bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weed community differences in row crops with varying input levels in Ghana
Authors: Oreja Fernando H. , Arthur Stephen , Bolfrey-Arku Grace , Mochiah Moses B. , Klutse Victoria , Yorke Maxwell , Hukporti Solomon , Dzomeku Israel K. , Mahama Georgie Y. , Nboyine Jerry A. , Seidu Ahmed , Akromah Richard , Sarkodie-Addo Joseph , Jordan David L. , Leon Ramon G. 
Published: October 2024

AbstractPeanut (Arachis hypogaea L.) and maize (Zea mays L.) are essential crops for Ghana’s economy and food security, but weed infestation poses a significant threat to their cultivation. Crop rotations influence weed communities, but little is known about these processes in peanut-cropping systems in West Africa. This study investigated the impact of different crop rotations and input levels on weed communities in Ghana over 3 yr. Results showed that low inputs (absence of herbicide and fertilization) favored species richness, while higher input levels (weed control with herbicides and fertilizer use) reduced it. Diversity and evenness were also affected by inputs, with varying patterns across locations and seasons. Weed population growth rates (λ) varied significantly by location and treatment; all management programs resulted in increasing weed populations. Principal component analysis revealed distinct associations between weed species and crop management. The majority of weed species exhibited a generalist behavior and did not associate with a particular management. However, billygoat weed (Ageratum conyzoides L.) and Benghal dayflower (Commelina benghalensis L.) were positively associated with high-input systems, while purple nutsedge (Cyperus rotundus L.) exhibited strong associations with low and medium inputs. The weed–crop rotation dynamics described here demonstrate how management drives the selection of weed species that are more pervasive and interfere with important food crops in Ghanaian agriculture.
A New Cyclo‐Synchrotron Model for Lunar‐Based Observations of Earth's Radiation Belts
Authors: Marc G. , Sicard A. , Nénon Q. , Belmont R. 
Published: October 2024

AbstractThe energetic electrons trapped in the terrestrial radiation belts spontaneously emit radiation due to magnetic deflection. The observation of this radiation can offer insights into the space and energy distribution of the electrons, as well as their temporal variability. Given the energy range of the electrons in the Earth's radiation belts (0.1 keV to 10 MeV), the emission corresponds to cyclo‐synchrotron radiation, an intermediate radiation regime between the low‐energy cyclotron radiation and the extremely relativistic synchrotron emission. Terrestrial cyclo‐synchrotron radiation cannot be observed from Earth as it is emitted at frequencies below the ionospheric cutoff frequency (f < 10 MHz). However, a lunar near‐side observation could provide real time measurements of the dynamics of the Earth radiation belts. In this study, we present the development of a full cyclo‐synchrotron model for the electron radiation belt emissions, building upon a preliminary synchrotron model. While previous simulations focused on >1 MeV electrons, our new model is able to simulate the radiation of >100 keV electrons which have much larger fluxes than MeV electrons. This new model accurately simulates the cyclo‐synchrotron radiation emitted by Earth's radiation belts as observed from the lunar surface, which would help the design of lunar‐based radio interferometers and would offer a new perspective on radiation belts research and monitoring.
The Global Characteristics of Electrons Near the Inner Edge of the Inner Radiation Belt
Authors: Walton S. D. , Lejosne S. , Claudepierre S. G. 
Published: October 2024

AbstractEnergetic electrons around the inner edge of the inner radiation belt (L1.3) have not been studied to the extent of the rest of the inner belt and certainly not to that of the outer radiation belt. Yet, the behavior of electrons at the inner edge of the inner belt could improve our understanding of important dynamics deep within Earth's magnetosphere. Previous work has analyzed these electrons during either isolated events or via significantly limited statistical studies, and it remains unclear what the particular drivers of electron flux enhancements in this region may be. Here, we present a broad statistical study of electrons around the inner edge of the inner radiation belt, utilizing the 7‐year data set of the MagEIS particle detectors aboard both Van Allen Probes spacecraft. Moreover, we separate electron flux measurements into stably trapped and quasi‐trapped electrons and directly compare their behavior. We find both populations to be variable in L and energy, as well as showing a clear magnetic local time (MLT) asymmetry. Potential drivers are also explored, where we demonstrate an association between increased electron fluxes in this region and heightened solar wind speed, Sym‐H, dynamic pressure, southward IMF and most prominently with the AU and AL indices.
AXIN1 boosts antiviral response through IRF3 stabilization and induced phase separation
Authors: Dai Dan-Ling , Xie Chu , Zhong Lan-Yi , Liu Shang-Xin , Zhang Le-Le , Zhang Hua , Wu Xing-Ping , Wu Zhou-Ming , Kang Kexin , Li Yan , Sun Ya-Meng , Xia Tian-Liang , Zhang Chen-Song , Zhang Ao , Shi Ming , Sun Cong , Chen Mei-Ling , Zhao Ge-Xin , Bu Guo-Long , Liu Yuan-Tao , Huang Kui-Yuan , Zhao Zheng , Li Shu-Xin , Zhang Xiao-Yong , Yuan Yun-Fei , Wen Shi-Jun , Zhang Lingqiang , Li Bin-Kui , Zhong Qian , Zeng Mu-Sheng 
Published: October 2024

