bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treasure Bowl: PM2.5 Aggregation in the Eye of a Tropical Cyclone
Authors: Wang Ruiwen , Wang Hao , Zhang Chunlin , Gong Daocheng , Ma Fangyuan , He Congrong , Chen Duohong , Shen Jin , Zhou Yan , Ristovski Zoran , Liu Shaw Chen , Wang Boguang 
Published: January 2025

AbstractA local tropical cyclone (TC) in South China Sea was observed making its first complete landfall on an island. Following the arrival of the TC eye, PM2.5 concentration rose from 4 µg/m³ to 44 µg/m³. Mass reconstruction results reveal that sea salt emerged as the primary source. The similar molar ratios of elements before and after landfall confirm that the source of PM2.5 is associated with the local terrigenous sediment. The ratio of Na+/Cl− in the TC eyewall is approximately 5:1 indicating the existence of chlorine depletion. Meanwhile, the concentration of Cl− and molar ratios like Si/Fe inside the TC eyewall show a rapid increase, and reach a peak in the TC eye, indicating that marine particulate matter invades and presents a treasure‐bowl‐like stepwise aggregation. Our findings provide statistical and theoretical foundations for understanding extreme air pollution events, offering direct evidence of sea‐land transport throughout the entire TC.
Monitoring and Modeling the Soil‐Plant System Toward Understanding Soil Health
Authors: Zeng Yijian , Verhoef Anne , Vereecken Harry , Ben‐Dor Eyal , Veldkamp Tom , Shaw Liz , Van Der Ploeg Martine , Wang Yunfei , Su Zhongbo 
Published: January 2025

AbstractThe soil health assessment has evolved from focusing primarily on agricultural productivity to an integrated evaluation of soil biota and biotic processes that impact soil properties. Consequently, soil health assessment has shifted from a predominantly physicochemical approach to incorporating ecological, biological and molecular microbiology indicators. This shift enables a comprehensive exploration of soil microbial community properties and their responses to environmental changes arising from climate change and anthropogenic disturbances. Despite the increasing availability of soil health indicators (physical, chemical, and biological) and data, a holistic mechanistic linkage has not yet been fully established between indicators and soil functions across multiple spatiotemporal scales. This article reviews the state‐of‐the‐art of soil health monitoring, focusing on understanding how soil‐microbiome‐plant processes contribute to feedback mechanisms and causes of changes in soil properties, as well as the impact these changes have on soil functions. Furthermore, we survey the opportunities afforded by the soil‐plant digital twin approach, an integrative framework that amalgamates process‐based models, Earth Observation data, data assimilation, and physics‐informed machine learning, to achieve a nuanced comprehension of soil health. This review delineates the prospective trajectory for monitoring soil health by embracing a digital twin approach to systematically observe and model the soil‐plant system. We further identify gaps and opportunities, and provide perspectives for future research for an enhanced understanding of the intricate interplay between soil properties, soil hydrological processes, soil‐plant hydraulics, soil microbiome, and landscape genomics.
Machine Learning Prediction of Tritium‐Helium Groundwater Ages in the Central Valley, California, USA
Authors: Azhar Abdullah , Chakraborty Indrasis , Visser Ate , Liu Yang , Lerback Jory Chapin , Oerter Erik 
Published: January 2025

AbstractGroundwater ages provides insight into recharge rates, flow velocities, and vulnerability to contaminants. The ability to predict groundwater ages based on more accessible parameters via Machine Learning (ML) would advance our ability to guide sustainable management of groundwater resources. In this study, ML models were trained and tested on a large data set of tritium concentrations and tritium‐helium groundwater ages from the California Central Valley, a large groundwater basin with complex land use, irrigation, and water management practices. The ML models were trained on 63 features, including location, well construction information, landscape characteristics, and climate variables, water chemistry, and stable isotopes. The Bagging regressor method can accurately classify (F1‐score = 0.91) groundwater samples as either modern or pre‐modern whereas the accuracy of the ML prediction of continuous tritium‐helium groundwater ages is limited and explains only of the variability in this data set. In general, ML groundwater age prediction relies mostly on features related to (a) the source of groundwater recharge, (b) contaminant history, (c) aquifer materials, (d) well construction, and (e) geochemical reactions along flow paths.
Dissociating social reward learning and behavior in alcohol use disorder
Authors: Jangard Simon , Lindström Björn , Khemiri Lotfi , Jayaram-Lindström Nitya , Olsson Andreas 
Published: January 2025

Abstract

Background
Alcohol use disorder (AUD) is associated with deficits in social cognition and behavior, but why these deficits are acquired is unknown. We hypothesized that a reduced association between actions and outcomes for others, i.e., social reward learning, would explain prevalent social deficiencies in AUD.

