bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving Weather Fronts Increases the Large‐Scale Circulation Response to Gulf Stream SST Anomalies in Variable‐Resolution CESM2 Simulations
Authors: Wills Robert C. J. , Herrington Adam R. , Simpson Isla R. , Battisti David S. 
Published: July 2024

AbstractCanonical understanding based on general circulation models (GCMs) is that the atmospheric circulation response to midlatitude sea‐surface temperature (SST) anomalies is weak compared to the larger influence of tropical SST anomalies. However, the ∼100‐km horizontal resolution of modern GCMs is too coarse to resolve strong updrafts within weather fronts, which could provide a pathway for surface anomalies to be communicated aloft. Here, we investigate the large‐scale atmospheric circulation response to idealized Gulf Stream SST anomalies in Community Atmosphere Model (CAM6) simulations with 14‐km regional grid refinement over the North Atlantic, and compare it to the responses in simulations with 28‐km regional refinement and uniform 111‐km resolution. The highest resolution simulations show a large positive response of the wintertime North Atlantic Oscillation (NAO) to positive SST anomalies in the Gulf Stream, a 0.4‐standard‐deviation anomaly in the seasonal‐mean NAO for 2°C SST anomalies. The lower‐resolution simulations show a weaker response with a different spatial structure. The enhanced large‐scale circulation response results from an increase in resolved vertical motions with resolution and an associated increase in the influence of SST anomalies on transient‐eddy heat and momentum fluxes in the free troposphere. In response to positive SST anomalies, these processes lead to a stronger and less variable North Atlantic jet, as is characteristic of positive NAO anomalies. Our results suggest that the atmosphere responds differently to midlatitude SST anomalies in higher‐resolution models and that regional refinement in key regions offers a potential pathway to improve multi‐year regional climate predictions based on midlatitude SSTs.
Insights for River Restoration: The Impacts of Vegetation Canopy Length and Canopy Discontinuity on Riverbed Evolution
Authors: Li Fujian , Shan Yuqi , Li Ming , Guo Yakun , Liu Chao 
Published: July 2024

AbstractRiver restoration projects often involve vegetation planting to retain sediment and stabilize riverbanks. Laboratory experiments have explored the impact of rigid emergent vegetation canopies on bed morphology. Inside canopies, bed erosion is attributed to vegetation‐induced turbulent kinetic energy (TKE). Based on the in‐canopy local TKE and the criteria for sediment movement, a method is established and validated for predicting the length of the bed erosion region. In the bare channel, bed erosion is related to the ratio of canopy length to flow adjustment distance, L/LI, and exhibits two trends. At L/LI < 1, the maximum depth, ds(bare), and length, Ls(bare), of the bed erosion region increase with increasing canopy length. At L/LI ≥ 1, ds(bare) and Ls(bare) are not influenced by the canopy length and remain constant. In vegetated regions with the same length and plant density, discontinuous canopies (streamwise interval s ≥ canopy width D) yield weaker bed erosion than continuous canopies. The mutual influence between two canopies must be considered if the canopy interval satisfies s < 3D. These results provide insights for designing vegetation canopies for river restoration projects.
Projected Thermally Driven Elderly Mortality for Beijing Under Greenhouse Gas and Stratospheric Aerosol Geoengineering Scenarios
Authors: Wang Jun , Zhao Liyun , Moore John C. 
Published: July 2024

AbstractBeijing is undergoing multiple challenges including urbanization, warming and aging. The Beijing megalopolis of 20 million people now suffers more cold‐related than heat‐related deaths. Stratospheric aerosol injection (SAI) geoengineering is designed to lower surface temperatures, so if SAI were ever done, it may reduce future heat‐related mortality, while also increasing cold‐related mortality. Here we use four Earth System Models (ESM) downscaled to 10 km resolution with the Weather Research and Forecasting (WRF) system to capture urban temperature, humidity and wind speeds. Temperature‐related mortality risk were calculated using a distributed lag nonlinear model (DLNM) of the elderly (over 65s) under the dynamically downscaled moderate (RCP4.5) and extreme (RCP8.5) greenhouse gas, and the G4 SAI scenarios. We used population demographics for all five shared socioeconomic pathways (SSP) and various adaptation measures. Heat‐related excess deaths under G4 are 630∼3,160 per year fewer than RCP4.5, while cold‐related deaths are 370∼1,990 more than RCP4.5 during 2060–2069, with a marginally significant net reduction. G4 significantly reduces the excess deaths relative to RCP8.5. Both heat‐related and cold‐related mortality will increase by 240∼490% when the aging population is accounted for, and decrease by 11%, 23% and 44% under low, medium and high adaptation relative to a no adaptation scenario. Dynamical downscaling produces better quality climate simulations than commonly used statistical approaches, and in the case of Beijing, significantly fewer heat‐related deaths. The marginal health benefits of modest future SAI in Beijing may be representative of the population impacts in the extra‐tropics where deaths due to cold are more than those caused by heat.
Electron Dynamics Associated With Advection and Diffusion in Self‐Consistent Wave‐Particle Interactions With Oblique Chorus Waves
Authors: Chen Huayue , Wang Xueyi , Zhao Hong , Lin Yu , Chen Lunjin , Omura Yoshiharu , Chen Rui , Hsieh Yi‐Kai 
Published: July 2024

