bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking Changes in Plant Growth and Nutrient Stoichiometry With Nitrogen Enrichment in a Meadow Steppe
Authors: Wang Yinliu , Niu Guoxiang , Yang Guojiao , Hasi Muqier , Li Ang , Xue Jianguo , Lü Xiaotao , Han Xingguo , Huang Jianhui 
Published: January 2025

AbstractExogenous nitrogen (N) inputs can significantly influence the availability of N and other nutrients in terrestrial ecosystems. However, the connections between soil nutrient dynamics following N enrichment and plant nutrient uptake as well as plant growth responses within a community remain underexplored. Here, we examined the effects of N addition on the dynamics of several macro and micronutrients in soil and three dominant plants on a meadow steppe in China. The results showed that (a) the exchangeable Ca and Mg in the soil initially increased when the N addition rate was lower than 10 g N m−2 yr−1 and then decreased at higher N addition rates (10–50 g N m−2 yr−1), whereas the available P and extractable Fe, Mn, and Cu remained relatively stable at low N addition rates but increased at high N addition rates. (b) The response of plant nutrient concentrations and the stoichiometry of these nutrients to N addition was not only species‐specific but also showed marked differences especially for those micronutrients. (c) Species with lower variation in nutrient concentrations, such as Leymus chinensis (Lc) and Thermopsis lanceolata (Tl), exhibited increased (for Lc) or stable (for Tl) biomass after N addition, whereas species such as Carex duriuscula, with greater nutrient variability, experienced reduced biomass. These findings suggest that soil acidification induced by exogenous N inputs alters soil nutrient availability and further results in imbalanced plant nutrient uptake and stoichiometries, which will affect the dynamics and structures of plant communities under global change scenarios.
Electrophysiology-based screening identifies neuronal HtrA serine peptidase 2 (HTRA2) as a synaptic plasticity regulator participating in tauopathy
Authors: Zheng Naizhen , Li Kun , Cao Jing , Wang Zijie , Zhang Liang , Zhao Zihao , He Jiawei , Wang Yong , Zhu Xiang , Chen Yiqing , Meng Jian , Zhao Dongdong , Niu Mengxi , Luo Hong , Zhang Xian , Sun Hao , Zhang Yun-wu 
Published: January 2025

AbstractLong-term potentiation (LTP) and long-term depression (LTD) are widely used to study synaptic plasticity. However, whether proteins regulating LTP and LTD are altered in cognitive disorders and contribute to disease onset remains to be determined. Herein, we induced LTP and LTD in the hippocampal CA3-CA1 Schaffer collateral pathway, respectively, and then performed proteomic analysis of the CA1 region. We identified 20 differentially expressed proteins (DEPs) shared by the LTP and the LTD processes. Among them, we found that HtrA serine peptidase 2 (HTRA2) was mainly expressed in neurons and that HTRA2 levels were increased in both the LTP and the LTD processes in C57BL/6 mice. HTRA2 downregulation impaired synapses and reduced ATP production in cultured primary neurons. Furthermore, adeno-associated virus (AAV)-mediated HTRA2 downregulation in the hippocampus impaired synaptic plasticity and cognitive function in C57BL/6 mice. Moreover, we found that HTRA2 expression decreased in the brains of Alzheimer’s disease patients, frontotemporal lobar degeneration with ubiquitin inclusions patients, and tauopathy model mice. Finally, we showed that lentivirus-mediated HTRA2 overexpression in the hippocampus rescued PP2B reduction, alleviated tau hyperphosphorylation, and partially attenuated synaptic plasticity and cognitive deficits in the PS19 tauopathy model mice. Our study not only indicates that HTRA2 in neurons plays an important role in regulating synaptic plasticity under both physiological and pathological conditions, but also provides a novel, electrophysiology-based strategy to identify proteins regulating synaptic plasticity systematically.
N6-methyladenosine-modification of USP15 regulates chemotherapy resistance by inhibiting LGALS3 ubiquitin-mediated degradation via AKT/mTOR signaling activation pathway in hepatocellular carcinoma
Authors: Fang Ronghuan , Jia Zhigang , Xin Yuhang , Zhao Kai , Qin Wei , Lu Haoran , Zhou Yi , Yang Yongsheng , Fang He 
Published: January 2025