AbstractAxis inhibition protein 1 (AXIN1), a scaffold protein interacting with various critical molecules, plays a vital role in determining cell fate. However, its impact on the antiviral innate immune response remains largely unknown. Here, we identify that AXIN1 acts as an effective regulator of antiviral innate immunity against both DNA and RNA virus infections. In the resting state, AXIN1 maintains the stability of the transcription factor interferon regulatory factor 3 (IRF3) by preventing p62-mediated autophagic degradation of IRF3. This is achieved by recruiting ubiquitin-specific peptidase 35 (USP35), which removes lysine (K) 48-linked ubiquitination at IRF3 K366. Upon virus infection, AXIN1 undergoes a phase separation triggered by phosphorylated TANK-binding kinase 1 (TBK1). This leads to increased phosphorylation of IRF3 and a boost in IFN-I production. Moreover, KYA1797K, a small molecule that binds to the AXIN1 RGS domain, enhances the AXIN1-IRF3 interaction and promotes the elimination of various highly pathogenic viruses. Clinically, patients with HBV-associated hepatocellular carcinoma (HCC) who show reduced AXIN1 expression in pericarcinoma tissues have low overall and disease-free survival rates, as well as higher HBV levels in their blood. Overall, our findings reveal how AXIN1 regulates IRF3 signaling and phase separation-mediated antiviral immune responses, underscoring the potential of the AXIN1 agonist KYA1797K as an effective antiviral agent.
Envafolimab plus lenvatinib and transcatheter arterial chemoembolization for unresectable hepatocellular carcinoma: a prospective, single-arm, phase II study
Authors: Chen Yiwen , Zhang Junlei , Hu Wendi , Li Xiang , Sun Ke , Shen Yan , Zhang Min , Wu Jian , Gao Shunliang , Yu Jun , Que Risheng , Zhang Yun , Yang Fuchun , Xia Weiliang , Zhang Aibin , Tang Xiaofeng , Bai Xueli , Liang Tingbo 
Published: October 2024

AbstractEvidences regarding the feasibility of transcatheter arterial chemoembolization (TACE)-based therapy for unresectable hepatocellular carcinoma (uHCC) remains limited. This study aimed to investigate the efficacy and safety of TACE combined with envafolimab and lenvatinib for uHCC. Eligible patients with uHCC received envafolimab and lenvatinib after TACE until disease progression, conversion to surgery, intolerable toxicities, or death. The primary endpoint was the objective response rate (ORR) assessed according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 criteria. Between March 2022 and July 2022, 38 patients were included for safety analysis, and 36 patients were included for efficacy analysis. As of the data cutoff (13 December 2023), the median follow-up was 16.9 months. The ORR was 50%, and disease control rate (DCR) was 83.3% per RECIST 1.1 (ORR and DCR of both 83.3% per modified RECIST (mRECIST)). The median progression-free survival (PFS) was 7.58 months. Of 36 patients, 17 patients were converted to resectable HCC with a surgical conversion rate of 47.2%, and 16 patients underwent surgery with R0 resection rate of 100%, pathologic complete response (pCR) rate of 31.3%. Overall incidences of treatment-related adverse events (TRAEs) of any grade was 97.4%. Grade ≥ 3 TRAEs were observed in 52.6% patients. No treatment-related deaths occurred. Image mass cytometry (IMC) analysis revealed that combined treatment improved the immune status of the tumor microenvironment, and resident macrophages had the potential to predict efficacy of this treatment. Envafolimab plus lenvatinib and TACE yielded promising survival outcomes and conversion efficiency with a tolerable safety profile. Trial registration Clinical trials: NCT05213221.
Genome-wide association studies of COVID-19 vaccine seroconversion and breakthrough outcomes in UK Biobank
Authors: Alcalde-Herraiz Marta , Català Martí , Prats-Uribe Albert , Paredes Roger , Xie JunQing , Prieto-Alhambra Daniel 
Published: October 2024

