bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategies for integrating ChatGPT and generative AI into clinical studies
Authors: Lee Jeong-Moo 
Published: December 2024

Abstract
Large language models, specifically ChatGPT, are revolutionizing clinical research by improving content creation and providing specific useful features. These technologies can transform clinical research, including data collection, analysis, interpretation, and results sharing. However, integrating these technologies into the academic writing workflow poses significant challenges. In this review, I investigated the integration of large-language model-based AI tools into clinical research, focusing on practical implementation strategies and addressing the ethical considerations associated with their use. Additionally, I provide examples of the safe and sound use of generative AI in clinical research and emphasize the need to ensure that AI-generated outputs are reliable and valid in scholarly writing settings. In conclusion, large language models are a powerful tool for organizing and expressing ideas efficiently; however, they have limitations. Writing an academic paper requires critical analysis and intellectual input from the authors. Moreover, AI-generated text must be carefully reviewed to reflect the authors’ insights. These AI tools significantly enhance the efficiency of repetitive research tasks, although challenges related to plagiarism detection and ethical use persist.
Incidence and outcomes of subsequent malignancy after allogeneic hematopoietic stem cell transplantation in adult patients with severe aplastic anemia
Authors: Kwag Daehun , Park Sung-Soo , Lee Sung-Eun , Kim Hee-Je , Lee Jong Wook 
Published: December 2024

Abstract
Purpose
This study investigated the occurrence of subsequent malignancies (SM) in adult patients with severe aplastic anemia (SAA) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) to address the lack of large-scale, long-term data on this complication.

Methods
A retrospective cohort analysis of 376 adult patients with SAA who underwent allo-HSCT between 2002 and 2021 at a single center was conducted. The incidence, risk factors, and survival impact of SM were also examined.

Results
During the follow-up period, 31 cases of SM (8.2%) were identified. Approximately one-third (32.3%) of SM cases were hematologic malignancies, including post-transplant lymphoproliferative disorder (16.1%), myelodysplastic neoplasm (6.5%), and acute myeloid leukemia (3.2%). Solid tumors accounted for 67.7% of cases, with thyroid cancer being the most prevalent (25.8%). The 15-year cumulative incidence of SM was 11.2%, and the hazard ratio for overall survival according to the development of SM was 16.25 (p < 0.001). High-dose total body irradiation (TBI), anti-thymocyte globulin (ATG), and moderate-to-severe chronic graft-versus-host disease (GVHD) were identified as significant risk factors for subsequent malignancy. Post-transplant SAA patients exhibited a 3.54-fold higher observed cancer incidence than the expected incidence calculated from the age-, sex-, and calendar year-matched general population.

Conclusion
SM is a significant long-term complication in patients with posttransplant SAA and has a substantial survival impact. Patients receiving high-dose TBI or ATG, and those with moderate-to-severe chronic GVHD, require vigilant long-term monitoring.
The incidence and risk factors of fetuses with mirror-image dextrocardia with solitus inversus
Authors: Xu Wenjiao , Wei Yajuan , Gao Xinru , Yang Xiaoxue , Wang Liping , Gao Wenlian , Zhu Xumin , Liu Baomin 
Published: December 2024

AbstractObjective:This research seeks to ascertain the prevalence and determinants of mirror-image dextrocardia in fetusesStudy design:With December 2022 as the reference point, we compiled colleted data on pregnant women who carried fetuses with mirror-image dextrocardia in Xi’an, Shaanxi Province: September–October 2022, November 2022, and December 2022–January 2023. An online questionnaire was distributed to 209 pregnant across China who had contracted COVID-19. The case group comprised women whose final menstrual cycle occurred in November 2022 and who had a fetus with mirror-image dextrocardia. Women with a November 2022 final menstrual period and a fetus without this condition made up the control group. To identify the risk factors associated with fetal mirror-image dextrocardia, both univariate and multivariate logistic regression analyses were employed.Results:A significant difference was noted in the gestational age at COVID-19 infection women with a September to October 2022 and December 2022 to January 2023 final menstrual period who did not bear a fetus with mirror-image dextrocardia, and those with a November 2022 final menstrual period whose fetus exhibited this condition. The univariate and multivariate analyses conducted on pregnant women with a final menstrual period in November 2022 who had contracted COVID-19 revealed significant differences in the presence and duration of fever between those bearing fetuses with mirror-image dextrocardia and those without (P = 0.000).Conclusion:The findings suggest two critical factors to the increased prevalence of fetal mirror-image dextrocardia: 1) the infection timing which occurs between the 4th and 6th week of pregnancy and 2) the presence of fever and its prolonged duration.
Performance of Common Land Model in Simulating the Land Surface Thermal and Hydrological Processes Over China Improved by Including the Sub‐Grid Terrain Solar Radiative Effect
Authors: Zhang Xindan , Huang Anning , Yang Xianyu , Gu Chunlei , Cai Shuxin , Luo Jiangxin 
Published: December 2024