AbstractChorus waves are intense electromagnetic emissions critical in modulating electron dynamics. In this study, we perform two‐dimensional particle‐in‐cell simulations to investigate self‐consistent wave‐particle interactions with oblique chorus waves. We first analyze the electron dynamics sampled from cyclotron and Landau resonances with waves, and then quantify the advection and diffusion coefficients through statistical studies. It is found that phase‐trapped cyclotron resonant electrons satisfy the second‐order resonance condition and gain energy from waves. While phase‐bunched cyclotron resonant electrons cannot remain in resonance for long periods. They transfer energy to waves and are scattered to smaller pitch angles. Landau resonant electrons are primarily energized by waves. For both types of resonances, advection coefficients are greater than diffusion coefficients when the wave amplitude is large. Our study highlights the important role of advection in electron dynamics modulation resulting from nonlinear wave‐particle interactions.
The Vertical Tilt of Mesoscale Eddy in the Northern South China Sea in a High‐Resolution Numerical Simulation
Authors: Men Guorui , Wan Xiuquan , Ma Weiwei 
Published: July 2024

AbstractUsing a high‐resolution numerical model, we investigate the influence of slope topography on the vertical tilted structure of mesoscale eddies in the northern South China Sea (NSCS). The model effectively captures key features including trajectories, intensities, and three‐dimensional tilted structures of these eddies. By compositing all NSCS eddies on the slope and in the basin, a more pronounced southwestward tilt in slope eddies is found from the sea surface down to the deep, compared to basin eddies. The tilt distance of slope eddies is approximately 1.8 times that of basin eddies, with the strongest eddy tilt near the Dongsha Islands. Variations in topography gradient induce noticeable changes in both the magnitude and direction of the eddy tilt. Due to potential vorticity conservation, the eddies' lower part follows isobaths, while the upper part drifts southwestward. This rapidly increases a southward eddy tilt during the upslope phase (USP) and a gradual transition to a southwestward tilt in the downslope phase (DSP). Moreover, the lower eddy part responds more significantly and earlier (about 20 days) to topography than the upper eddy part, moving faster and tilt‐developing more rapidly. The lower eddy part tilts larger during the USP, roughly 2.5 times than that of the upper eddy part. In the subsequent DSP, the tilt of lower eddy part decreases, about half of that in the upper eddy part. This study reveals the complex interactions between mesoscale eddies and steep slope topography, aiding further understanding the dynamics of eddy tilt and propagation.
Summertime Ozone Production at Carlsbad Caverns National Park, New Mexico: Influence of Oil and Natural Gas Development
Authors: Marsavin Andrey , Pan Da , Pollack Ilana B. , Zhou Yong , Sullivan Amy P. , Naimie Lillian E. , Benedict Katherine B. , Juncosa Calahoranno Julieta F. , Fischer Emily V. , Prenni Anthony J. , Schichtel Bret A. , Sive Barkley C. , Collett Jeffrey L. 
Published: July 2024

