bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of antidepressants with cataracts and glaucoma: a disproportionality analysis using the reports to the United States Food and Drug Administration Adverse Event Reporting System (FAERS) pharmacovigilance database
Authors: Le Gia Han , Wong Sabrina , Kwan Angela T.H. , Rosenblat Joshua D. , Mansur Rodrigo B. , Teopiz Kayla M. , Ho Roger , Rhee Taeho Greg , Vinberg Maj , Cao Bing , Liao Sonya , McIntyre Roger S. 
Published: January 2025

AbstractBackgroundAntidepressants are commonly prescribed for mood disorders. Epidemiological studies suggest antidepressant use may be associated with cataracts and glaucoma. We aim to investigate the association between antidepressants and cataracts and glaucoma.MethodsData was collected from the United States Food and Drug Administration Adverse Event Reporting System. Reporting odds ratio (ROR) and Bayesian information components (IC025) were calculated for antidepressants (ie, selective serotonin reuptake inhibitors [SSRIs], selective norepinephrine reuptake inhibitors [SNRIs], serotonin-norepinephrine-dopamine reuptake inhibitors, serotonin modulators and stimulators, serotonin antagonists and reuptake inhibitors [SARIs], norepinephrine reuptake inhibitors, norepinephrine-dopamine reuptake inhibitors, tricyclic antidepressants [TCAs], tetracyclic antidepressants [TeCAs], and monoamine oxidase inhibitors [MAOIs]). The reference agent was acetaminophen.ResultsTeCAs and MAOIs were significantly associated with a decreased risk of cataracts (ROR = 0.11-0.65 and 0.16-0.69, respectively). TCAs, brexanolone, esketamine, and opipramol reported an increased cataract risk (ROR = 1.31-12.81). For glaucoma, SSRIs, SNRIs, SARIs, TCAs, MAOIs, and other investigated antidepressants reported significant RORs ranging from 1.034 to 21.17. There was a nonsignificant association of angle closure glaucoma (ACG) and open angle glaucoma (OAG) with the investigated antidepressants.LimitationsFor adverse event cases, multiple suspected product names are listed, and as cases are not routinely verified, there may be a possibility of duplicate reports and causality cannot be established.ConclusionMost of the investigated antidepressants were associated with a lower risk of cataract reporting. TCAs, brexanolone, esketamine, and opipramol were associated with greater odds of cataract. For most antidepressants, there was an insignificant increase in reports of ACG and OAG.
Radial and Latitudinal Distributions of the Exohiss Under the Effect of Landau Damping
Authors: Ding Xiangling , He Zhaoguo , Wu Zhiyong , Yu Jiang , Li Kun , Ye Yuguang , Zong Qiugang 
Published: January 2025

AbstractExohiss serves as a typical imprint of the outward energy release from plasmaspheric hiss. The distribution of exohiss under the effect of Landau damping has not been thoroughly evaluate. On the basis of observations from the Van Allen Probes on 17 February 2014, we performed two‐dimensional ray tracing simulations to model the evolution of hiss waves propagating from the geomagnetic equator in plasmasphere. The results show that the hiss wave power decreases rapidly as the waves enter the plasmatrough under the enhanced Landau damping effect of hot electrons. Furthermore, we perform a statistical analysis of the simulation results from multiple rays and obtain the radial, latitudinal, and frequency distributions of the exohiss wave power. The modeled distribution characteristics of exohiss align well with observations, suggesting that Landau damping is crucial in shaping the morphology of exohiss in the inner magnetosphere.
Ionospheric Conductances at the Giant Planets of the Solar System: A Comparative Study of Ionization Sources and the Impact of Meteoric Ions
Authors: Clément Noé , Nakamura Yuki , Blanc Michel , Wang Yuxian , Al Saati Sariah 
Published: January 2025

