bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scenario Superposition Method for Real‐Time Tsunami Prediction Using a Bayesian Approach
Authors: Fujita Saneiki , Nomura Reika , Moriguchi Shuji , Otake Yu , LeVeque Randall J. , Terada Kenjiro 
Published: December 2024

AbstractIn this study, we propose a scenario superposition method for real‐time tsunami wave prediction. In the offline phase, prior to actual tsunami occurrence, hypothetical tsunami scenarios are created, and their wave data are decomposed into spatial modes and scenario‐specific coefficients by the singular value decomposition. Then, once an actual tsunami event is observed, the proposed method executes an online phase, which is a novel contribution of this study. Specifically, the predicted waveform is represented by a linear combination of training scenarios consisting of precomputed tsunami simulation results. To make such a prediction, a set of weight parameters that allow for appropriate scenario superposition is identified by the Bayesian update process. At the same time, the probability distribution of the weight parameters is obtained as reference information regarding the reliability of the prediction. Then, the waveforms are predicted by superposition with the estimated weight parameters multiplied by the waveforms of the corresponding scenarios. To validate the performance and benefits of the proposed method, a series of synthetic experiments are performed for the Shikoku coastal region of Japan with the subduction zone of the Nankai Trough. All tsunami data are derived from numerical simulations and divided into a training data set used as scenario superposition components and a test data set for an unknown real event. The predicted waveforms at the synthetic gauges closest to the Shikoku Islands are compared to those obtained using our previous prediction method incorporating sequential Bayesian updating.
Revealing Circulation Patterns Responsible for Extreme Precipitation Events Over the Hai River Basin From Moisture Transport Perspective
Authors: Li Weidong , Li Tiejian , Zhao Jie , Cao Yuan , Li Zhaoxi , Zhong Deyu 
Published: December 2024

AbstractIn July 2023, an extreme precipitation event (EPE) caused severe damage and nearly 100 fatalities in the Hai River basin, North China. Using a Lagrangian approach, we investigated the moisture transport regime and identified the circulation pattern responsible for the EPE. The primary moisture sources were the northwest Pacific (24%), southeast China (21%), and the South China Sea (20%). The circulation pattern, featuring the western Pacific subtropical high to the northeast, tropical cyclone KHANUN in the northwest Pacific, and a low‐pressure system southwest of the Hai River Basin, predominantly controlled the moisture transport. We discovered that an unprecedented EPE in 1963 exhibited a similar circulation pattern. By classifying historical EPEs into three categories based on seven atmospheric predictors, we identified circulation patterns associated with disaster‐prone events. The most frequent category is characterized by a circulation pattern with positive geopotential height anomalies in northeast Asia and negative anomalies to the south, extending from the northwest Pacific to the Hai River Basin. This classification provides insights into the atmospheric conditions conducive to severe EPEs in the region.
Spatial and Seasonal Variability of Remote and Urban Speciated Fine Particulate Matter in the United States
Authors: Hand J. L. , Prenni A. J. , Raffuse S. M. , Hyslop N. P. , Malm W. C. , Schichtel B. A. 
Published: December 2024

AbstractThe spatial and seasonal variability in the composition of major PM2.5 (particles with aerodynamic diameters less than 2.5 μm) aerosol species in the United States were characterized using data from ground‐based aerosol monitoring networks. The IMPROVE (Interagency Monitoring of Protected Visual Environments) network and the Chemical Speciation Network (CSN) operate in mostly rural/remote or urban/suburban sites, respectively. The networks have similar sampling schedules and analysis methods. Regional, monthly, and annual mean concentrations from 2019 to 2022 were calculated for ammonium sulfate (AS), ammonium nitrate (AN), particulate organic matter (POM), elemental carbon (EC), fine dust (FD), and sea salt (SS), as well as their relative contributions to reconstructed PM2.5 mass (RCFM). Organic aerosols were the largest contributor to RCFM across the United States (>40% annually, up to 80% monthly), with significant impacts from biomass smoke on POM and EC concentrations, contributions, and seasonality. AS concentrations and contributions were similar in urban and rural regions and contributed <20% annually to RCFM, considerably less than two decades ago. In general, urban concentrations were greater for AN, POM, and EC, suggesting additional urban sources. Some species, such as POM, FD, and AN, exhibited strong seasonal variability due to episodic source impacts or seasonal formation conditions. Evaluating the urban and rural monthly variability of major aerosol species is necessary for understanding the impacts of emission sources, regional transport, and atmospheric processes governing aerosol concentrations in the atmosphere.
Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate
Authors: Pecsi E. L. , Forbes S. , Guillemette F. 
Published: December 2024