Methods
We conducted one laboratory study (n = 234) and one confirmatory online study (n = 258), comparing young adults with AUD to age-, gender-, and education-matched healthy controls on a standardized reward learning task. In the task, participants learned to maximize reward for another person and for oneself. To elucidate the potential relation between reward learning and social behavior in AUD, we administered two measures: a dictator game task and a self-report measure. Finally, we applied reinforcement learning models to examine the computational properties of learning.

Results
Social and individual learning, expressed in choice behavior, were comparable in individuals with AUD and healthy controls. Individual differences in learning were not associated with reduced social behavior in AUD. Computational modeling suggested that the learning mechanisms are comparable in AUD and healthy controls and indifferent to whether learning maximizes reward for another person or oneself.

Conclusions
Individuals with AUD demonstrated preserved reward learning abilities that do not vary with social behavior. Together, these results indicate that reward processes may not be relevant for understanding compromised social behavior in AUD.
Autophagic flux-lipid droplet biogenesis cascade sustains mitochondrial fitness in colorectal cancer cells adapted to acidosis
Authors: Liu Xiaojie , Sun Xue , Mu Wenqing , Li Yanan , Bu Wenqing , Yang Tingting , Zhang Jia , Liu Rui , Ren Jiayu , Zhou Jin , Li Peishan , Shi Yufang , Shao Changshun 
Published: January 2025

Abstract
Cancer development is associated with adaptation to various stressful conditions, such as extracellular acidosis. The adverse tumor microenvironment also selects for increased malignancy. Mitochondria are integral in stress sensing to allow for tumor cells to adapt to stressful conditions. Here, we show that colorectal cancer cells adapted to acidic microenvironment (CRC-AA) are more reliant on oxidative phosphorylation than their parental cells, and the acetyl-CoA in CRC-AA cells are generated from fatty acids and glutamine, but not from glucose. Consistently, CRC-AA cells exhibit increased mitochondrial mass and fitness that depends on an upregulated autophagic flux-lipid droplet axis. Lipid droplets (LDs) function as a buffering system to store the fatty acids derived from autophagy and to protect mitochondria from lipotoxicity in CRC-AA cells. Blockade of LD biogenesis causes mitochondrial dysfunction that can be rescued by inhibiting carnitine palmitoyltransferase 1 α (CPT1α). High level of mitochondrial superoxide is essential for the AMPK activation, resistance to apoptosis, high autophagic flux and mitochondrial function in CRC-AA cells. Thus, our results demonstrate that the cascade of autophagic flux and LD formation plays an essential role in sustaining mitochondrial fitness to promote cancer cell survival under chronic acidosis. Our findings provide insight into the pro-survival metabolic plasticity in cancer cells under microenvironmental or therapeutic stress and imply that this pro-survival cascade may potentially be targeted in cancer therapy.
Rapid iPSC-derived neuromuscular junction model uncovers motor neuron dominance in amyotrophic lateral sclerosis cytopathy
Authors: Ting Hsiao-Chien , Guo Yun-Ting , Su Hong-Lin , Chen Yu-Shuan , Lin Shinn-Zong , Harn Horng-Jyh , Chang Chia-Yu 
Published: January 2025