AbstractThe sub‐grid terrain solar radiative effect (STSRE) significantly affects the heterogeneity of the surface downward solar radiation (SDSR) over mountainous areas, which further exerts remarkable influences on simulations of surface energy budgets and hydrological processes. Given that two thirds of China is mountainous, we have systematically revealed the noticeable STSRE impacts on the performance of the Common Land Model (CoLM) in simulating land surface thermal and hydrological processes over China. Validations indicate that adopting the three dimensional (3D) STSRE scheme clearly improves the CoLM's ability in simulating the land thermal and moist characteristics over China in almost all seasons, and the improvements increase with the terrain complexity increasing. Over the regions with the most rugged terrain, adopting the 3D STSRE scheme can remarkably reduce the overestimated SDSR and thereafter land surface temperature (LST) warm biases in the CoLM with the plane‐parallel radiative scheme. The modeled snow cover increases corresponding to the reduced LST with the Taylor score improved the most by 52.84% in summer, and the modeled evapotranspiration (ET) over southeastern Tibet and the Hengduan Mountains is also notably improved in summer. Further analysis indicates that the surface net radiation well corrected by the 3D STSRE scheme firstly reduces the warm biases of LST simulation using the plane‐parallel radiative scheme over strong terrain shaded areas, directly leading to the depressed sensible heat flux and ET and more snow accumulation, then the inhibited ET and increased snow accumulation jointly affect the runoff and soil moisture simulations and thereafter latent heat simulation.
Contributions of Tropical Cyclones and Internal Tides To Deep Near‐Inertial Kinetic Energy Under Eddy Modulation
Authors: Zhang Zhixiang , Gao Jing , Wang Jianing , Wang Fan 
Published: December 2024

AbstractNear‐inertial waves (NIWs) are essential energy sources for deep diapycnal mixing. However, the mechanisms for generating deep and abyssal NIWs are largely unknown. Here, using 3 year full‐depth mooring data at 130°E/15°N, we demonstrate that downward propagating tropical cyclone (TC)‐induced NIWs and parametric subharmonic instability (PSI) can contribute to the intensification of near‐inertial kinetic energy (NIKE) over 1,000–3,000 m. The deep warm core eddy (WCE) is found to facilitate the downward propagation of TC‐induced NIWs with fast vertical group velocity and the intensified PSI efficiency that improves the energy transfer from diurnal internal tides (DITs) to NIWs at the site poleward of critical latitude for DITs. Quantitative regression analysis suggests that compared to the PSI, downward penetrating TC‐induced NIWs contribute more to the deep NIKE. Our study emphasizes that accurately representing deep eddy activities and TC's wind intensity in numerical models is crucial to simulating the deep NIKE.
Bayesian Preprocessing for Palaeomagnetic Sediment Records Using a Flexible Lock‐In Function Approach
Authors: Bohsung L. , Schanner M. , Korte M. , Holschneider M. 
Published: December 2024

AbstractGeomagnetic field models covering past millennia rely on two main data sources: archaeomagnetic data, that provide snapshots of the geomagnetic field at specific locations, and sediment records, that deliver time series of the geomagnetic field from individual cores. The limited temporal and spatial global coverage with archaeomagnetic data necessitates use of sediment data, especially when models go further back in time. However, the accurate preprocessing and interpretation of sediment data is crucial. Unlike archaeomagnetic data, sediment data does not provide absolute values for intensities and declinations; instead, it represents relative variations. The detrital remanent magnetization (DRM) of sediment records is influenced by various depositional (dDRM) effects that can result in inclination shallowing, as well as post‐depositional (pDRM) processes that cause a delayed and smoothed signal. To address the distortion associated with the pDRM effects, a novel class of flexible parameterized lock‐in functions has been proposed. These lock‐in functions involve four parameters, which are estimated using a Bayesian modeling technique and archaeomagnetic data. By extending the space of hyperparameters to include the calibration factor for intensities, the declination offsets and the inclination shallowing factor, we present a fully Bayesian preprocessing method for sediment records in form of a Python package, called sedprep. By applying the estimated parameters to the raw sediment data sedprep is able to provide a calibrated and preprocessed palaeomagnetic record.
A Numerical Study of the Impact of Topography on the July 2021 Extreme Rainfall Event in Zhengzhou, China
Authors: Wang Jingju , Zhang Shaoqing , Yu Xiaolin , Jin Yishuai , Liu Xing , Qi Yiling , Yang Gao , Li Mingkui 
Published: December 2024

