bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding Causal Gateways of Precipitation Over the Contiguous United States
Authors: Yang Xueli , Wang Zhi‐Hua , Wang Chenghao , Lai Ying‐Cheng 
Published: February 2023

AbstractIdentifying regions that mediate regional propagation of atmospheric perturbations is important to assessing the susceptibility and resilience of complex hydroclimate systems. Detecting the regional gateways through causal inference, can help unravel the interplay of physical processes and inform projections of future changes. In this study, we characterize the causal interactions among nine climate regions in the contiguous United States using long‐term (1901–2018) precipitation data. The constructed causal networks reveal the cross‐regional propagation of precipitation perturbations. Results show that the Ohio Valley region acts as an atmospheric gateway for precipitation and moisture transport in the U.S., which is largely regulated by the regional convective uplift. The findings have implications for improving predicative capacity of hydroclimate modeling of regional precipitation.
On Current Sheets and Associated Density Spikes in Titan’s Ionosphere as Seen From Cassini
Authors: Kim Konstantin , Edberg Niklas J. T. , Shebanits Oleg , Wahlund Jan‐Erik , Vigren Erik , Bertucci Cesar 
Published: February 2023

AbstractThe Cassini spacecraft made in‐situ measurements of Titan's plasma environment during 126 close encounters between 2004 and 2017. Here we report on observations from the Radio and Plasma Waves System/Langmuir probe instrument (RPWS/LP) from which we have observed, primarily on the outbound leg, a localized increase of the electron density by up to 150 cm−3 with respect to the background. This feature, appearing as an electron density spike in the data, is found during 28 of the 126 flybys. The data from RPWS/LP, the electron spectrometer from the Cassini Plasma Spectrometer package , and the magnetometer is used to calculate electron densities and magnetic field characteristics. The location of these structures around Titan with respect to the nominal corotation direction and the sun direction is investigated. We find that the electron density spikes are primarily observed on the dayside and ramside of Titan. We also observe magnetic field signatures that could suggest the presence of current sheets in most cases. The density spikes are extended along the trajectory of the spacecraft with the horizontal scale of ∼537 ± 160 km and vertical scale ∼399 ± 163 km. We suggest that the density spikes are formed as a result of the current sheet formation.
Extreme Copper Isotope Fractionation Driven by Redox Oscillation During Gleysols Weathering in Mun River Basin, Northeast Thailand
Authors: Zheng Xiaodi , Han Guilin , Zhang Qian , Liang Bin , Liu Man , Yu Changxun , Liu Linan , Zhao Ye , Song Zhaoliang 
Published: February 2023

AbstractCopper (Cu) isotopes are utilized to track Cu geochemical cycling in weathered gleysols of tropical zones. A significant isotope fractionation of Cu in these soils is primarily redox‐controlled; however, it is rarely reported how the frequency of redox fluctuations affects the soil Cu isotope signature. This study investigated the variations of Cu content and isotope fractionation in two low‐humic gleysol profiles (S1 and S2) from a dry tropical savanna zone. Owing to redox oscillation during weathering, δ65Cu values in profile S2 showed a stronger positive correlation with the mafic index of alteration of reducing environment than S1, and isotopically light Cu is more retained in the Zone II of profile S2 than S1. As the frequency of redox fluctuation increased, the retained stable Cu(I) species and light Cu isotopes increased in the residual soils through re‐adsorption or re‐precipitation by iron oxyhydroxide (i.e., ferrihydrite). Importantly, an Mn‐enriched zone was formed after reduction events in profile S2, and found to be enriched in light Cu isotopes. The heavier Cu fraction might be lost by adsorption on Fe oxyhydroxides in the Mn‐rich zone, while the relatively light Cu might be retained through adsorption on Mn oxyhydroxides. Additionally, a significant Soil Organic Carbon (SOC) contribution to Cu was found due to the high δ65Cu‐SOC correlation (R2 = 0.80) in S1 (depth <1 m). Therefore, our study shows that the Cu isotope signature can respond to redox changes in the terrestrial ecosystem, and these Cu isotope signatures may have significant implications for assessing soil ecological vulnerability under future climate change scenarios.
Surface and Crustal Response to Deep Subduction Dynamics: Insights From the Apennines, Italy
Authors: Lanari R. , Reitano R. , Faccenna C. , Agostinetti N. Piana , Ballato P. 
Published: February 2023