AbstractUnderstanding the genetic basis of COVID-19 vaccine seroconversion is crucial to study the role of genetics on vaccine effectiveness. In our study, we used UK Biobank data to find the genetic determinants of COVID-19 vaccine-induced seropositivity and breakthrough infections. We conducted four genome-wide association studies among vaccinated participants for COVID-19 vaccine seroconversion and breakthrough susceptibility and severity. Our findings confirmed a link between the HLA region and seroconversion after the first and second doses. Additionally, we identified 10 genomic regions associated with breakthrough infection (SLC6A20, ST6GAL1, MUC16, FUT6, MXI1, MUC4, HMGN2P18-KRTCAP2, NFKBIZ and APOC1), and one with breakthrough severity (APOE). No significant evidence of genetic colocalisation was found between those traits. Our study highlights the roles of individual genetic make-up in the varied antibody responses to COVID-19 vaccines and provides insights into the potential mechanisms behind breakthrough infections occurred even after the vaccination.
Complex transcriptional regulations of a hyperparasitic quadripartite system in giant viruses infecting protists
Authors: Bessenay Alexandra , Bisio Hugo , Belmudes Lucid , Couté Yohann , Bertaux Lionel , Claverie Jean-Michel , Abergel Chantal , Jeudy Sandra , Legendre Matthieu 
Published: October 2024

AbstractHyperparasitism is a common pattern in nature that is not limited to cellular organisms. Giant viruses infecting protists can be hyperparasitized by smaller ones named virophages. In addition, both may carry episomal DNA molecules known as transpovirons in their particles. They all share transcriptional regulatory elements that dictate the expression of their genes within viral factories built by giant viruses in the host cytoplasm. This suggests the existence of interactions between their respective transcriptional networks. Here we investigated Acanthamoeba castellanii cells infected by a giant virus (megavirus chilensis), and coinfected with a virophage (zamilon vitis) and/or a transpoviron (megavirus vitis transpoviron). Infectious cycles were monitored through time-course RNA sequencing to decipher the transcriptional program of each partner and its impact on the gene expression of the others. We found highly diverse transcriptional responses. While the giant virus drastically reshaped the host cell transcriptome, the transpoviron had no effect on the gene expression of any of the players. In contrast, the virophage strongly modified the giant virus gene expression, albeit transiently, without altering the protein composition of mature viral particles. The virophage also induced the overexpression of transpoviron genes, likely through the indirect upregulation of giant virus-encoded transcription factors. Together, these analyses document the intricated transcriptionally regulated networks taking place in the infected cell.
High fidelity DNA ligation prevents single base insertions in the yeast genome
Authors: Williams Jessica S. , Lujan Scott. A. , Arana Mercedes E. , Burkholder Adam B. , Tumbale Percy P. , Williams R. Scott , Kunkel Thomas A. 
Published: October 2024

AbstractFinalization of eukaryotic nuclear DNA replication relies on DNA ligase 1 (LIG1) to seal DNA nicks generated during Okazaki Fragment Maturation (OFM). Using a mutational reporter in Saccharomyces cerevisiae, we previously showed that mutation of the high-fidelity magnesium binding site of LIG1Cdc9 strongly increases the rate of single-base insertions. Here we show that this rate is increased across the nuclear genome, that it is synergistically increased by concomitant loss of DNA mismatch repair (MMR), and that the additions occur in highly specific sequence contexts. These discoveries are all consistent with incorporation of an extra base into the nascent lagging DNA strand that can be corrected by MMR following mutagenic ligation by the Cdc9-EEAA variant. There is a strong preference for insertion of either dGTP or dTTP into 3–5 base pair mononucleotide sequences with stringent flanking nucleotide requirements. The results reveal unique LIG1Cdc9-dependent mutational motifs where high fidelity DNA ligation of a subset of OFs is critical for preventing mutagenesis across the genome.
A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage
Authors: Barrett James , Naduthodi Mihris I. S. , Mao Yuwei , Dégut Clément , Musiał Sabina , Salter Aidan , Leake Mark C. , Plevin Michael J. , McCormick Alistair J. , Blaza James N. , Mackinder Luke C. M. 
Published: October 2024