AbstractAn unprecedented extreme rainfall event occurred in Zhengzhou, Henan Province, China, in July 2021. To understand the impact of local topography on this extreme rainfall event, the Weather Research and Forecasting model is configured with 27 and 9 km model grid spacings (MGS), along with United States Geological Survey (USGS) topography data at 8.3 and 0.9 km resolutions, called MGS27_USGS8.3, MGS9_USGS8.3, and MGS9_USGS0.9. Results show that the 9 km MGS, permitting activities with coarse γ scales (∼20 km), successfully reproduces the generation of mesoscale cyclones. However, the finer topography enables a more accurate representation of orographic blocking and lifting effects, thereby adjusting the position of the mesoscale cyclone. It can depict the location of adiabatic processes, local circulation, and vertical pressure gradient forces more accurately, thereby adjusting the position of topography‐induced vertical motions. The turbulence diagnostics show that the topography‐induced lifting motion enhances clouds that block longwave radiation, leading to local environment warming, which in turn enhances turbulence and further amplifies the updrafts, ultimately improving the spatial distribution and temporal variation of precipitation. This study provides insights for an in‐depth understanding of the mechanisms of topography on extreme rainfall.
Structural Difference on the Response of Microphysical and Precipitation Processes to Aerosol Perturbation in a Quasi‐Stationary Southwest Vortex System
Authors: He Yuhang , Zhao Pengguo , Xiao Hui , Zhao Chuanfeng 
Published: December 2024

AbstractUsing the WRF coupled with Thompson aerosol‐aware microphysics scheme, a quasi‐stationary southwest vortex (SWV) precipitation process occurring in the Sichuan Basin is simulated. Based on three experiments with low aerosol concentration background (“Low”), medium aerosol concentration background (“Medium”), and high aerosol concentration background (“High”), the effects of hydrophilic aerosol serving as Cloud Condensation Nuclei (CCN) on microphysical and precipitation processes are investigated. Results indicate the impact of hydrophilic aerosol on clouds and precipitation structure exhibits structural difference. Aerosol increases from “Low” to “Medium”, precipitation in middle circle of SWV decreases, precipitation in outer circle of SWV increases. Because the outer circle of SWV with strong convection competes with the middle circle of SWV for liquid droplets, leading to a reduction in ice‐phase particles in middle circle of SWV. In contrast, more ice‐phase particles are formed in outer circle of SWV. The increased ice‐phase particles melt into raindrops, leading to an increase in precipitation. Aerosol increases from “Medium” to “High”, precipitation in middle circle of SWV increases, precipitation in outer circle of SWV decreases. The size of liquid droplets formed in outer circle of SWV further becomes smaller. This is not conducive to the formation of ice‐phase particles, leading to weaker convection, which makes it becomes less competitive. A large number of small cloud droplets in middle circle of SWV are transported above the freezing layer and participate in the formation of ice‐phase particles. The released latent heat promotes convective development, resulting in more precipitation.
Predicting the Onset of Subglacial Drainage Channels
Authors: Warburton K. L. P. , Meyer C. R. , Sommers A. N. 
Published: December 2024

AbstractThe sliding speed of glaciers depends strongly on the water pressure at the ice‐sediment interface, which is controlled by the efficiency of water transport through a subglacial hydrological system. The least efficient component of the system consists of “distributed” flow everywhere beneath the ice, whereas the “channelized” drainage through large, thermally eroded conduits is more efficient. To understand the conditions under which the subglacial network channelizes, we perform a linear stability analysis of distributed flow, considering competition between thermal erosion and viscous ice collapse. The calculated growth rate gives a stability criterion, describing the minimum subglacial meltwater flux needed for channels to form, but also indicates the tendency to generate infinitely narrow channels in existing models. We demonstrate the need to include lateral heat diffusion when modeling melt incision to resolve channel widths, which allows continuum models to recover Röthlisberger channel behavior. We also show that low numerical resolution can suppress channel formation and lead to overestimates of water pressure. Our derived channelization criterion can be used to predict the character of subglacial hydrological systems without recourse to numerical simulations, with practical implications for understanding changes in ice velocity due to changes in surface melt runoff.
Sensitivity Analysis of a Dynamic Vegetation‐Sediment Transport Model Using Equadratures: Exploring Inorganic Accretion on a Marsh Platform
Authors: Allen R. M. , Ganju N. K. , Kalra T. S. , Aretxabaleta A. L. , Lacy J. R. 
Published: December 2024