AbstractSoutheastern New Mexico's Carlsbad Caverns National Park (CAVE) has increasingly experienced summertime ozone (O3) exceeding an 8‐hr average of 70 parts per billion by volume (ppbv). The park is located in the western part of the Permian oil and natural gas (O&G) basin, where production rates have increased fivefold in the last decade. We investigate O3–precursor relationships by constraining the F0AM box model to observations of nitrogen oxides (NOx = NO + NO2) and a suite of volatile organic compounds (VOCs) collected at CAVE during summer 2019. O&G‐related VOCs dominated the calculated VOC reactivity with hydroxyl radicals (OH) on days when O3 concentrations were primarily controlled by local photochemistry. Radical budget analysis showed that NOx levels were high enough to impose VOC sensitivity on O3 production in the morning hours, while subsequent NOx loss through photochemical consumption led to NOx‐sensitive conditions in the afternoon. Maximum daily O3 was responsive to both NOx and O&G‐related VOC reductions, with NOx reductions proving most effective. The model underestimated observed O3 during a 5‐day high O3 episode that was influenced by photochemically aged O&G emissions, as indicated by back‐trajectory analysis, low i‐/n‐pentane ratios, enhanced secondary VOCs, and low ratios of NOx to total reactive oxidized nitrogen (NOy). Model‐observation agreement was improved by constraining model NOx with observed NOy, which approximates NOx at the time of emission, indicating that a large fraction of O3 during this episode was formed nonlocally.
Is game-based therapy effective for treating cognitive deficits in adults with schizophrenia? Evidence from a randomized controlled trial
Authors: Wang Junkai , Zhang Jie , Xu Peng , Qian Tianyi , Tan Shuping , Liang Peipeng 
Published: July 2024

AbstractCognitive deficits in schizophrenia are a major contributor to poor functional outcomes and everyday functioning, making them a promising therapeutic target. Recent years have witnessed a dramatic increase in the use of digital interventions, such as game-based therapy, targeting various domains of cognition to treat mental disorders. Game-based digital interventions have been suggested to have therapeutic value in health care for people with schizophrenia. To support this idea, a novel, online training program (Komori Life) that targets cognitive deficits in schizophrenia was tested for feasibility of use and initial efficiency. Inpatients with schizophrenia were randomized to complete 20 sessions of either Komori Life (N = 40 completers) or treatment as usual (N = 40 completers). Cognitive and clinical assessments were performed at enrollment and after completion of the training intervention for all patients. In addition, 32 healthy volunteers were recruited as controls, and an eye-tracking paradigm was employed to assess attentional biases to emotional information before and after game intervention for all subjects. The results showed that there were no group differences in cognitive or clinical assessments at baseline between the two patient groups. After game training, there were still no group × time interactions on cognitive or clinical assessment scores. Regarding eye movement measurements, both patient groups showed increased attention to threatening stimuli compared to healthy controls in terms of attentional maintenance at baseline. After game training, the game training group revealed greater improvement in attentional bias towards threatening scenes (decreased percentage of total duration and percentage of total fixations towards threatening stimuli) relative to the treatment as usual group. Moreover, our results partially indicated that training effectiveness was associated with cognitive improvement and that heightened attentional maintenance to threats was associated with worse cognitive performance. This study provides initial evidence that a remote, online cognitive training program is feasible and effective in improving cognitive function in schizophrenia. This form of training may serve as a complementary therapy to existing psychiatric care. Clinical trial registration: the trial is registered at http://www.chictr.org.cn, identifier ChiCTR2100048403.
Gut proinflammatory bacteria is associated with abnormal functional connectivity of hippocampus in unmedicated patients with major depressive disorder
Authors: Xiao Shu , Yang Zibin , Yan Hong , Chen Guanmao , Zhong Shuming , Chen Pan , Zhong Hui , Yang Hengwen , Jia Yanbin , Yin Zhinan , Gong Jiaying , Huang Li , Wang Ying 
Published: July 2024