Abstract
The neuromuscular junction (NMJ) is essential for transmitting signals from motor neurons (MNs) to skeletal muscles (SKMs), and its dysfunction can lead to severe motor disorders. However, our understanding of the NMJ is limited by the absence of accurate human models. Although human induced pluripotent stem cell (iPSC)-derived models have advanced NMJ research, their application is constrained by challenges such as limited differentiation efficiency, lengthy generation times, and cryopreservation difficulties. To overcome these limitations, we developed a rapid human NMJ model using cryopreserved MNs and SKMs derived from iPSCs. Within 12 days of coculture, we successfully recreated NMJ-specific connectivity that closely mirrors in vivo synapse formation. Using this model, we investigated amyotrophic lateral sclerosis (ALS) and replicated ALS-specific NMJ cytopathies with SOD1 mutant and corrected isogenic iPSC lines. Quantitative analysis of 3D confocal microscopy images revealed a critical role of MNs in initiating ALS-related NMJ cytopathies, characterized by alterations in the volume, number, intensity, and distribution of acetylcholine receptors, ultimately leading to impaired muscle contractions. Our rapid and precise in vitro NMJ model offers significant potential for advancing research on NMJ physiology and pathology, as well as for developing treatments for NMJ-related diseases.
Anthracyclines disaggregate and restore mutant p63 function: a potential therapeutic approach for AEC syndrome
Authors: Boncimino Fabiana , D’Auria Ludovica , Todorova Kristina , van der Zanden Sabina Y. , Neefjes Jacques , Mandinova Anna , Missero Caterina , Sol Stefano 
Published: January 2025

Abstract
Ankyloblepharon-Ectodermal Defects-Cleft Lip/Palate (AEC) syndrome is a rare genetic disorder caused by mutations in the TP63 gene, which encodes a transcription factor essential for epidermal gene expression. A key feature of AEC syndrome is chronic skin erosion, for which no effective treatment currently exists. Our previous studies demonstrated that mutations associated with AEC syndrome lead to p63 protein misfolding and aggregation, exerting a dominant-negative effect. By performing a high-throughput screening of epigenetic and FDA-approved compounds in a co-transfection model of wild-type and mutant p63, we found that two compounds, Doxorubicin and Epirubicin, alleviate protein aggregation and restore p63 transactivation function. Moreover, treatment with these compounds reduced protein aggregation and restored the expression of keratinocyte-specific p63 target genes in primary keratinocytes derived from a conditional ΔNp63αL514F knock-in AEC mouse model, which mimics the ectodermal defects and skin erosions characteristic of AEC syndrome. A chemical analog of Doxorubicin, diMe-Doxorubicin, which exhibits lower tissue and organ toxicity, was also found to be effective in promoting the disaggregation of mutant p63 and rescuing its transcriptional activity. Our findings identify compounds that can partially resolve mutant p63 aggregation, increase its monomeric isoform, and reactivate its transcriptional function. These results suggest potential therapeutic efficacy for treating skin erosions in AEC syndrome.
Epigenetic variation in light of population genetic practice
Authors: Mueller Sarah A. , Merondun Justin , Lečić Sonja , Wolf Jochen B. W. 
Published: January 2025

Abstract
The evolutionary impact of epigenetic variation depends on its transgenerational stability and source - whether genetically determined, environmentally induced, or due to spontaneous, genotype-independent mutations. Here, we evaluate current approaches for investigating an independent role of epigenetics in evolution, pinpointing methodological challenges. We further identify opportunities arising from integrating epigenetic data with population genetic analyses in natural populations. Efforts to advance data quality, study design, and statistical treatment are encouraged to consolidate our understanding of the source of heritable epigenetic variation, quantify its autonomous potential for evolution, and enrich population genetic analyses with an additional layer of information.
Diversity-oriented synthesis of stereodefined tetrasubstituted alkenes via a modular alkyne gem-addition strategy
Authors: Di Xuan , Zhou Sitian , Qin Yali , Li Wenjun , Zhang Yue , Zhang Jie , Shen Xu , Han Jie , Xie Jin , Jin Hongming 
Published: January 2025