AbstractOrganic by‐products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois‐Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein‐like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic‐like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A‐horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold‐climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.
Spatial and Temporal Bayesian Hierarchical Model Over Large Domains With Application to Holocene Sea Surface Temperature Reconstruction in the Equatorial Pacific
Authors: Ossandón Álvaro , Gual Javier , Rajagopalan Balaji , Kleiber William , Marchitto Thomas 
Published: December 2024

AbstractWe present a novel space‐time Bayesian hierarchical model (BHM) to reconstruct annual Sea Surface Temperature (SST) over a large domain based on SST at limited proxy (i.e., sediment core) locations. The model is tested in the equatorial Pacific. The BHM leverages Principal Component Analysis to identify dominant space‐time modes of contemporary variability of the SST field at the proxy locations and employs these modes in a Gaussian process framework to estimate SSTs across the entire domain. The BHM allows us to model the mean field and covariance, varying in space and time in the process layers of the hierarchy. Using the Markov Chain Monte Carlo (MCMC) method and suitable priors on the model parameters, posterior distributions of the model parameters and, consequently, posterior distributions of the SST fields and the attendant uncertainties are obtained for any desired year. The BHM is calibrated and validated in the contemporary period (1854–2014) and subsequently applied to reconstruct SST fields during the Holocene (0–10 ka). Results are consistent with prior inferences of La Niña‐like conditions during the Holocene. This modeling framework opens exciting prospects for modeling and reconstruction of other fields, such as precipitation, drought indices, and vegetation.
Diachronous Cretaceous Closure of the Bangong‐Nujiang‐Shyok Ocean (Westernmost Central Tibet)
Authors: Ma Anlin , Hu Xiumian , Garzanti Eduardo , Xue Weiwei , Schlagintweit Felix , Xu Yiwei , Lai Wen 
Published: December 2024

AbstractPrecisely reconstructing the diachroneity of continental collision along various Paleo‐, Meso‐, and Neo‐Tethyan branches has proved to be challenging, which limited our understanding of the dynamics of terrane suturing and associated topographic inheritance in the Tibetan Plateau. In this study, we present stratigraphic and sedimentological evidence to support, for the first time, the presence of a late Early Cretaceous remnant deep‐water basin active at least until 110 Ma in the westernmost Bangong‐Nujiang suture in central Tibet. This basin was confined by shallow‐marine deposition in the north, east, and southeast, as indicated by obitolinid biostratigraphy and maximum depositional ages for six lithostratigraphic units, while the corresponding ocean had already closed in the east by Aptian‐Albian time. Detrital zircon U‐Pb age data (n = 965), forward numerical mixture modeling, and in situ εHf(t) values point at syn‐collisional magmatic rocks along strike in the east as the main sediment source, with additional variable input from uplifted Jurassic‐lowermost Cretaceous turbidites. Our paleogeographic reconstruction indicates that the closure of the Bangong‐Nujiang Ocean progressed markedly diachronously from east to west, culminating in the final closure of the Shyok oceanic branch during the Late Cretaceous (probably by 95 and no later than 85 Ma). This westward‐younging ocean closure corresponds to a shorter duration of continental convergence in the west, resulting in less crustal shortening and tectonic uplift than in the east. This may have played a pivotal role in shaping Cenozoic topography, characterized by higher elevations in the east compared to the west along the Bangong‐Nujiang‐suture valley.
Noncoding RNA as a crucial epigenetic modulator in the degeneration of the ligamentum flavum
Authors: Zhao Yongzhao , Xiang Qian , Tian Shuo , Wu Zhenquan , Lin Jialiang , Wang Longjie , Sun Zhuoran , Li Weishi 
Published: December 2024