AbstractThe dynamics of giant planet magnetospheres is controlled by a complex interplay between their fast rotation, their interaction with the solar wind, and their diverse internal plasma and momentum sources. In the ionosphere, the Hall and Pedersen conductances are two key parameters that regulate the intensity of currents coupling the magnetosphere and the ionosphere, and the rate of angular momentum transfer and power carried by these currents. We perform a comparative study of Hall and Pedersen conductivities and conductances in the four giant planets of our Solar System ‐ Jupiter, Saturn, Uranus and Neptune. We use a generic ionospheric model (restraining the studied ions to , , and meteoric ions) to study the dependence of conductances on the structure and composition of these planets' upper atmospheres and on the main ionization sources (photoionization, ionization by precipitating electrons, and meteoroid ablation). After checking that our model reproduces the conclusions of Nakamura et al. (2022), https://doi.org/10.1029/2022ja030312 at Jupiter, that is, the contribution of meteoric ions to the height‐integrated conductances is non‐negligible, we show that this contribution could also be non‐negligible at Saturn, Uranus and Neptune, compared with ionization processes caused by precipitating electrons of energies lower than a few keV (typical energies on these planets). However, because of their weaker magnetic field, the conductive layer of these planets is higher than the layer where meteoric ions are mainly produced, limiting their role in magnetosphere‐ionosphere coupling.
Microseism Amplitude and Wave Power in the Mediterranean Sea (1996–2023)
Authors: Borzì Alfio Marco , Cannata Andrea , Panzera Francesco , D’Amico Sebastiano , Lo Re Carlo , Aster Richard C. 
Published: January 2025

AbstractIn this work, we integrate seismic data recorded by nine coastal Mediterranean seismic stations and wave hindcast data for 1 January 1996 through 15 October 2023. We examine the relationships between the ocean wave‐generated microseism signal (the most continuous and ubiquitous seismic signal on Earth) in terms of temporally varying spectral content, root mean square amplitude, and microseism power spectral density, with the main features of principal ocean wave attributes, specifically significant wave heights, wave period and wave power. To explore relationships between microseism and sea state, we performed a correlation analysis between seismic root square mean amplitude and significant wave height time series for the entire Mediterranean Sea for 1996–2023, including retrieving long‐term trends for microseism energy and independently estimated wave power and calculating the Spearman correlation coefficient between the two trend time series. Despite the small number of stations available the analysis allows for a useful exploratory study on the microseism and its relationship with Mediterranean Sea state and wave power spanning 27 years. Given the recent increase in the number of regional seismic stations, the growth of data sharing, and the intensification of global warming and climate extreme events, the results and methods explored here can be further implemented and developed in coming years for coastal monitoring purposes in complement with other data sources.
Intraseasonal Variations in the Indian Ocean Cross‐Equatorial Cell During the Subsequent Boreal Summer of ENSO
Authors: Liu Yu , Xu Kang , Wang Weiqiang , Chen Sheng , He Zhuoqi , Xie Qiang , Arulananthan K. , Kumara P. B. Terney Pradeep 
Published: January 2025

AbstractThe interannual relationships between the cross‐equatorial cell (CEC) in the Indian Ocean (IO) and the El Niño‐Southern Oscillation (ENSO) are examined through observational data and numerical simulations. The findings indicate a notable intraseasonal variation in the boreal summer IO CEC responses to preceding ENSO events, showing a weakening in early summer (May–June) and a strengthening in late summer (August–September) subsequent to an El Niño events. These contrasting responses are primarily driven by opposite meridional Ekman transport anomalies, characterized by anomalous northward Ekman transport in early summer and southward transport in late summer. Further analysis reveals that ENSO‐induced surface zonal wind anomalies predominantly influence these anomalous meridional Ekman transport in the upper layer, accounting for over 80% of the variation. In early summer, an antisymmetric wind pattern over the IO, induced by El Niño in the decaying spring, along with the westward extension of the anomalous western North Pacific anticyclone (WNPAC), generates anomalous easterlies over the North IO (NIO), leading to weakened meridional Ekman transport and a diminished CEC. Simultaneously, those anomalous easterlies and the associated weakened CEC in early summer trigger a wind‐CEC‐SST (WCS) negative feedback mechanism. The resulting anomalous northward transport and reduced upwelling lead to sea surface temperature (SST) warming in the northern NIO, creating a northward surface ocean temperature gradient in the July–August period. This gradient, along with the eastward retreat of the WNPAC, causes anomalous NIO westerlies in late summer, enhancing meridional Ekman transport and ultimately strengthening the CEC.
An Analytical Framework for Risk Evaluation and Design of Infiltration Basins for Managed Aquifer Recharge
Authors: Fiori Aldo , de Barros Felipe P. J. , Bellin Alberto 
Published: January 2025

