bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Antecedent Topography on Complex Crater Formation
Authors: Hood Don R. , Young Brennan W. , Cohen‐Zada Aviv L. , James Peter B. , Ewing Ryan C. , Lee Jeffery S. 
Published: July 2024

AbstractImpact craters that form on every planetary body provide a record of planetary surface evolution. On heavily cratered surfaces, new craters that form often overlap antecedent craters, but it is unknown how the presence of antecedent craters alters impact crater formation. We use overlapping complex crater pairs on the lunar surface to constrain this process and find that crater rims are systematically lower where they intersect antecedent crater basins. The rim morphology of the new crater depends on the depth of the antecedent crater and the degree of overlap between the craters. Our observations suggest that new craters do not always obliterate underlying topography and that transient rim collapse is altered by antecedent topography. This study represents the first formalization of the influence of antecedent topography on rim morphology and provides process insight into a common impact scenario relevant to the geology of potential Artemis landing sites.
Why Do DJF 2023/24 Upper‐Level 200‐hPa Geopotential Height Forecasts Look Different From the Expected El Niño Response?
Authors: Chen Mingyue , Kumar Arun , L’Heureux Michelle , Peng Peitao , Zhang Tao , Hoerling Martin P. , Diaz Henry F. 
Published: July 2024

AbstractWe investigate why the North American Multi‐Model Ensemble (NMME) upper‐level height forecast for December–February (DJF) 2023/24 differs from the expected El Niño response. These atypical height anomalies emerged despite the fact a strong El Niño was forecast. The analysis focuses on diagnosing the NMME forecasts of DJF 2023/24 for SSTs and 200‐hPa heights initialized at the beginning of November 2023 relative to other ensemble mean NMME DJF forecasts dating back to 1982. The results demonstrate that forecasts of the 200‐hPa height anomalies had a large contribution from warming trends in global SSTs. It is the combination of trends and the expected El Niño teleconnection that results in the forecast height anomalies. Increasingly, for forecasts of geopotential height anomalies during the recent El Niño winters, the amplitude of trends is nearly equal to the signal from El Niño and has implications for the climatological base period selection for seasonal forecasts.
Association of High‐Latitude Geomagnetic Perturbations and Pi1 and Pi2 Pulsations With the Three Steps of Auroral Onset Arc Development at Substorm Onset
Authors: Talha Madeeha , Miyashita Yukinaga 
Published: July 2024

AbstractUsing Time History of Events and Macroscale Interactions during Substorms (THEMIS) data, we studied the stepwise development in high‐latitude geomagnetic perturbations and Pi1 and Pi2 pulsations during substorm onsets and their association with stepwise auroral onset arc development by analyzing four substorm events. We found that the geomagnetic perturbations and pulsations which are magnetic signatures of the substorm on the ground show stepwise changes and excitation similar to the development of the auroral onset arc which is the visual manifestation of the substorm. We observed minor to small changes in magnetic perturbations and excitation of Pi2 pulsations before initial brightening (IB), and the subsequent excitation of Pi1 and the second Pi2 at or around the further enhancement of onset arc (FE). Then, a steep fall in the magnetic northward component, and the largest‐amplitude and highest‐frequency Pi1 and Pi2 pulsations appeared at or after poleward expansion (PE). The appearance of FE in all four events and its association with magnetic perturbations and pulsations suggest that FE is an important step in addition to IB and PE. The detailed analysis of the FE step using ground‐ and space‐based data may provide information on the substorm triggering mechanism, the sequence of mechanisms behind the substorm, as well as the mechanisms responsible for the excitation of Pi1 and Pi2 pulsations.
Updating Measures of CME Arrival Time Errors
Authors: Kay C. , Palmerio E. , Riley P. , Mays M. L. , Nieves‐Chinchilla T. , Romano M. , Collado‐Vega Y. M. , Wiegand C. , Chulaki A. 
Published: July 2024