AbstractLigamentum flavum degeneration, including hypertrophy and ossification of the ligamentum flavum, leads to degenerative spinal stenosis in older adults. However, the underlying mechanisms of ligamentum flavum degeneration remain unclear, and therapeutic strategies are limited. Noncoding RNAs include microRNAs, circular RNAs, and long noncoding RNAs. As important epigenetic modifications, noncoding RNAs are involved in the progression of several age-related diseases, including ligamentum flavum degeneration. Previous studies have shown that noncoding RNAs can regulate the osteogenic differentiation and fibrosis of ligamentum flavum cells by regulating the expression of related genes. In this review, we discuss noncoding RNAs and their role in ligamentum flavum degeneration.
Infection of Helicobacter pylori contributes to the progression of gastric cancer through ferroptosis
Authors: Liu Yun , Miao Renjie , Xia Jinxuan , Zhou Yong , Yao Jun , Shao Shihe 
Published: December 2024

AbstractHelicobacter pylori (H. pylori) is a gram-negative pathogen that colonizes gastric epithelial cells, and its chronic infection is the primary risk factor for the development of gastric cancer (GC). Ferroptosis is an iron-dependent form of cell death characterized by intracellular lipid peroxide accumulation and reactive oxygen species (ROS) imbalance. There is evidence suggesting that pathogens can manipulate ferroptosis to facilitate their replication, transmission, and pathogenesis. However, the interaction between ferroptosis and H. pylori infection requires further elucidation. We reviewed the mechanism of ferroptosis and found that H. pylori virulence factors such as cytotoxin-associated gene A (CagA), vacuolating cytotoxin A (VacA), neutrophil-activating protein A (NapA), superoxide dismutase B (SodB), γ-glutamyl transpeptidase (gGT), lipopolysaccharide (LPS), and outer inflammatory protein A (OipA) affected glutathione (GSH), ROS, and lipid oxidation to regulate ferroptosis. It also affected the progression of GC by regulating ferroptosis-related indicators through abnormal gene expression after H. pylori infected gastric mucosa cells. Finally, we discuss the potential application value of ferroptosis inducers, inhibitors and other drugs in treating H. pylori-infected GC patients while acknowledging that their interactions are still not fully understood.
EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences
Authors: Sieber Alina , Parr Marina , von Ehr Julian , Dhamotharan Karthikeyan , Kielkowski Pavel , Brewer Tess , Schäpers Anna , Krafczyk Ralph , Qi Fei , Schlundt Andreas , Frishman Dmitrij , Lassak Jürgen 
Published: December 2024