AbstractCO2 fixation is commonly limited by inefficiency of the CO2-fixing enzyme Rubisco. Eukaryotic algae concentrate and fix CO2 in phase-separated condensates called pyrenoids, which complete up to one-third of global CO2 fixation. Condensation of Rubisco in pyrenoids is dependent on interaction with disordered linker proteins that show little conservation between species. We developed a sequence-independent bioinformatic pipeline to identify linker proteins in green algae. We report the linker from Chlorella and demonstrate that it binds a conserved site on the Rubisco large subunit. We show that the Chlorella linker phase separates Chlamydomonas Rubisco and that despite their separation by ~800 million years of evolution, the Chlorella linker can support the formation of a functional pyrenoid in Chlamydomonas. This cross-species reactivity extends to plants, with the Chlorella linker able to drive condensation of some native plant Rubiscos in vitro and in planta. Our results represent an exciting frontier for pyrenoid engineering in plants, which is modelled to increase crop yields.
Wind turbine condition monitoring dataset of Fraunhofer LBF
Authors: Mostafavi Atabak , Friedmann Andreas 
Published: October 2024

AbstractFraunhofer wind turbine dataset contains monitoring data from a 750 W wind turbine, including accelerometers and tachometer, to capture structural response, bearing vibrations and rotational velocity. Additionally, temperatures, wind speed and wind direction have been measured, while weather conditions have been acquired from selected sources. Various damage scenarios, including mass imbalance, and aerodynamic imbalance as well as damages on bearings’ outer race, inner race and roller element have been implemented. The availability of time series data makes the dataset well suited for both machine learning and signal processing-based condition monitoring applications. The availability of heterogeneous sensors has created a dataset particularly suited for information fusion, data fusion, multi-sensor approaches, and holistic monitoring. Experiments were conducted in real-world conditions outside of a controlled laboratory environment, thereby introducing challenges such as variable rotor speed, noise, overloads, and other environmental factors. Consequently, the dataset is qualified for tasks involving uncertainty quantification and signal pre-processing. This document will detail the test equipment, experimental procedures, simulated damage cases and measurement parameters.
Advanced nano modification of ecofriendly glauconite clay for high efficiency methylene blue dye adsorption
Authors: Saad Eman M. , Wagdy Manar , Orabi Adel S. 
Published: October 2024

AbstractThis research focuses on the utilization of nano glauconite clay as an environmentally friendly sorbent for the removal of cationic dyes, particularly Methylene Blue (MB), from polluted water. The glauconite clay was sourced from the El Gidida region of Egypt and subjected to grinding in a laboratory-type ball mill to ensure homogeneity and increase the active sites available for the adsorption process. The resulting ball milled nano clay (BMNC) was characterized using techniques such as X-ray fluorescence (XRF), Fourier transform infrared (FT-IR) spectroscopy, transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD). The concentration of MB dye was monitored using UV–Vis spectroscopy to assess the adsorption capacity of BMNC under various conditions including pH, time, dose, and temperature. The optimal conditions for the adsorption process were determined to be a pH range of 7–8, a contact time of 60 min, and a dose of 200 ppm, resulting in an adsorption capacity of 128 mg/g. This process demonstrated both low cost and high speed. The adsorption mechanism of MB on the BMNC surface was evaluated through kinetics, adsorption isotherms, and thermodynamics. The experimental data indicated an endothermic, spontaneous, and thermodynamically favourable adsorption process, which was further supported by simulated modelling results using Forcite program. The in-silico data aligned well with the experimental findings. Additionally, the study assessed the interference of salts, metal ions, and other dyes on MB adsorption onto BMNC, showing promising results. These findings strongly support the effectiveness of our sorbent substrate under challenging conditions.
Drug-associated congenital anomalies of the external ear identified in the United States food and drug administration adverse event reporting system database
Authors: Li Xinyu , Hao Jiajia , Li Datao , Zhang Ruhong 
Published: October 2024