AbstractThe topography of orogenic belts responds to several contributions operating at short and long temporal and spatial (i.e., wavelengths) scales, from the surface to the deep mantle. Here, we aim to investigate the connection between morphometric characteristics, exhumation, and crustal deformation along and across the Italian Apennines, by comparing superficial with deeper data. Specifically, we present four sets of observations that are constructed by gathering previous data and adding new analyses and inferences, that include: (a) a new geomorphological set of analyses; (b) a database of available low temperature thermochronological cooling ages; (c) a reconstruction of drainage divide evolution in time and space based on the age of the youngest lacustrine deposits within each extensional basin; (d) Moho depth from receiver functions, gathering previous estimates and 13 new ones. From these sets of data, it emerges that across the main drainage divide of the Apennines, the morphological characteristics, the style of deformation and the spatial distribution of exhumation correlate with the geometries of the Moho and are associated with a strong asymmetry in the Northern‐Apennines and a clear symmetry in the Central‐Apennines. We interpret these results as evidence of a strong coupling between shallower and deeper geometries, that are most likely related to complex along‐strike variations in the Apennines geodynamic setting.
Effects of Large Macropores on Saline Water Evaporation From Marsh Soil
Authors: Xu Xinghua , Xin Pei , Zhou Tingzhang , Yu Xiayang 
Published: February 2023

AbstractMacropores such as crab burrows are a common feature of salt marsh sediment and are recognized as an important factor influencing pore‐water flow in salt marshes. In this study, we examined the effect of macropores on saline water evaporation and pore‐water salinity based on laboratory experiments and numerical simulations. Soil columns with and without an artificial macropore were packed with clay‐loam and were set with different hydraulic heads fixed at the bottom. The results showed that increase in pore‐water salinity significantly reduced evaporation rates. The preferential flow induced by macropores recharged the soil surrounding macropores and maintained higher evaporation rates in comparison with homogeneous soil without macropores. As macropores induced lateral flow, the pore‐water salinity in shallow soil around the macropores was reduced but that in the area away from the macropores was increased. These impacts were more remarkable on the soil layers with higher hydraulic heads. A sensitivity analysis showed that with a higher initial pore‐water salinity, the macropore's impact on soil evaporation rates was more remarkable for both clay‐loam and silt‐loam. These results revealed the effect of macropores on soil evaporation processes and soil conditions, and also shed light on associated biogeochemical processes in salt marshes.
Changes at glutamate tripartite synapses in the prefrontal cortex of a new animal model of resilience/vulnerability to acute stress
Authors: Bonifacino Tiziana , Mingardi Jessica , Facchinetti Roberta , Sala Nathalie , Frumento Giulia , Ndoj Elona , Valenza Marta , Paoli Caterina , Ieraci Alessandro , Torazza Carola , Balbi Matilde , Guerinoni Michele , Muhammad Nadeem , Russo Isabella , Milanese Marco , Scuderi Caterina , Barbon Alessandro , Steardo Luca , Bonanno Giambattista , Popoli Maurizio , Musazzi Laura 
Published: February 2023