AbstractCoronal mass ejections (CMEs) drive space weather effects at Earth and the heliosphere. Predicting their arrival is a major part of space weather forecasting. In 2013, the Community Coordinated Modeling Center started collecting predictions from the community, developing an Arrival Time Scoreboard (ATSB). Riley et al. (2018, https://doi.org/10.1029/2018sw001962) analyzed the first 5 years of the ATSB, finding a bias of a few hours and uncertainty of order 15 hr. These metrics have been routinely quoted since 2018, but have not been updated despite continued predictions. We revise analysis of the ATSB using a sample 3.5 times the size of that in the original study. We find generally the same overall metrics, a bias of −2.5 hr, mean absolute error of 13.2 hr, and standard deviation of 17.4 hr, with only a slight improvement comparing between the previously‐used and new sets. The most well‐established, frequently‐submitted model results tend to outperform those from seldomly‐contributed models. These “best” models show a slight improvement over the 11 year span, with more scatter between the models during early times and a convergence toward the same error metrics in recent years. We find little evidence of any correlations between the arrival time errors and any other properties. The one noticeable exception is a tendency for late predictions for short transit times and vice versa. We propose that any model‐driven systematic errors may be washed out by the uncertainties in CME reconstructions in characterization of the background solar wind, and suggest that improving these may be the key to better predictions.
Knowledge Extraction via Machine Learning Guides a Topology‐Based Permeability Prediction Model
Authors: Zhang Jia , Ma Gang , Yang Zhibing , Mei Jiangzhou , Zhang Daren , Zhou Wei , Chang Xiaolin 
Published: July 2024

AbstractThe complexity and heterogeneity of pore structure present significant challenges in accurate permeability estimation. Commonly used empirical formulas neglect its microscopic and topological characteristics, thus lacking accuracy and adaptability. While machine learning (ML) and deep learning (DL) models demonstrate promising performance, but encounter challenges of data availability, computational cost, and model interpretability. The present study aims to develop a more robust and accurate permeability prediction model via knowledge extraction from ML model. We first establish an ML model between permeability and the geometry‐topology characteristics of porous media using Extreme Gradient Boosting (XGBoost) algorithm. The data set used to fit ML model is prepared from 458 samples of different types of porous media. Using the SHapley Additive exPlanations (SHAP) value, the influence of each feature on permeability prediction is quantified. It is found that the closeness centrality (topology feature), tortuosity, porosity (macroscopic features) and throat diameter, throat length, pore diameter (pore network features) are vital for permeability prediction. Guided by partial dependence calculation, the unknown function relationship between permeability and the top six important features is established. The novel permeability prediction model incorporating topology feature improves the prediction accuracy and demonstrates strong applicability across diverse data sets. This new model presents an optimal balance between simplicity and performance, rendering it a compelling alternative for permeability prediction in porous media. The research provides a novel referable framework of knowledge extraction via ML to reveal the important features and establish the potential relationship that can be extended and applied in other research fields.
Long‐Term Performance on Drought Mitigation of Soil Slope Through Bio‐Approach of MICP: Evidence and Insight from Both Field and Laboratory Tests
Authors: Ji Xin‐Lun , Tang Chao‐Sheng , Pan Xiao‐Hua , Cai Zhao‐Lin , Liu Bo , Wang Dian‐Long 
Published: July 2024

AbstractDrought is a serious global environmental issue that causes water resource scarcity and threatens agriculture and food supplements. This study aims to investigate the long‐term performance of an eco‐friendly technique‐microbial induced carbonate precipitation (MICP) on drought mitigation at field and laboratory scales. Seven in‐situ slopes treated with different MICP rounds and cementation solution concentrations were subjected to 16‐month weathering. Tests were conducted to evaluate the evaporation characteristics, water retention capacity, and CaCO3 distribution. Laboratory soil samples were further prepared to provide evidence related to underlying weathering mechanisms. The results show that MICP has a time‐dependent performance on drought mitigation. After MICP treatment, soil performs a remarkable evaporation suppression ability and the evaporation rate can decrease by 50%. This is attributed to the soluble salts which increase soil water retention capability and dense hard crust which inhibits water vapor migration into the atmosphere. However, the soluble salts and crust are sensitive to weathering thus leading to degradation of MICP. Suffering 16‐month weathering, the MICP‐induced CaCO3 decreases by more than 60%. The evaporation rate of soil increases with MICP rounds and cementation solution concentrations and can reach nearly two times of untreated soil. MICP‐treated field soil exhibits weaker water retention capacity than untreated soil because MICP alters soil microstructure which expands macropores and decreases volume of micropores. Connected macropores act as favorable evaporation channels and accelerate evaporation. To ensure MICP long‐term effects, periodical treatments are necessary. The most effective MICP treatment scheme is four to six treatment rounds and 1.0 M cementation solution.
AXDND1 is required to balance spermatogonial commitment and for sperm tail formation in mice and humans
Authors: Houston Brendan J. , Nguyen Joseph , Merriner D. Jo , O’Connor Anne E. , Lopes Alexandra M. , Nagirnaja Liina , Friedrich Corinna , Kliesch Sabine , Tüttelmann Frank , Aston Kenneth I. , Conrad Donald F. , Hobbs Robin M. , Dunleavy Jessica E. M. , O’Bryan Moira K. 
Published: July 2024