AbstractManaged Aquifer Recharge (MAR) plays an important role in improving and supplementing groundwater storage. Many natural factors, ranging from climatic conditions to soil characteristics, can impact the efficiency of an infiltration basin. Other factors, such as engineered variables, will also influence the basin performance and the risks associated with groundwater contamination. The latter depends on the interplay between the hydraulic characteristics of the system and the soil and solute properties. The design of infiltration basins has been performed so far with the main objective of mitigating the tendency of the basin to reduce the infiltration rate with time due to clogging of the basin's bottom. Less attention has been paid to the risk of groundwater contamination by the infiltrating water. To understand the complex interplay between natural and engineering parameters on MAR efficiency and the contamination risk, we propose a risk‐oriented analytical framework. The framework allows to investigate the interplay between soil parameters, engineering design and climatic factors on the efficiency of an infiltration basin. Our framework relies on novel analytical solutions that relates the geometrical and hydrological features of the infiltration basin to its efficiency and groundwater contamination risk. The solutions incorporates the randomness associated with inflows (precipitation) and soil properties. We explore the trade‐off between efficiency and the risk of contamination and delineate a design procedure that balances these two opposing needs. Although the framework relies on simplifying assumptions, it provides a computationally efficient manner to obtain physical insights and relate model input parameters to decision making.
Anti-PD-1 exacerbates bleomycin-induced lung injury in mice via Caspase-3/GSDME-mediated pyroptosis
Authors: Wang Fei , Deng Haiyi , Zhou Maolin , Yang Yilin , Zhou Jiankui , Wang Yansheng , Xie Xiaohong , Lin Xinqing , Liu Ming , Sun Gengyun , Zhou Chengzhi 
Published: January 2025

AbstractImmune checkpoint inhibitors (ICIs) have significant therapeutic effects but can also cause fatal lung injury. However, the lack of mouse animal models of ICI-related lung injury (ICI-LI) has limited the in-depth exploration of its pathogenesis. In clinical practice, underlying lung diseases increase the risk of lung injury. Thus, we used a mouse model of lung injury induced by bleomycin (BLM) and then administered anti-programmed cell death 1 (aPD-1) antibodies to induce ICI-LI. Compared with the BLM group, the aPD-1 + BLM group presented more significant weight loss, greater levels of lung inflammation and fibrosis, and decreased lung function. In this ICI-LI model, high levels of caspase-3/gasdermin E (GSDME) were detected in the lung tissue of mice, and the JNK inhibitor SP600125 mitigated lung damage by inhibiting GSDME-mediated pyroptosis. Consistent with the findings in the animal model, immunofluorescence and RNA sequencing of lung tissue from ICI-LI patients revealed upregulation of the expression of genes related to the GSDME-related pyroptosis pathway. Our results suggest that GSDME-mediated pyroptosis may be associated with the pathogenesis of ICI-LI, indicating that targeting GSDME could be a potential therapeutic strategy for treating ICI-LI.
Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation
Authors: Wan Yue , Wu Jialu , Hou Tingjun , Hsieh Chang-Yu , Jia Xiaowei 
Published: January 2025