AbstractStress represents a main risk factor for psychiatric disorders. Whereas it is known that even a single trauma may induce psychiatric disorders in humans, the mechanisms of vulnerability to acute stressors have been little investigated. In this study, we generated a new animal model of resilience/vulnerability to acute footshock (FS) stress in rats and analyzed early functional, molecular, and morphological determinants of stress vulnerability at tripartite glutamate synapses in the prefrontal cortex (PFC). We found that adult male rats subjected to FS can be deemed resilient (FS-R) or vulnerable (FS-V), based on their anhedonic phenotype 24 h after stress exposure, and that these two populations are phenotypically distinguishable up to two weeks afterwards. Basal presynaptic glutamate release was increased in the PFC of FS-V rats, while depolarization-evoked glutamate release and synapsin I phosphorylation at Ser9 were increased in both FS-R and FS-V. In FS-R and FS-V rats the synaptic expression of GluN2A and apical dendritic length of prelimbic PFC layers II–III pyramidal neurons were decreased, while BDNF expression was selectively reduced in FS-V. Depolarization-evoked (carrier-mediated) glutamate release from astroglia perisynaptic processes (gliosomes) was selectively increased in the PFC of FS-V rats, while GLT1 and xCt levels were higher and GS expression reduced in purified PFC gliosomes from FS-R. Overall, we show for the first time that the application of the sucrose intake test to rats exposed to acute FS led to the generation of a novel animal model of resilience/vulnerability to acute stress, which we used to identify early determinants of maladaptive response related to behavioral vulnerability to stress.
Evaluation of red-complex bacteria loads in complete denture patients: a pilot study
Authors: Veseli Enis , Staka Gloria , Tovani-Palone Marcos Roberto 
Published: February 2023

Abstract
Objective
This pilot study aimed to evaluate red-complex bacteria (RCB) loads in edentulous patients, before and after dentures’ insertion.

Materials and methods
Thirty patients were included in the study. Deoxyribonucleic acid (DNA) isolated from bacterial samples were obtained from the dorsum of the tongue before and 3 months after complete dentures (CDs) insertion in order to identify the presence of RCB (Tannerella forsythia, Porphyromonas gingivalis, and Treponema denticola) and quantify their loads, using real-time polymerase chain reaction (RT-PCR). Bacterial loads were represented as “Lg (genome equivalents/sample)” and the data classified according to the “ParodontoScreen” test.

Results
Significant changes in bacterial loads were observed before and 3 months after the CDs insertion for: P. gingivalis (0.40 ± 0.90 vs 1.29 ± 1.64, p = 0.0007), T. forsythia (0.36 ±0.94 vs 0.87 ± 1.45, p = 0.005), and T. denticola (0.11 ± 0.41 vs 0.33 ± 0.75, p = 0.03). Before the CDs insertion, all patients had a normal bacterial prevalence range (100%) for all analyzed bacteria. Three months after the insertion, 2 (6.7%) of them had a moderate bacterial prevalence range for P. gingivalis, while 28 (93.3%) had a normal bacterial prevalence range.

Conclusion
The use of CDs has a significant impact on increasing RCB loads in edentulous patients.
Delivery of microRNA-302a-3p by APTES modified hydroxyapatite nanoparticles to promote osteogenic differentiation in vitro
Authors: Limlawan Pirawish , Marger Laurine , Durual Stéphane , Vacharaksa Anjalee 
Published: February 2023

Abstract
Objective
To demonstrate the miRNA delivery by hydroxyapatite nanoparticles modified with APTES (HA-NPs-APTES) and promote osteogenic gene expression.

Materials and methods
Osteosarcoma cells (HOS, MG-63) and primary human mandibular osteoblasts (HmOBs) were co-cultured with HA-NPs-APTES conjugated with miRNA-302a-3p. Resazurin reduction assay was performed to evaluate HA-NPs-APTES biocompatibility. Intracellular uptake was demonstrated by confocal fluorescent and scanning electron microscopy. The miRNA-302a-3p and its mRNA targets expression levels including COUP-TFII and other osteogenic genes were assessed by qPCR on day1 or day5 post-delivery. Calcium deposition induced by the osteogenic gene upregulation was shown by alizarin red staining on day7 and 14 post-delivery.