Abstract
Stereocontrolled construction of tetrasubstituted olefins has been an attractive issue yet remains challenging for synthetic chemists. In this manuscript, alkynyl selenides, when treated with ArBCl2, are subject to an exclusive 1,1-carboboration, affording tetrasubstituted alkenes with excellent levels of E-selectivity. Detailed mechanistic studies, supported by DFT calculations, elucidates the role of selenium in this 1,1-addition process. Coupled with subsequent C-B and C-Se bond transformations, this 1,1-addition protocol constitutes a modular access to stereodefined all-carbon tetrasubstituted alkenes. The merit of this approach is demonstrated by programmed assembly of diverse functionalized multi-arylated alkenes, especially enabling the stereospecific synthesis of all six possible stereoisomers of tetraarylethene (TAE) derived from the random permutation of four distinct aryl substituents around the double bond. The diversity-oriented synthesis is further utilized to explore different TAE luminogenic properties and potential Se-containing antitumor lead compounds.
The α-globin super-enhancer acts in an orientation-dependent manner
Authors: Kassouf Mira T. , Francis Helena S. , Gosden Matthew , Suciu Maria C. , Downes Damien J. , Harrold Caroline , Larke Martin , Oudelaar Marieke , Cornell Lucy , Blayney Joseph , Telenius Jelena , Xella Barbara , Shen Yuki , Sousos Nikolaos , Sharpe Jacqueline A. , Sloane-Stanley Jacqueline , Smith Andrew J. H. , Babbs Christian , Hughes Jim R. , Higgs Douglas R. 
Published: January 2025

Abstract
Individual enhancers are defined as short genomic regulatory elements, bound by transcription factors, and able to activate cell-specific gene expression at a distance, in an orientation-independent manner. Within mammalian genomes, enhancer-like elements may be found individually or within clusters referred to as locus control regions or super-enhancers (SEs). While these behave similarly to individual enhancers with respect to cell specificity, distribution and distance, their orientation-dependence has not been formally tested. Here, using the α-globin locus as a model, we show that while an individual enhancer works in an orientation-independent manner, the direction of activity of a SE changes with its orientation. When the SE is inverted within its normal chromosomal context, expression of its normal targets, the α-globin genes, is severely reduced and the normally silent genes lying upstream of the α-globin locus are upregulated. These findings add to our understanding of enhancer-promoter specificity that precisely activate transcription.
The effect of avatar identity on spontaneous perspective-taking in patients with schizophrenia
Authors: Xie Pei , Huang ChaoZheng , Wang XiaoQuan , Sang HanBin , Zhou AiBao 
Published: January 2025

Abstract
Controversy exists regarding whether the spontaneity of altercentric intrusion is impaired in patients with schizophrenia during implicit visual perspective-taking tasks. This study explored the characteristics of spontaneous visual perspective-taking in patients with schizophrenia and the effect of an avatar identity on their perspective-taking. We recruited 65 patients with schizophrenia and 65 healthy participants to complete 4 visual perspective-taking experiments for uncued other-avatar and self-avatar tasks and cued other-avatar and self-avatar tasks. In uncued other-avatar experiments, healthy controls showed a significant reduction in accuracy and an increase in response latency when the number of visible discs differed from that seen by the other-avatar (inconsistent condition), indicating altercentric intrusion. However, patients with schizophrenia did not exhibit this effect. In uncued self-avatar experiments, when the avatar was defined as the participant themselves, patients with schizophrenia did not show spontaneous perspective-taking. However, in cued other-avatar experiments, they showed altercentric intrusion in response latency, and in cued self-avatar experiments, they showed altercentric intrusion in accuracy and response latency. These results suggest that patients with schizophrenia have the tendency to spontaneously adopt the perspective of others, which is predicated on their awareness of the existence of perspectives. In addition, the avatar’s identity as a stranger hinders the spontaneous perspective-taking processes in patients with schizophrenia.
DeepExtremeCubes: Earth system spatio-temporal data for assessing compound heatwave and drought impacts
Authors: Ji Chaonan , Fincke Tonio , Benson Vitus , Camps-Valls Gustau , Fernández-Torres Miguel-Ángel , Gans Fabian , Kraemer Guido , Martinuzzi Francesco , Montero David , Mora Karin , Pellicer-Valero Oscar J. , Robin Claire , Söchting Maximilian , Weynants Mélanie , Mahecha Miguel D. 
Published: January 2025