AbstractReliable molecular property prediction is essential for various scientific endeavors and industrial applications, such as drug discovery. However, the data scarcity, combined with the highly non-linear causal relationships between physicochemical and biological properties and conventional molecular featurization schemes, complicates the development of robust molecular machine learning models. Self-supervised learning (SSL) has emerged as a popular solution, utilizing large-scale, unannotated molecular data to learn a foundational representation of chemical space that might be advantageous for downstream tasks. Yet, existing molecular SSL methods largely overlook chemical knowledge, including molecular structure similarity, scaffold composition, and the context-dependent aspects of molecular properties when operating over the chemical space. They also struggle to learn the subtle variations in structure-activity relationship. This paper introduces a multi-channel pre-training framework that learns robust and generalizable chemical knowledge. It leverages the structural hierarchy within the molecule, embeds them through distinct pre-training tasks across channels, and aggregates channel information in a task-specific manner during fine-tuning. Our approach demonstrates competitive performance across various molecular property benchmarks and offers strong advantages in particularly challenging yet ubiquitous scenarios like activity cliffs.
Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals
Authors: Fackelmann Gloria , Manghi Paolo , Carlino Niccolò , Heidrich Vitor , Piccinno Gianmarco , Ricci Liviana , Piperni Elisa , Arrè Alberto , Bakker Elco , Creedon Alice C. , Francis Lucy , Capdevila Pujol Joan , Davies Richard , Wolf Jonathan , Bermingham Kate M. , Berry Sarah E. , Spector Tim D. , Asnicar Francesco , Segata Nicola 
Published: January 2025

Abstract
As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology.
Engineering covalent small molecule–RNA complexes in living cells
Authors: Bereiter Raphael , Flemmich Laurin , Nykiel Kamila , Heel Sarah , Geley Stephan , Hanisch Malou , Eichler Clemens , Breuker Kathrin , Lusser Alexandra , Micura Ronald 
Published: January 2025

AbstractCovalent labeling of RNA in living cells poses many challenges. Here we describe a structure-guided approach to engineer covalent RNA aptamer–ligand complexes. The key is to modify the cognate ligand with an electrophilic handle that allows it to react with a guanine at the RNA binding site. We illustrate this for the preQ1-I riboswitch, in vitro and in vivo. Further, we demonstrate the versatility of the approach with a covalent fluorescent light-up aptamer. The coPepper system maintains strong fluorescence in live-cell imaging even after washing, can be used for super-resolution microscopy and, most notably, is uniquely suited for fluorescence recovery after photobleaching to monitor intracellular RNA dynamics. In addition, we have generated a Pepper ligand with a second handle for bioorthogonal chemistry to allow easily traceable pull-down of the covalently linked target RNA. Finally, we provide evidence for the suitability of this tethering strategy for drug targeting.
Context-dependent decision-making in the primate hippocampal–prefrontal circuit
Authors: Elston Thomas W. , Wallis Joni D. 
Published: January 2025

Abstract
What is good in one scenario may be bad in another. Despite the ubiquity of such contextual reasoning in everyday choice, how the brain flexibly uses different valuation schemes across contexts remains unknown. We addressed this question by monitoring neural activity from the hippocampus (HPC) and orbitofrontal cortex (OFC) of two monkeys performing a state-dependent choice task. We found that HPC neurons encoded state information as it became available and then, at the time of choice, relayed this information to the OFC via theta synchronization. During choice, the OFC represented value in a state-dependent manner; many OFC neurons uniquely coded for value in only one state but not the other. This suggests a functional dissociation whereby the HPC encodes contextual information that is broadcast to the OFC via theta synchronization to select a state-appropriate value subcircuit, thereby allowing for contextual reasoning in value-based choice.
Multimodal transcriptomics reveal neurogenic aging trajectories and age-related regional inflammation in the dentate gyrus
Authors: Wu Yicheng , Korobeynyk Vladyslav I. , Zamboni Margherita , Waern Felix , Cole John Darby , Mundt Sarah , Greter Melanie , Frisén Jonas , Llorens-Bobadilla Enric , Jessberger Sebastian 
Published: January 2025

Abstract
The mammalian dentate gyrus (DG) is involved in certain forms of learning and memory, and DG dysfunction has been implicated in age-related diseases. Although neurogenic potential is maintained throughout life in the DG as neural stem cells (NSCs) continue to generate new neurons, neurogenesis decreases with advancing age, with implications for age-related cognitive decline and disease. In this study, we used single-cell RNA sequencing to characterize transcriptomic signatures of neurogenic cells and their surrounding DG niche, identifying molecular changes associated with neurogenic aging from the activation of quiescent NSCs to the maturation of fate-committed progeny. By integrating spatial transcriptomics data, we identified the regional invasion of inflammatory cells into the hippocampus with age and show here that early-onset neuroinflammation decreases neurogenic activity. Our data reveal the lifelong molecular dynamics of NSCs and their surrounding neurogenic DG niche with age and provide a powerful resource to understand age-related molecular alterations in the aging hippocampus.
Capture, mutual inhibition and release mechanism for aPKC–Par6 and its multisite polarity substrate Lgl
Authors: Earl Christopher P. , Cobbaut Mathias , Barros-Carvalho André , Ivanova Marina E. , Briggs David C. , Morais-de-Sá Eurico , Parker Peter J. , McDonald Neil Q. 
Published: January 2025