AbstractHepatocellular carcinoma (HCC) is among the most malignant tumors and seriously threatens human health worldwide, and its incidence rate is increasing annually. USP15 is a member of the ubiquitination-specific protease (USP) family, which can regulate protein ubiquitination, thereby affecting their stability, and is dysregulated in many cancers, but its expression and regulatory mechanism in HCC are unclear. The aims of this study were to explore the role and mechanism of USP15 in regulating HCC cell stemness, proliferation, and lenvatinib resistance. Immunohistochemistry and high-throughput sequencing analyses of tumor and adjacent normal tissue samples from 52 patients with HCC were conducted. Functional analyses of immortalized human liver and HCC cell lines were conducted, including quantitative real-time PCR; western blot; plasmid, lentivirus, and siRNA transfection; co-immunoprecipitation; mass spectrometry; MeRIP-qPCR; and ubiquitination, cell growth, colony formation, and spheroid formation assays. HCC tumor growth was also assessed using cell transplantation in nude mice. We found that USP15 is upregulated in HCC and affects patient prognosis. Our results demonstrated that USP15 can increase LGALS3 stability in HCC through deubiquitination modification, and affect the stemness, proliferation, and lenvatinib resistance of HCC cells by activating the AKT/mTOR pathway. USP15 expression levels were positively correlated with HCC cell stemness, proliferation, and lenvatinib resistance. In addition, methyltransferase-like protein 3 (Mettl3) N6-methyladenosine (m6A) modified USP15 to upregulate its levels by increasing its mRNA stability. These findings provide a theoretical basis for the potential discovery of new HCC oncogenes, as well as the identification of effective targets and development of novel anti-HCC drugs and clinical applications.
The proline-rich antimicrobial peptide Api137 disrupts large ribosomal subunit assembly and induces misfolding
Authors: Lauer Simon Malte , Gasse Jakob , Krizsan Andor , Reepmeyer Maren , Sprink Thiemo , Nikolay Rainer , Spahn Christian M. T. , Hoffmann Ralf 
Published: January 2025

AbstractThe proline-rich antimicrobial designer peptide Api137 inhibits protein expression in bacteria by binding simultaneously to the ribosomal polypeptide exit tunnel and the release factor (RF), depleting the cellular RF pool and leading to ribosomal arrest at stop codons. This study investigates the additional effect of Api137 on the assembly of ribosomes using an Escherichia coli reporter strain expressing one ribosomal protein per 30S and 50S subunit tagged with mCherry and EGFP, respectively. Separation of cellular extracts derived from cells exposed to Api137 in a sucrose gradient reveals elevated levels of partially assembled and not fully matured precursors of the 50S subunit (pre-50S). High-resolution structures obtained by cryogenic electron microscopy demonstrate that a large proportion of pre-50S states are missing up to five proteins (uL22, bL32, uL29, bL23, and uL16) and have misfolded helices in 23S rRNA domain IV. These data suggest a second mechanism for Api137, wherein it disrupts 50S subunit assembly by inducing the formation of misfolded precursor particles potentially incapable of evolving into active ribosomes, suggesting a bactericidal mechanism.
Engineered Mycobacterium tuberculosis triple-kill-switch strain provides controlled tuberculosis infection in animal models
Authors: Wang Xin , Su Hongwei , Wallach Joshua B. , Wagner Jeffrey C. , Braunecker Benjamin J. , Gardner Michelle , Guinn Kristine M. , Howard Nicole C. , Klevorn Thais , Lin Kan , Liu Yue J. , Liu Yao , Mugahid Douaa , Rodgers Mark , Sixsmith Jaimie , Wakabayashi Shoko , Zhu Junhao , Zimmerman Matthew , Dartois Véronique , Flynn JoAnne L. , Lin Philana Ling , Ehrt Sabine , Fortune Sarah M. , Rubin Eric J. , Schnappinger Dirk 
Published: January 2025