AbstractDynein complexes are large, multi-unit assemblies involved in many biological processes via their critical roles in protein transport and axoneme motility. Using next-generation sequencing of infertile men presenting with low or no sperm in their ejaculates, we identified damaging variants in the dynein-related gene AXDND1. We thus hypothesised that AXDND1 is a critical regulator of male fertility. To test this hypothesis, we produced a knockout mouse model. Axdnd1−/− males were sterile at all ages but presented with an evolving testis phenotype wherein they could undergo one round of histologically replete spermatogenesis followed by a rapid depletion of the seminiferous epithelium. Marker experiments identified a role for AXDND1 in maintaining the balance between differentiation-committed and self-renewing spermatogonial populations, resulting in disproportionate production of differentiating cells in the absence of AXDND1 and increased sperm production during initial spermatogenic waves. Moreover, long-term spermatogonial maintenance in the Axdnd1 knockout was compromised, ultimately leading to catastrophic germ cell loss, destruction of blood–testis barrier integrity and immune cell infiltration. In addition, sperm produced during the first wave of spermatogenesis were immotile due to abnormal axoneme structure, including the presence of ectopic vesicles and abnormalities in outer dense fibres and microtubule doublet structures. Sperm output was additionally compromised by a severe spermiation defect and abnormal sperm individualisation. Collectively these data identify AXDND1 as an atypical dynein complex-related protein with a role in protein/vesicle transport of relevance to spermatogonial function and sperm tail formation in mice and humans. This study underscores the importance of studying the consequences of gene loss-of-function on both the establishment and maintenance of male fertility.
Increased ONECUT2 induced by Helicobacter pylori promotes gastric cancer cell stemness via an AKT-related pathway
Authors: Lin Mi , Tu Ru-Hong , Wu Sheng-Ze , Zhong Qing , Weng Kai , Wu Yu-Kai , Lin Guang-Tan , Wang Jia-Bin , Zheng Chao-Hui , Xie Jian-Wei , Lin Jian-Xian , Chen Qi-Yue , Huang Chang-Ming , Cao Long-Long , Li Ping 
Published: July 2024

AbstractHelicobacter pylori (HP) infection initiates and promotes gastric carcinogenesis. ONECUT2 shows promise for tumor diagnosis, prognosis, and treatment. This study explored ONECUT2’s role and the specific mechanism underlying HP infection-associated gastric carcinogenesis to suggest a basis for targeting ONECUT2 as a therapeutic strategy for gastric cancer (GC). Multidimensional data supported an association between ONECUT2, HP infection, and GC pathogenesis. HP infection upregulated ONECUT2 transcriptional activity via NFκB. In vitro and in vivo experiments demonstrated that ONECUT2 increased the stemness of GC cells. ONECUT2 was also shown to inhibit PPP2R4 transcription, resulting in reduced PP2A activity, which in turn increased AKT/β-catenin phosphorylation. AKT/β-catenin phosphorylation facilitates β-catenin translocation to the nucleus, initiating transcription of downstream stemness-associated genes in GC cells. HP infection upregulated the reduction of AKT and β-catenin phosphorylation triggered by ONECUT2 downregulation via ONECUT2 induction. Clinical survival analysis indicated that high ONECUT2 expression may indicate poor prognosis in GC. This study highlights a critical role played by ONECUT2 in promoting HP infection-associated GC by enhancing cell stemness through the PPP2R4/AKT/β-catenin signaling pathway. These findings suggest promising therapeutic strategies and potential targets for GC treatment.
Biological impact and therapeutic implication of tumor-associated macrophages in hepatocellular carcinoma
Authors: Li Deming , Zhang Ting , Guo Ye , Bi Cong , Liu Ming , Wang Gang 
Published: July 2024