AbstractCongenital anomalies of the external ear can have a significant impact on a child’s development and quality of life. While genetic factors play a crucial role in the etiology of these anomalies, environmental factors such as drug exposure during pregnancy may also contribute to their occurrence. This study aims to investigate the association between drug exposure and congenital anomalies of the external ear using data from an adverse drug reaction report database. Using OpenVigil 2.1, we queried the FAERS database to retrieve adverse event reports from the first quarter of 2004 to the first quarter of 2024. To identify relevant cases, we used Medical Dictionary for Regulatory Activities terms focusing on congenital anomalies of the external ear. Drug generic names were sourced from the DrugBank database. To assess safety signals and rank drugs by their signal strength, we conducted a disproportionality analysis, generating reporting odds ratios (ROR) and proportional reporting ratios (PRR). A total of 20,754,281 AE reports were identified in the FAERS database from Q1 2004 to Q1 2024, of which 1763 were related to congenital anomalies of the external ear. Valproic acid (122 cases) was associated with the most cases, followed by mycophenolate mofetil (105 cases) and lamotrigine (65 cases). According to the disproportionality analysis, the top five drugs with the highest ROR and PRR were primidone (ROR: 397.05, 95% CI 147.21, 1070.9; PRR: 388.71, 95% CI 145.89, 1035.7), valproic acid (ROR: 239.46, 95% CI 123.75, 463.37; PRR: 236.42, 95% CI 123.82, 451.43), tapazole (ROR: 198.35, 95% CI 63.49, 619.67; PRR: 196.25, 95% CI 62.97, 611.67), nevirapine (ROR: 138.24, 95% CI 82.9, 230.51; PRR: 137.23, 95% CI 82.44, 228.44), and sebivo (ROR: 117.1, 95% CI 48.51, 282.67; PRR: 116.37, 95% CI 48.17, 281.12). This study identified several drugs significantly associated with congenital anomalies of the external ear in the FAERS database using disproportionality analysis. The findings can help healthcare professionals better recognize and manage drug-induced congenital anomalies of the external ear, particularly when prescribing high-risk medications. Further research is needed to elucidate the mechanisms underlying these associations and develop strategies for preventing and mitigating drug-induced congenital anomalies of the external ear.
A machine learning algorithm to explore the drivers of carbon emissions in Chinese cities
Authors: Yu Wenmei , Xia Lina , Cao Qiang 
Published: October 2024

AbstractAs the world’s largest energy consumer and carbon emitter, the task of carbon emission reduction is imminent. In order to realize the dual-carbon goal at an early date, it is necessary to study the key factors affecting China’s carbon emissions and their non-linear relationships. This paper compares the performance of six machine learning algorithms to that of traditional econometric models in predicting carbon emissions in China from 2011 to 2020 using panel data from 254 cities in China. Specifically, it analyzes the comparative importance of domestic economic, external economic, and policy uncertainty factors as well as the nonparametric relationship between these factors and carbon emissions based on the Extra-trees model. Results show that energy consumption (ENC) remains the root cause of increased carbon emissions among domestic economic factors, although government intervention (GOV) and digital finance (DIG) can significantly reduce it. Next, among the external economic and policy uncertainty factors, foreign direct investment (FDI) and economic policy uncertainty (EPU) are important factors influencing carbon emissions, and the partial dependence plots (PDPs) confirm the pollution haven hypothesis and also reveal the role of EPU in reducing carbon emissions. The heterogeneity of factors affecting carbon emissions is also analyzed under different city sizes, and it is found that ENC is a common driving factor in cities of different sizes, but there are some differences. Finally, appropriate policy recommendations are proposed by us to help China move rapidly towards a green and sustainable development path.
Fast low-temperature irradiation creep driven by athermal defect dynamics
Authors: Feichtmayer Alexander , Boleininger Max , Riesch Johann , Mason Daniel R. , Reali Luca , Höschen Till , Fuhr Maximilian , Schwarz-Selinger Thomas , Neu Rudolf , Dudarev Sergei L. 
Published: October 2024

AbstractThe occurrence of high stress concentrations in reactor components is a still intractable phenomenon encountered in fusion reactor design. Here, we observe and quantitatively model a non-linear high-dose radiation mediated microstructure evolution effect that facilitates fast stress relaxation in the most challenging low-temperature limit. In situ observations of a tensioned tungsten wire exposed to a high-energy ion beam show that internal stress of up to 2 GPa relaxes within minutes, with the extent and time-scale of relaxation accurately predicted by a parameter-free multiscale model informed by atomistic simulations. As opposed to conventional notions of radiation creep, the effect arises from the self-organisation of nanoscale crystal defects, athermally coalescing into extended polarized dislocation networks that compensate and alleviate the external stress.