AbstractAccumulating evidence has revealed the gut bacteria dysbiosis and brain hippocampal functional and structural alterations in major depressive disorder (MDD). However, the potential relationship between the gut microbiota and hippocampal function alterations in patients with MDD is still very limited. Data of resting-state functional magnetic resonance imaging were acquired from 44 unmedicated MDD patients and 42 demographically matched healthy controls (HCs). Severn pairs of hippocampus subregions (the bilateral cornu ammonis [CA1-CA3], dentate gyrus (DG), entorhinal cortex, hippocampal–amygdaloid transition area, and subiculum) were selected as the seeds in the functional connectivity (FC) analysis. Additionally, fecal samples of participants were collected and 16S rDNA amplicon sequencing was used to identify the altered relative abundance of gut microbiota. Then, association analysis was conducted to investigate the potential relationships between the abnormal hippocampal subregions FC and microbiome features. Also, the altered hippocampal subregion FC values and gut microbiota levels were used as features separately or together in the support vector machine models distinguishing the MDD patients and HCs. Compared with HCs, patients with MDD exhibited increased FC between the left hippocampus (CA2, CA3 and DG) and right hippocampus (CA2 and CA3), and decreased FC between the right hippocampal CA3 and bilateral posterior cingulate cortex. In addition, we found that the level of proinflammatory bacteria (i.e., Enterobacteriaceae) was significantly increased, whereas the level of short-chain fatty acids producing-bacteria (i.e., Prevotellaceae, Agathobacter and Clostridium) were significantly decreased in MDD patients. Furthermore, FC values of the left hippocampal CA3- right hippocampus (CA2 and CA3) was positively correlated with the relative abundance of Enterobacteriaceae in patients with MDD. Moreover, altered hippocampal FC patterns and gut microbiota level were considered in combination, the best discrimination was obtained (AUC = 0.92). These findings may provide insights into the potential role of gut microbiota in the underlying neuropathology of MDD patients.
NOP2 facilitates EZH2-mediated epithelial–mesenchymal transition by enhancing EZH2 mRNA stability via m5C methylation in lung cancer progression
Authors: Yang Ying , Fan Hongzhao , Liu Hongyang , Lou Xueling , Xiao Nan , Zhang Chenxing , Chen Huanxiang , Chen Shuangshuang , Gu Huihui , Liu Hongchun , Wan Junhu 
Published: July 2024

AbstractNOP2, a member of the NOL1/NOP2/SUN domain (NSUN) family, is responsible for catalyzing the posttranscriptional modification of RNA through 5-methylcytosine (m5C). Dysregulation of m5C modification has been linked to the pathogenesis of various malignant tumors. Herein, we investigated the expression of NOP2 in lung adenocarcinoma (LUAD) tissues and cells, and found that it was significantly upregulated. Moreover, lentivirus-mediated overexpression of NOP2 in vitro resulted in enhanced migration and invasion capabilities of lung cancer cells, while in vivo experiments demonstrated its ability to promote the growth and metastasis of xenograft tumors. In contrast, knockdown of NOP2 effectively inhibited the growth and metastasis of lung cancer cells. RNA-sequencing was conducted to ascertain the downstream targets of NOP2, and the findings revealed a significant upregulation in EZH2 mRNA expression upon overexpression of NOP2. Subsequent validation experiments demonstrated that NOP2 exerted an m5C-dependent influence on the stability of EZH2 mRNA. Additionally, our investigations revealed a co-regulatory relationship between NOP2 and the m5C reader protein ALYREF in modulating the stability of EZH2 mRNA. Notably, the NOP2/EZH2 axis facilitated the malignant phenotype of lung cancer cells by inducing epithelial–mesenchymal transition (EMT) both in vitro and in vivo. Mechanistically, ChIP analysis proved that EZH2 counteracted the impact of NOP2 on the occupancy capacity of EZH2 and H3K27me3 in the promoter regions of E-cadherin, a gene crucial for regulating EMT. In a word, our research highlights the significant role of NOP2 in LUAD and offers novel mechanistic insights into the NOP2/ALYREF/EZH2 axis, which holds promise as a potential target for lung cancer therapy.
TACSTD2 in gelatinous drop-like corneal dystrophy: variant functional analysis and expression in the cornea after limbal stem cell transplantation
Authors: Skorodumova Liubov O. , Grafskaia Ekaterina N. , Kharlampieva Daria D. , Maltsev Dmitry I. , Petrova Tatiana V. , Kanygina Alexandra V. , Fedoseeva Elena V. , Makarov Pavel V. , Malyugin Boris E. 
Published: July 2024