AbstractThe tumor microenvironment is a complex space comprised of normal, cancer and immune cells. The macrophages are considered as the most abundant immune cells in tumor microenvironment and their function in tumorigenesis is interesting. Macrophages can be present as M1 and M2 polarization that show anti-cancer and oncogenic activities, respectively. Tumor-associated macrophages (TAMs) mainly have M2 polarization and they increase tumorigenesis due to secretion of factors, cytokines and affecting molecular pathways. Hepatocellular carcinoma (HCC) is among predominant tumors of liver that in spite of understanding its pathogenesis, the role of tumor microenvironment in its progression still requires more attention. The presence of TAMs in HCC causes an increase in growth and invasion of HCC cells and one of the reasons is induction of glycolysis that such metabolic reprogramming makes HCC distinct from normal cells and promotes its malignancy. Since M2 polarization of TAMs stimulates tumorigenesis in HCC, molecular networks regulating M2 to M1 conversion have been highlighted and moreover, drugs and compounds with the ability of targeting TAMs and suppressing their M2 phenotypes or at least their tumorigenesis activity have been utilized. TAMs increase aggressive behavior and biological functions of HCC cells that can result in development of therapy resistance. Macrophages can provide cell–cell communication in HCC by secreting exosomes having various types of biomolecules that transfer among cells and change their activity. Finally, non-coding RNA transcripts can mainly affect polarization of TAMs in HCC.
Single-shot laser-driven neutron resonance spectroscopy for temperature profiling
Authors: Lan Zechen , Arikawa Yasunobu , Mirfayzi Seyed Reza , Morace Alessio , Hayakawa Takehito , Sato Hirotaka , Kamiyama Takashi , Wei Tianyun , Tatsumi Yuta , Koizumi Mitsuo , Abe Yuki , Fujioka Shinsuke , Mima Kunioki , Kodama Ryosuke , Yogo Akifumi 
Published: July 2024

AbstractThe temperature measurement of material inside of an object is one of the key technologies for control of dynamical processes. For this purpose, various techniques such as laser-based thermography and phase-contrast imaging thermography have been studied. However, it is, in principle, impossible to measure the temperature of an element inside of an object using these techniques. One of the possible solutions is measurements of Doppler brooding effect in neutron resonance absorption (NRA). Here we present a method to measure the temperature of an element or an isotope inside of an object using NRA with a single neutron pulse of approximately 100 ns width provided from a high-power laser. We demonstrate temperature measurements of a tantalum (Ta) metallic foil heated from the room temperature up to 617 K. Although the neutron energy resolution is fluctuated from shot to shot, we obtain the temperature dependence of resonance Doppler broadening using a reference of a silver (Ag) foil kept to the room temperature. A free gas model well reproduces the results. This method enables element(isotope)-sensitive thermometry to detect the instantaneous temperature rise in dynamical processes.
Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation
Authors: Cyriaque Valentine , Ibarra-Chávez Rodrigo , Kuchina Anna , Seelig Georg , Nesme Joseph , Madsen Jonas Stenløkke 
Published: July 2024

AbstractTranscriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.
Therapeutic potential of the secreted Kazal-type serine protease inhibitor SPINK4 in colitis
Authors: Wang Ying , Han Jing , Yang Guang , Zheng Shuhui , Zhou Gaoshi , Liu Xinjuan , Cao Xiaocang , Li Guang , Zhang Bowen , Xie Zhuo , Li Li , Zhang Mudan , Li Xiaoling , Chen Minhu , Zhang Shenghong 
Published: July 2024