Results
Proliferation of HOS cells treated with HA-NPs-APTES was similar to that of untreated cells. HA-NPs-APTES was visualized in cell cytoplasm within 24 hours. MiRNA-302a-3p level was upregulated in HOS, MG-63 and HmOBs as compared to untreated cells. As a result, COUP-TFII mRNA expression was reduced, followed by an increase of RUNX2 and other osteogenic genes mRNA expression. Calcium deposition induced by HA-NPs-APTES-miR-302a-3p in HmOBs was significantly higher than in untreated cells.

Conclusion
HA-NPs-APTES may support the delivery of miRNA-302a-3p into bone cells, as assessed by osteogenic gene expression and differentiation improvement once this combination is used on osteoblast cultures.
m5C-dependent cross-regulation between nuclear reader ALYREF and writer NSUN2 promotes urothelial bladder cancer malignancy through facilitating RABL6/TK1 mRNAs splicing and stabilization
Authors: Wang Ning , Chen Ri-xin , Deng Min-hua , Wei Wen-su , Zhou Zhao-hui , Ning Kang , Li Yong-hong , Li Xiang-dong , Ye Yun-lin , Wen Jun-hua , Dong Biao , Zhang Xue-pei , Liu Zhuo-wei , Zhou Fang-jian 
Published: February 2023

AbstractThe significance of 5-methylcytosine (m5C) methylation in human malignancies has become an increasing focus of investigation. Here, we show that m5C regulators including writers, readers and erasers, are predominantly upregulated in urothelial carcinoma of the bladder (UCB) derived from Sun Yat-sen University Cancer Center and The Cancer Genome Atlas cohort. In addition, NOP2/Sun RNA methyltransferase family member 2 (NSUN2) as a methyltransferase and Aly/REF export factor (ALYREF) as a nuclear m5C reader, are frequently coexpressed in UCB. By applying patient-derived organoids model and orthotopic xenograft mice model, we demonstrate that ALYREF enhances proliferation and invasion of UCB cells in an m5C-dependent manner. Integration of tanscriptome-wide RNA bisulphite sequencing (BisSeq), RNA-sequencing (RNA-seq) and RNA Immunoprecipitation (RIP)-seq analysis revealed that ALYREF specifically binds to hypermethylated m5C site in RAB, member RAS oncogene family like 6 (RABL6) and thymidine kinase 1 (TK1) mRNA via its K171 domain. ALYREF controls UCB malignancies through promoting hypermethylated RABL6 and TK1 mRNA for splicing and stabilization. Moreover, ALYREF recognizes hypermethylated m5C site of NSUN2, resulting in NSUN2 upregulation in UCB. Clinically, the patients with high coexpression of ALYREF/RABL6/TK1 axis had the poorest overall survival. Our study unveils an m5C dependent cross-regulation between nuclear reader ALYREF and m5C writer NSUN2 in activation of hypermethylated m5C oncogenic RNA through promoting splicing and maintaining stabilization, consequently leading to tumor progression, which provides profound insights into therapeutic strategy for UCB.
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics
Authors: Jun Seong-Hwan , Toosi Hosein , Mold Jeff , Engblom Camilla , Chen Xinsong , O’Flanagan Ciara , Hagemann-Jensen Michael , Sandberg Rickard , Aparicio Samuel , Hartman Johan , Roth Andrew , Lagergren Jens 
Published: February 2023

AbstractFunctional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer’s proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.
Prolonged experimental CD4+ T-cell depletion does not cause disease progression in SIV-infected African green monkeys
Authors: Le Hingrat Quentin , Sette Paola , Xu Cuiling , Rahmberg Andrew R. , Tarnus Lilas , Annapureddy Haritha , Kleinman Adam , Brocca-Cofano Egidio , Sivanandham Ranjit , Sivanandham Sindhuja , He Tianyu , Capreri Daniel J. , Ma Dongzhu , Estes Jacob D. , Brenchley Jason M. , Apetrei Cristian , Pandrea Ivona 
Published: February 2023