AbstractSalt marsh systems require a net import of inorganic sediment to maintain their structure in response to sea‐level rise. Marshes are affected by physical processes including tides, waves, sediment transport, and the influence of vegetation, and these processes interact in complex ways leading to sediment accretion or erosion. We implement a 3‐D hydrodynamic sediment transport model in an idealized marsh‐bay complex with a gently sloping edge, and use it as a laboratory to explore the processes leading to bed elevation change through the bay‐marsh continuum. We use the novel equadratures method for efficient sensitivity analysis to test the roles of wave, vegetation, and sediment parameters on wave dissipation, bed shear stress, sediment fluxes, and deposition and erosion across a transect spanning bay shallows to the marsh. Within the explored bounds of parameter uncertainty, significant wave height , settling velocity , and critical shear stress most strongly affect accretion on the marsh platform. Deposition is affected more by parameter‐parameter interactions, that is, both and or both and , than by a single parameter varying alone. The sediment that accretes on the marsh platform originates beyond the marsh edge, indicating that the dynamics of the adjacent mudflat are important for predicting the fate of the marsh. Applying efficient sensitivity analysis techniques can empower process‐based models to test more parameters, larger ranges, and longer timeframes, enabling future predictions of marsh response to sea‐level rise based on physical processes.
Toripalimab plus chemotherapy for first line treatment of advanced non-small cell lung cancer (CHOICE-01): final OS and biomarker exploration of a randomized, double-blind, phase 3 trial
Authors: Zhong Jia , Fei Kailun , Wu Lin , Li Baolan , Wang Zhijie , Cheng Ying , Li Xiaoling , Wang Xicheng , Han Liang , Wu Xiaohong , Fan Yun , Yu Yan , Lv Dongqing , Shi Jianhua , Huang Jianjin , Zhou Shaozhang , Han Baohui , Sun Guogui , Guo Qisen , Ji Youxin , Zhu Xiaoli , Hu Sheng , Zhang Wei , Wang Qiming , Jia Yuming , Wang Ziping , Song Yong , Wu Jingxun , Shi Meiqi , Li Xingya , Han Zhigang , Liu Yunpeng , Yu Zhuang , Liu An-Wen , Wang Xiuwen , Zhou Caicun , Zhong Diansheng , Miao Liyun , Zhang Zhihong , Zhao Hui , Yang Jun , Wang Dong , Wang Yingyi , Li Qiang , Zhang Xiaodong , Ji Mei , Yang Zhenzhou , Cui Jiuwei , Gao Beili , Wang Buhai , Liu Hu , Nie Lei , He Mei , Jin Shi , Gu Wei , Shu Yongqian , Zhou Tong , Feng Jian , Yang Xinmei , Huang Cheng , Zhu Bo , Yao Yu , Yao Sheng , Yu Jianjun , Cai Shang li , Cai Yiran , Xu Jiachen , Zhuang Wei , Luo Xianmin , Duan Jianchun , Wang Jie 
Published: December 2024