AbstractMucus injury associated with goblet cell (GC) depletion constitutes an early event in inflammatory bowel disease (IBD). Using single-cell sequencing to detect critical events in mucus dysfunction, we discover that the Kazal-type serine protease inhibitor SPINK4 is dynamically regulated in colitic intestine in parallel with disease activities. Under chemically induced colitic conditions, the grim status in Spink4-conditional knockout mice is successfully rescued by recombinant murine SPINK4. Notably, its therapeutic potential is synergistic with existing TNF-α inhibitor infliximab in colitis treatment. Mechanistically, SPINK4 promotes GC differentiation using a Kazal-like motif to modulate EGFR-Wnt/β-catenin and -Hippo pathways. Microbiota-derived diacylated lipoprotein Pam2CSK4 triggers SPINK4 production. We also show that monitoring SPINK4 in circulation is a reliable noninvasive technique to distinguish IBD patients from healthy controls and assess disease activity. Thus, SPINK4 serves as a serologic biomarker of IBD and has therapeutic potential for colitis via intrinsic EGFR activation in intestinal homeostasis.
High-efficiency dysprosium-ion extraction enabled by a biomimetic nanofluidic channel
Authors: Xin Weiwen , Cui Yanglansen , Qian Yongchao , Liu Tianchi , Kong Xiang-Yu , Ling Haoyang , Chen Weipeng , Zhang Zhehua , Hu Yuhao , Jiang Lei , Wen Liping 
Published: July 2024

AbstractBiological ion channels exhibit high selectivity and permeability of ions because of their asymmetrical pore structures and surface chemistries. Here, we demonstrate a biomimetic nanofluidic channel (BNC) with an asymmetrical structure and glycyl-L-proline (GLP) -functionalization for ultrafast, selective, and unidirectional Dy3+ extraction over other lanthanide (Ln3+) ions with very similar electronic configurations. The selective extraction mainly depends on the amplified chemical affinity differences between the Ln3+ ions and GLPs in nanoconfinement. In particular, the conductivities of Ln3+ ions across the BNC even reach up to two orders of magnitude higher than in a bulk solution, and a high Dy3+/Nd3+ selectivity of approximately 60 could be achieved. The designed BNC can effectively extract Dy3+ ions with ultralow concentrations and thereby purify Nd3+ ions to an ultimate content of 99.8 wt.%, which contribute to the recycling of rare earth resources and environmental protection. Theoretical simulations reveal that the BNC preferentially binds to Dy3+ ion due to its highest affinity among Ln3+ ions in nanoconfinement, which attributes to the coupling of ion radius and coordination matching. These findings suggest that BNC-based ion selectivity system provides alternative routes to achieving highly efficient lanthanide separation.
Rare de novo damaging DNA variants are enriched in attention-deficit/hyperactivity disorder and implicate risk genes
Authors: Olfson Emily , Farhat Luis C. , Liu Wenzhong , Vitulano Lawrence A. , Zai Gwyneth , Lima Monicke O. , Parent Justin , Polanczyk Guilherme V. , Cappi Carolina , Kennedy James L. , Fernandez Thomas V. 
Published: July 2024

AbstractResearch demonstrates the important role of genetic factors in attention-deficit/hyperactivity disorder (ADHD). DNA sequencing of families provides a powerful approach for identifying de novo (spontaneous) variants, leading to the discovery of hundreds of clinically informative risk genes for other childhood neurodevelopmental disorders. This approach has yet to be extensively leveraged in ADHD. We conduct whole-exome DNA sequencing in 152 families, comprising a child with ADHD and both biological parents, and demonstrate a significant enrichment of rare and ultra-rare de novo gene-damaging mutations in ADHD cases compared to unaffected controls. Combining these results with a large independent case-control DNA sequencing cohort (3206 ADHD cases and 5002 controls), we identify lysine demethylase 5B (KDM5B) as a high-confidence risk gene for ADHD and estimate that 1057 genes contribute to ADHD risk. Using our list of genes harboring ultra-rare de novo damaging variants, we show that these genes overlap with previously reported risk genes for other neuropsychiatric conditions and are enriched in several canonical biological pathways, suggesting early neurodevelopmental underpinnings of ADHD. This work provides insight into the biology of ADHD and demonstrates the discovery potential of DNA sequencing in larger parent-child trio cohorts.