AbstractPolyproline sequences are deleterious to cells because they stall ribosomes. In bacteria, EF-P plays an important role in overcoming such polyproline sequence-induced ribosome stalling. Additionally, numerous bacteria possess an EF-P paralog called EfpL (also known as YeiP) of unknown function. Here, we functionally and structurally characterize EfpL from Escherichia coli and demonstrate its role in the translational stress response. Through ribosome profiling, we analyze the EfpL arrest motif spectrum and find additional sequences beyond the canonical polyproline motifs that both EF-P and EfpL can resolve. Notably, the two factors can also induce pauses. We further report that EfpL can sense the metabolic state of the cell via lysine acylation. Overall, our work characterizes the role of EfpL in ribosome rescue at proline-containing sequences, and provides evidence that co-occurrence of EF-P and EfpL is an evolutionary driver for higher bacterial growth rates.
Hospital-wide access to genomic data advanced pediatric rare disease research and clinical outcomes
Authors: French Courtney E. , Andrews Nancy C. , Beggs Alan H. , Boone Philip M. , Brownstein Catherine A. , Chopra Maya , Chou Janet , Chung Wendy K. , D’Gama Alissa M. , Doan Ryan N. , Ebrahimi-Fakhari Darius , Goldstein Richard D. , Irons Mira , Jacobsen Christina , Kenna Margaret , Lee Ted , Madden Jill A. , Majmundar Amar J. , Mann Nina , Morton Sarah U. , Poduri Annapurna , Randolph Adrienne G. , Roberts Amy E. , Roberts Stephanie , Sampson Matthew G. , Shao Diane D. , Shao Wanqing , Sharma Aditi , Shearer Eliot , Shimamura Akiko , Snapper Scott B. , Srivastava Siddharth , Thiagarajah Jay R. , Whitman Mary C. , Wojcik Monica H. , Rockowitz Shira , Sliz Piotr 
Published: December 2024

AbstractBoston Children’s Hospital has established a genomic sequencing and analysis research initiative to improve clinical care for pediatric rare disease patients. Through the Children’s Rare Disease Collaborative (CRDC), the hospital offers CLIA-grade exome and genome sequencing, along with other sequencing types, to patients enrolled in specialized rare disease research studies. The data, consented for broad research use, are harmonized and analyzed with CRDC-supported variant interpretation tools. Since its launch, 66 investigators representing 26 divisions and 45 phenotype-based cohorts have joined the CRDC. These studies enrolled 4653 families, with 35% of analyzed cases having a finding either confirmed or under further investigation. This accessible and harmonized genomics platform also supports additional institutional data collections, research and clinical, and now encompasses 13,800+ patients and their families. This has fostered new research projects and collaborations, increased genetic diagnoses and accelerated innovative research via integration of genomics research with clinical care.
Comparative transcriptomic, epigenomic and immunological analyses identify drivers of disparity in high-grade serous ovarian cancer
Authors: Huang Hao , Keathley Russel , Kim Ujin , Cardenas Horacio , Xie Ping , Wei Jianjun , Lengyel Ernst , Nephew Kenneth P. , Zhao Guangyuan , Fu Zhen , Barber Emma L. , Kocherginsky Masha , Bae-Jump Victoria , Zhang Bin , Matei Daniela 
Published: December 2024

AbstractBlack women face the highest mortality-to-incidence ratio from high grade serous ovarian cancer (HGSOC). This study investigated biological differences in HGSOC tumors from Black vs. White women. HGSOC from 35 Black and 31 White patients were analyzed by Infinium Methyation-EPIC array and RNA sequencing. 191 CpG sites were differentially methylated (FDR < 0.05, β value change> 10%) and 277 genes were differentially expressed (FDR < 0.05). Gene Ontology identified enriched pathways related to DNA damage response, p53/apoptosis signaling, and cholesterol/lipid metabolism directly connected with genes like INSR, FOXA1 and FOXB1. INSR and FOXA1 knockdown enhanced cisplatin sensitivity and inhibited cell proliferation and colony formation. Tumors from Black patients were infiltrated by fewer CD4+ naïve and regulatory T-cells. Overall, differences in DNA methylation, transcriptomic profiles and immune cell infiltration were detected in tumors from Black vs. White patients. Further investigation is warranted into how these differences may affect treatment response and outcomes in Black women.
Modeling the persistence of 4CMenB vaccine protection against real world meningococcal B disease in adolescents
Authors: Argante Lorenzo , Prunas Ottavia , Medini Duccio , Ypma Ellen 
Published: December 2024