Abstract
The mutually antagonistic relationship of atypical protein kinase C (aPKC) and partitioning-defective protein 6 (Par6) with the substrate lethal (2) giant larvae (Lgl) is essential for regulating polarity across many cell types. Although aPKC–Par6 phosphorylates Lgl at three serine sites to exclude it from the apical domain, aPKC–Par6 and Lgl paradoxically form a stable kinase–substrate complex, with conflicting roles proposed for Par6. We report the structure of human aPKCι–Par6α bound to full-length Llgl1, captured through an aPKCι docking site and a Par6PDZ contact. This complex traps a phospho-S663 Llgl1 intermediate bridging between aPKC and Par6, impeding phosphorylation progression. Thus, aPKCι is effectively inhibited by Llgl1pS663 while Llgl1 is captured by aPKCι–Par6. Mutational disruption of the Lgl–aPKC interaction impedes complex assembly and Lgl phosphorylation, whereas disrupting the Lgl–Par6PDZ contact promotes complex dissociation and Lgl phosphorylation. We demonstrate a Par6PDZ-regulated substrate capture-and-release model requiring binding by active Cdc42 and the apical partner Crumbs to drive complex disassembly. Our results suggest a mechanism for mutual regulation and spatial control of aPKC–Par6 and Lgl activities.
NEBULA101: an open dataset for the study of language aptitude in behaviour, brain structure and function
Authors: Rampinini Alessandra , Balboni Irene , Kepinska Olga , Berthele Raphael , Golestani Narly 
Published: January 2025

AbstractThis paper introduces the “NEBULA101 - Neuro-behavioural Understanding of Language Aptitude” dataset, which comprises behavioural and brain imaging data from 101 healthy adults to examine individual differences in language and cognition. Human language, a multifaceted behaviour, varies significantly among individuals, at different processing levels. Recent advances in cognitive science have embraced an integrated approach, combining behavioural and brain studies to explore these differences comprehensively. The NEBULA101 dataset offers brain structural, diffusion-weighted, task-based and resting-state MRI data, alongside extensive linguistic and non-linguistic behavioural measures to explore the complex interaction of language and cognition in a highly multilingual sample. By sharing this multimodal dataset, we hope to promote research on the neuroscience of language, cognition and multilingualism, enabling the field to deepen its understanding of the multivariate panorama of individual differences and ultimately contributing to open science.
Electro-polymerization of modified carbon paste sensor for detecting azithromycin
Authors: Mamdouh Salma , Shehata M. , Fekry A. M. , Ameer M. A. 
Published: January 2025

AbstractAzithromycin (AM) is one of the prescribed drugs in pandemic medication treatment which has paid great attention. We developed in this study a simply modified carbon paste electrode (CPE) to detect AM using poly-threonine (PT). PT or similar polymers are used as carriers to enhance the delivery and effectiveness of AM. The work was characterised via Cyclic Voltammetry (CV), electrochemical impedance spectroscopy (EIS) and scanning electron microscopy (SEM). We take into consideration the effects of pH, scan rate, accumulation time, interference, and calibration curve.A very sensitive response to the oxidation of 1.0 mM from AM in phosphate buffer solution (PBS) over a pH range of 5.0 to 10.0 was observed using the developed poly-threonine carbon paste electrode (PTCPE). The impact of different AM concentrations was investigated resulting in a detection limit of 0.32 µM and a quantification limit of 1.07 µM at PBS (pH 7.4). Finally, the recently used electrode realized acceptable sensitivity and consistency for AM detection in pharmaceutical drugs.