AbstractA randomized double-blind phase 3 trial (CHOICE-01, NCT03856411) demonstrated that combining toripalimab with chemotherapy substantially improves progression-free survival (PFS) in advanced non-small cell lung cancer (NSCLC) patients without pretreatment. This study presents the prespecified final analysis of overall survival (OS) and biomarkers utilizing circulating tumor DNA (ctDNA) and tissue-based sequencing. Additionally, the analysis revealed a higher median overall survival (OS, 23.8 months) in the toripalimab group than that in the control group (17.0 months). (HR = 0.69, 95%CI: 0.57–0.93, nominal P = 0.01). This survival benefit was particularly notable in the non-squamous subgroup. As the first phase 3 study to perform both baseline tissue whole-exome sequencing (WES) and peripheral blood ctDNA testing, we investigated efficacy predictive biomarkers based on both tissue and ctDNA, Genomic sequencing of ctDNA showed high concordance with tumor tissue independently confirmed that individuals exhibiting a high tumor mutational burden, as well as mutations in the FA-PI3K-Akt and IL-7 signaling pathways benefited more from the toripalimab treatment. Furthermore, a ctDNA response observed on cycle 3 day 1, was associated with improved clinical outcomes for patients treated with the combination therapy. In conclusion, Toripalimab plus chemotherapy yields significant improvements in OS as a first-line treatment. The study highlights the utility of ctDNA as a proxy for tumor tissue, providing novel prospects for predicting efficacy of immuno-chemotherapy through continuous ctDNA monitoring.
Genomic and transcriptomic profiling of radioresistant prostate and head and neck cancers implicate a BAHD1-dependent modification of DNA damage at the heterochromatin
Authors: Beh Chaw Yee , Yeo Celestia Pei Xuan , Hong Boon Hao , Tan Evelyn Mui Cheng , Tan Kah Min , Poon Dennis Jun Jie , Chu Pek Lim , Susanti Dewi , Tai Pei Ling , Ryu Monica , Proudfoot James , Yeo Eugenia Li Ling , Soo Khee Chee , Chua Melvin L. K. 
Published: December 2024

AbstractRadiotherapy is an integral modality in treating human cancers, but radioresistance remains a clinical challenge due to the involvement of multiple intrinsic cellular and extrinsic tumour microenvironment factors that govern radiosensitivity. To study the intrinsic factors that are associated with cancer radioresistance, we established 4 radioresistant prostate (22Rv1 and DU145) and head and neck cancer (FaDu and HK1) models by irradiating their wild-type parentals to 90 Gy, mimicking the fractionated radiotherapy schema that is often using in the clinic, and performed whole exome and transcriptome sequencing of the radioresistant and wild-type models. Comparative genomic analyses detected the enrichment of mismatch repair mutational signatures (SBS6, 14, 15, 20) across all the cell lines and several non-synonymous single nucleotide variants involved in pro-survival pathways. Despite significant inter-cell type heterogeneity of their transcriptomic profiles, 18 common dysregulated genes (5 upregulated and 13 downregulated) were identified across the 4 models, including the overexpression of bromo-adjacent homology domain containing 1 (BAHD1) gene, which is involved in heterochromatin formation. Interestingly, this coincided with our observation of increased histone 3 lysine 9 trimethylation (H3K9me3) and histone 3 lysine 27 trimethylation (H3K27me3) expression post-irradiation in our radioresistant cells. The dependency between BAHD1 and heterochromatin formation was confirmed by siRNA knockdown of BAHD1, indicating preferential reduction of H3K9me3 and H3K27me3 expression in the radioresistant cells, but not the wild-type parentals, and confirmed by clonogenic assays showing reversal of radioresistance post-siBAHD1 treatment. We further showed that inhibition of the BAHD1-heterochromatin formation axis led to reduced DNA double-strand break repair. Finally, analyses of treatment outcomes in 4 prostate and head and neck cancer radiotherapy cohorts suggested an increased risk of failures in tumours of high heterochromatin activity. Taken together, our results support a new model implicating BAHD1-dependent modulation of the heterochromatin in acquired radioresistance of prostate and head and neck cancers.
Emerging discoveries on the role of TRIM14: from diseases to immune regulation
Authors: Li Xinhao , Zhou Feilong , Niu Kaiyi , Wang Yizhu , Shi Yanlong , Li Yunxin , Gao Xin , Zhao Weijie , Chen Tianyi , Zhang Yewei 
Published: December 2024

AbstractTRIM14 is an important member of the TRIM family and is widely expressed in a variety of tissues. Like other members of the TRIM family, TRIM14 is also involved in ubiquitination modifications. TRIM14 was initially reported as an interferon-stimulated gene (ISG). In recent years, many studies have focused on the regulatory role of TRIM14 in signaling pathways such as the PI3K/Akt, NF-κB, and cGAS/STING pathways and revealed its mechanism of action in a variety of pathophysiological processes, and the regulation of TRIM14 has attracted the interest of many researchers as a new direction for the treatment of various diseases. However, there are no reviews on the role of TRIM14 in diseases. In this paper, we will describe the structure of TRIM14, review its role in cancer, cardiovascular disease, cervical spondylosis, inflammation and antiviral immunity, and provide an outlook on future research directions.