AbstractThe efficacy of the four-component 4CMenB vaccine is measured through the serum bactericidal antibody (SBA) assay on four meningococcal B (MenB) indicator strains. However, they are not epidemiologically relevant for disease, thus the real-world persistence of 4CMenB protection remains uncertain. Several mathematical models of waning immunity were fitted on longitudinal SBA data from persistence studies in adolescents, with up to eight years follow-up after 4CMenB priming vaccination. The best model was used to predict protection from indicator strains. MenB typing data from the United States were used to integrate antigen-level curves and predict the persistence of protection from real-world MenB strains, considering synergies between antigens. Models show that protection and its evolution varied by antigen and that 4CMenB likely elicits antibody-producing long-lived plasma cells. 4CMenB protection from real-world MenB disease persisted at 61.5% four years post-priming and 70.5% four years post-booster. This evidence could support decision-making on adolescent immunization programs.
Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics
Authors: Sakenova Nazgul , Cacace Elisabetta , Orakov Askarbek , Huber Florian , Varik Vallo , Kritikos George , Michiels Jan , Bork Peer , Cossart Pascale , Goemans Camille V. , Typas Athanasios 
Published: December 2024

Abstract
By acquiring or evolving resistance to one antibiotic, bacteria can become cross-resistant to a second antibiotic, which further limits therapeutic choices. In the opposite scenario, initial resistance leads to collateral sensitivity to a second antibiotic, which can inform cycling or combinatorial treatments. Despite their clinical relevance, our knowledge of both interactions is limited. We used published chemical genetics data of the Escherichia coli single-gene deletion library in 40 antibiotics and devised a metric that discriminates between known cross-resistance and collateral-sensitivity antibiotic interactions. Thereby we inferred 404 cases of cross-resistance and 267 of collateral-sensitivity, expanding the number of known interactions by over threefold. We further validated 64/70 inferred interactions using experimental evolution. By identifying mutants driving these interactions in chemical genetics, we demonstrated that a drug pair can exhibit both interactions depending on the resistance mechanism. Finally, we applied collateral-sensitive drug pairs in combination to reduce antibiotic-resistance development in vitro.
Reliability analysis of subsea control system using FMEA and FFTA
Authors: Liu Chao , Li Guangxin , Xiao Wensheng , Liu Jian , Tan Liping , Li Changjiang , Wang Teng , Yang Fengran , Xue Chengzhi 
Published: December 2024

AbstractReliability technology plays a significant role in ensuring the safe operation of the subsea control system. To perform a comprehensive analysis of the reliability of complex systems, a combination of Failure Mode and Effects Analysis (FMEA) and Fuzzy Fault Tree Approach (FFTA) is introduced. Firstly, the FMEA method is used to analyze the potential failure modes and causes of system failure by completing the qualitative analysis of system reliability from the perspective of multi-factor failure modes. And the risk matrix diagram is applied to determine the degree of harm of different failure modes to the system. Then, the system reliability is quantitatively analyzed using FFTA, and a fault tree model is established by dividing the system into "system-subsystem-component" and solving for the minimum cut set. In addition, the failure probability of the top-level event is quantitatively calculated by introducing fuzzy set theory, and the probabilistic importance of the bottom-level event is analyzed to find out the weak points of each subsystem. Finally, a qualitative and quantitative reliability analysis is conducted by using FMEA-FFTA method for subsea control system. Effective measures should be taken to focus on preventive protection and regular testing for the high risk, medium–high risk and medium risk modes for subsea control system.
Issues in federated learning: some experiments and preliminary results
Authors: Bhanbhro Jamsher , Nisticò Simona , Palopoli Luigi 
Published: December 2024

AbstractThe growing need for data privacy and security in machine learning has led to exploring novel approaches like federated learning (FL) that allow collaborative training on distributed datasets, offering a decentralized alternative to traditional data collection methods. A prime benefit of FL is its emphasis on privacy, enabling data to stay on local devices by moving models instead of data. Despite its pioneering nature, FL faces issues such as diversity in data types, model complexity, privacy concerns, and the need for efficient resource distribution. This paper illustrates an empirical analysis of these challenges within specially designed scenarios, each aimed at studying a specific problem. In particular, differently from existing literature, we isolate the issues that can arise in an FL framework to observe their nature without the interference of external factors.