Abstract
Gelatinous drop-like corneal dystrophy (GDLD) is a rare autosomal recessive eye disease. GDLD is characterized by the loss of barrier function in corneal epithelial cells (CECs) and amyloid deposition due to pathogenic variants in the TACSTD2 gene. Limbal stem cell transplantation (LSCT) has been suggested as an effective therapeutic alternative for patients with GDLD. However, despite LSCT, amyloid deposition recurs in some patients. The pathogenesis of recurrence is poorly studied. We present the case of a patient with GDLD. Genetic analysis revealed a homozygous deletion, NM_002353.3:c.653del, in the TACSTD2 gene. Functional analysis in a cell model system revealed the loss of the transmembrane domain and subcellular protein mislocalization. The patient with GDLD underwent direct allogeneic LSCT with epithelial debridement followed by deep anterior lamellar keratoplasty 10 months later due to amyloid deposition and deterioration of vision. Taken together, the results of transcriptome analysis and immunofluorescence staining of post-LSCT corneal sample with amyloid deposits obtained during keratoplasty demonstrated complete restoration of wild-type TACSTD2 expression, indicating that donor CECs replaced host CECs. Our study provides experimental evidence that amyloid deposition can recur after LSCT despite complete restoration of wild-type TACSTD2 expression.
PRC2-AgeIndex as a universal biomarker of aging and rejuvenation
Authors: Moqri Mahdi , Cipriano Andrea , Simpson Daniel J. , Rasouli Sajede , Murty Tara , de Jong Tineke Anna , Nachun Daniel , de Sena Brandine Guilherme , Ying Kejun , Tarkhov Andrei , Aberg Karolina A. , van den Oord Edwin , Zhou Wanding , Smith Andrew , Mackall Crystal , Gladyshev Vadim N. , Horvath Steve , Snyder Michael P. , Sebastiano Vittorio 
Published: July 2024

AbstractDNA methylation (DNAm) is one of the most reliable biomarkers of aging across mammalian tissues. While the age-dependent global loss of DNAm has been well characterized, DNAm gain is less characterized. Studies have demonstrated that CpGs which gain methylation with age are enriched in Polycomb Repressive Complex 2 (PRC2) targets. However, whole-genome examination of all PRC2 targets as well as determination of the pan-tissue or tissue-specific nature of these associations is lacking. Here, we show that low-methylated regions (LMRs) which are highly bound by PRC2 in embryonic stem cells (PRC2 LMRs) gain methylation with age in all examined somatic mitotic cells. We estimated that this epigenetic change represents around 90% of the age-dependent DNAm gain genome-wide. Therefore, we propose the “PRC2-AgeIndex,” defined as the average DNAm in PRC2 LMRs, as a universal biomarker of cellular aging in somatic cells which can distinguish the effect of different anti-aging interventions.
Distinct neural mechanisms for heading retrieval and context recognition in the hippocampus during spatial reorientation
Authors: Gagliardi Celia M. , Normandin Marc E. , Keinath Alexandra T. , Julian Joshua B. , Lopez Matthew R. , Ramos-Alvarez Manuel-Miguel , Epstein Russell A. , Muzzio Isabel A. 
Published: July 2024

AbstractReorientation, the process of regaining one’s bearings after becoming lost, requires identification of a spatial context (context recognition) and recovery of facing direction within that context (heading retrieval). We previously showed that these processes rely on the use of features and geometry, respectively. Here, we examine reorientation behavior in a task that creates contextual ambiguity over a long timescale to demonstrate that male mice learn to combine both featural and geometric cues to recover heading. At the neural level, most CA1 neurons persistently align to geometry, and this alignment predicts heading behavior. However, a small subset of cells remaps coherently in a context-sensitive manner, which serves to predict context. Efficient heading retrieval and context recognition correlate with rate changes reflecting integration of featural and geometric information in the active ensemble. These data illustrate how context recognition and heading retrieval are coded in CA1 and how these processes change with experience.
scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning
Authors: Wang Jingtao , Fonseca Gregory J. , Ding Jun 
Published: July 2024

AbstractSingle-cell sequencing is a crucial tool for dissecting the cellular intricacies of complex diseases. Its prohibitive cost, however, hampers its application in expansive biomedical studies. Traditional cellular deconvolution approaches can infer cell type proportions from more affordable bulk sequencing data, yet they fall short in providing the detailed resolution required for single-cell-level analyses. To overcome this challenge, we introduce “scSemiProfiler”, an innovative computational framework that marries deep generative models with active learning strategies. This method adeptly infers single-cell profiles across large cohorts by fusing bulk sequencing data with targeted single-cell sequencing from a few rigorously chosen representatives. Extensive validation across heterogeneous datasets verifies the precision of our semi-profiling approach, aligning closely with true single-cell profiling data and empowering refined cellular analyses. Originally developed for extensive disease cohorts, “scSemiProfiler” is adaptable for broad applications. It provides a scalable, cost-effective solution for single-cell profiling, facilitating in-depth cellular investigation in various biological domains.