AbstractCD4+ T-cell depletion is a hallmark of HIV infection, leading to impairment of cellular immunity and opportunistic infections, but its contribution to SIV/HIV-associated gut dysfunction is unknown. Chronically SIV-infected African Green Monkeys (AGMs) partially recover mucosal CD4+ T-cells, maintain gut integrity and do not progress to AIDS. Here we assess the impact of prolonged, antibody-mediated CD4 + T-cell depletion on gut integrity and natural history of SIV infection in AGMs. All circulating CD4+ T-cells and >90% of mucosal CD4+ T-cells are depleted. Plasma viral loads and cell-associated viral RNA in tissues are lower in CD4+-cell-depleted animals. CD4+-cell-depleted AGMs maintain gut integrity, control immune activation and do not progress to AIDS. We thus conclude that CD4+ T-cell depletion is not a determinant of SIV-related gut dysfunction, when gastrointestinal tract epithelial damage and inflammation are absent, suggesting that disease progression and resistance to AIDS are independent of CD4+ T-cell restoration in SIVagm-infected AGMs.
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses
Authors: Tan Qiao Wen , Lim Peng Ken , Chen Zhong , Pasha Asher , Provart Nicholas , Arend Marius , Nikoloski Zoran , Mutwil Marek 
Published: February 2023

AbstractAbiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy,Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression betweenArabidopsisandMarchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating thatMarchantiaperforms arithmetic multiplication to respond to multiple stresses. Lastly, two online resources (https://conekt.plant.toolsandhttp://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi) are provided to facilitate the study of gene expression inMarchantiaexposed to abiotic stresses.
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice
Authors: Nieweglowska Eliza S. , Brilot Axel F. , Méndez-Moran Melissa , Kokontis Claire , Baek Minkyung , Li Junrui , Cheng Yifan , Baker David , Bondy-Denomy Joseph , Agard David A. 
Published: February 2023

AbstractTo protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus—a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the phage nucleus while other phage and host proteins are excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that nucleus fragments isolated from ϕPA3 infected Pseudomonas aeruginosa form a 2-dimensional lattice, having p2 or p4 symmetry. We further demonstrate that recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into similar 2D sheets with p2 and p4 symmetry. We resolve the dominant p2 symmetric state to 3.9 Å by cryo-EM. Our structure reveals a two-domain core, organized into quasi-symmetric tetramers. Flexible loops and termini mediate adaptable inter-tetramer contacts that drive subunit assembly into a lattice and enable the adoption of different symmetric states. While the interfaces between subunits are mostly well packed, two are open, forming channels that likely have functional implications for the transport of proteins, mRNA, and small molecules.
Associations of timing of physical activity with all-cause and cause-specific mortality in a prospective cohort study
Authors: Feng Hongliang , Yang Lulu , Liang Yannis Yan , Ai Sizhi , Liu Yaping , Liu Yue , Jin Xinyi , Lei Binbin , Wang Jing , Zheng Nana , Chen Xinru , Chan Joey W. Y. , Sum Raymond Kim Wai , Chan Ngan Yin , Tan Xiao , Benedict Christian , Wing Yun Kwok , Zhang Jihui 
Published: February 2023

AbstractThere is a growing interest in the role of timing of daily behaviors in improving health. However, little is known about the optimal timing of physical activity to maximize health benefits. We perform a cohort study of 92,139 UK Biobank participants with valid accelerometer data and all-cause and cause-specific mortality outcomes, comprising over 7 years of median follow-up (638,825 person-years). Moderate-to-vigorous intensity physical activity (MVPA) at any time of day is associated with lower risks for all-cause, cardiovascular disease, and cancer mortality. In addition, compared with morning group (>50% of daily MVPA during 05:00-11:00), midday-afternoon (11:00-17:00) and mixed MVPA timing groups, but not evening group (17:00-24:00), have lower risks of all-cause and cardiovascular disease mortality. These protective associations are more pronounced among the elderly, males, less physically active participants, or those with preexisting cardiovascular diseases. Here, we show that MVPA timing may have the potential to improve public health.