Abstract
With climate extremes’ rising frequency and intensity, robust analytical tools are crucial to predict their impacts on terrestrial ecosystems. Machine learning techniques show promise but require well-structured, high-quality, and curated analysis-ready datasets. Earth observation datasets comprehensively monitor ecosystem dynamics and responses to climatic extremes, yet the data complexity can challenge the effectiveness of machine learning models. Despite recent progress in deep learning to ecosystem monitoring, there is a need for datasets specifically designed to analyse compound heatwave and drought extreme impact. Here, we introduce the DeepExtremeCubes database, tailored to map around these extremes, focusing on persistent natural vegetation. It comprises over 40,000 globally sampled small data cubes (i.e. minicubes), with a spatial coverage of 2.5 by 2.5 km. Each minicube includes (i) Sentinel-2 L2A images, (ii) ERA5-Land variables and generated extreme event cube covering 2016 to 2022, and (iii) ancillary land cover and topography maps. The paper aims to (1) streamline data accessibility, structuring, pre-processing, and enhance scientific reproducibility, and (2) facilitate biosphere dynamics forecasting in response to compound extremes.
Diversity and composition of vegetation and soil seed banks after sand dune restoration by oil mulching and plantations
Authors: Jalilian Banafsheh , Rostami Noredin , Heydari Mehdi , Kohzadian Mehrdad , Valkó Orsolya , Omidipour Reza 
Published: January 2025

Abstract
Soil seed bank (SSB) is valuable reserves of seeds hidden in the soil and are especially important for the preservation and establishment of vegetation under adverse environmental conditions. However, there is a lack of knowledge on the effects of restoration measures on SSB, especially in arid ecosystems. Here, we assess the impacts of oil mulching (1 and 3 years after mulching) and plantations (15-year-old) on the diversity and composition of SSB and aboveground vegetation (AGV) in comparison with those in non-restored areas (i.e., control). Based on the results, species richness was poor in the studied area (36 species belonging to 16 families), with a lower contribution of SSB than of AGV (11 and 34 species, respectively). The largest number of exclusive species was observed in the planted treatment for both SSB and AGV (4 and 5 species, respectively), while the lowest was found in the 1-yr mulching treatment. The mean comparison of the diversity indices revealed that the highest values occurred in the plantation and 3-yr-mulching plots. The seed density in the plantation area was significantly greater (4145 ± 694 seeds/m2) than that in the other areas (3-yr-mulching > 1-yr-mulching > control treatments (145 ± 53, 65 ± 28, and 43 ± 22, respectively). The results of the DCA showed that the plantation treatment was completely separated from the other treatments in terms of the plant composition of the AGV, and the treatment closest to that area was 3-yr mulching, which indicates the positive effect of time since mulching on plant composition. The results of this study suggest that there is a trade-off between the short-term and medium-term effects of oil mulching, such that in the early years, oil mulching has a negative effect on the AGV and SSB, but its positive effects increase with time since mulching. It can be concluded that mulching, along with afforestation, creates a favorable microclimate and improves the diversity and composition of AGV and SSB.
Atmospheric air plasma pre-activation and customizable covalent functionalization of PVDF-membranes of microtiter filter plates
Authors: Ádám Bálint Árpád , Spátay Sára , Jávor Bálint , László Szabolcs , Illés Levente , Fürjes Péter , Tóth Tünde , Huszthy Péter , Golcs Ádám 
Published: January 2025

Abstract
Microtiter-plate-based systems are unified platforms of high-throughput experimentation (HTE). These polymeric devices are used worldwide on a daily basis—mainly in the pharmaceutical industry—for parallel syntheses, reaction optimization, various preclinical studies and high-throughput screening methods. Accordingly, laboratory automation today aims to handle these commercially available multiwell plates, making developments focused on their modifications a priority area of modern applied research. We performed the covalent functionalization of the porous PVDF-membrane of microtiter filter plates as the essence of conventional and common sandwich plate systems by introducing a generalizable method. After surface-activation of the indifferent membrane polymer, customizable functionalization becomes feasible by covalently attached monofunctional molecular linkers. The study was designed with future adaptability, and thus, industrially widespread atmospheric plasma and two different chemical treatments were investigated and compared in terms of practical implementation, polarization effects, extent of labeling, effects on morphology and porosity as well as on permeability. For critical comparison, contact angle measurements, surface ATR-FTIR, 1H-NMR, 19F-NMR, UV–Vis spectroscopy, scanning electron microscopy and permeability tests were used.