Abstract
Human challenge experiments could accelerate tuberculosis vaccine development. This requires a safe Mycobacterium tuberculosis (Mtb) strain that can both replicate in the host and be reliably cleared. Here we genetically engineered Mtb strains encoding up to three kill switches: two mycobacteriophage lysin operons negatively regulated by tetracycline and a degron domain–NadE fusion, which induces ClpC1-dependent degradation of the essential enzyme NadE, negatively regulated by trimethoprim. The triple-kill-switch (TKS) strain showed similar growth kinetics and antibiotic susceptibilities to wild-type Mtb under permissive conditions but was rapidly killed in vitro without trimethoprim and doxycycline. It established infection in mice receiving antibiotics but was rapidly cleared upon cessation of treatment, and no relapse was observed in infected severe combined immunodeficiency mice or Rag−/− mice. The TKS strain had an escape mutation rate of less than 10−10 per genome per generation. These findings suggest that the TKS strain could be a safe, effective candidate for a human challenge model.
Comprehensive analysis of poly(A) tails in mouse testes and ovaries using Nanopore Direct RNA Sequencing
Authors: Czarnocka-Cieciura Agnieszka , Brouze Michał , Gumińska Natalia , Mroczek Seweryn , Gewartowska Olga , Krawczyk Paweł S. , Dziembowski Andrzej 
Published: January 2025

AbstractGametogenesis is a process in which dysfunctions lead to infertility, a growing health and social problem worldwide. In both spermatogenesis and oogenesis, post-transcriptional gene expression regulation is crucial. Essentially, all mRNAs possess non-templated poly(A) tails, whose composition and dynamics (elongation, shortening, and modifications) determine the fate of mRNA. Moreover, gametogenesis, especially oogenesis, represents a unique instance of the complexity of poly(A) tails metabolism, with oocyte-specific waves of cytoplasmic polyadenylation. In this context, we provide a comprehensive transcriptomic dataset focusing on mRNA poly(A) tail composition and dynamics in murine testes and ovaries. It consists of RNA samples isolated from wild-type and transgenic mice lacking TENT5 polymerases, which can extend poly(A) tails in the cytoplasm. TENT5 deficiencies have serious consequences. For instance, the defect of TENT5D causes infertility in humans. The data described here are generated mainly using the Oxford Nanopore Direct RNA Sequencing (DRS) method, which provides ground-truth information about mRNA molecules, including poly(A) tail length and nucleotide content. For instance, we show the prevalence of uridilated tails in testicular mRNAs.
Laboratory validation of patient-specific templating for total knee arthroplasty
Authors: Hafez Mahmoud A. , Jansen Arne , Portheine Frank , Jaramaz Branislav 
Published: January 2025

AbstractPatient-specific templating (PST), which is a sister procedure to patient-specific instrumentation (PSI) but hospital-based, is relatively less complex and less expensive than robotics and navigation. However, there are some concerns about the PST including the process of preoperative planning, 3D printing and material, positioning of PST intraoperatively, availability, and clinical value. The purpose of this study was to validate the technical accuracy and reliability of the PST technique in the lab and to report the outcomes of clinical application. To test the reliability of the PST technique, five observers positioned the PST templates five times over the distal femur and proximal tibial whilst a navigation system was used to measure the level of bone cutting, coronal and sagittal alignment, and rotation in both femur and tibia. The mean alignment error in all planes was 0.67° (maximum 2.5°). Concerning the bone (femoral and tibial) cutting, the mean error was 0.32 mm (maximum 1 mm). The qualitative and quantitative analysis showed an overall agreement between observers (p < 0.05). The laboratory part of this study showed that the positioning of the PST over the proximal tibia and distal femur during TKA is reliable. There were statistically insignificant intraobserver and interobserver variations.
Machine learning identified novel players in lipid metabolism, endosomal trafficking, and iron metabolism of the ALS spinal cord
Authors: Cheng Jack , Wu Bor-Tsang , Liu Hsin-Ping , Lin Wei-Yong 
Published: January 2025

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease affecting motor neurons. Although genes causing familial cases have been identified, those of sporadic ALS, which occupies the majority of patients, are still elusive. In this study, we adopted machine learning to build binary classifiers based on the New York Genome Center (NYGC) ALS Consortium’s RNA-seq data of the postmortem spinal cord of ALS and non-neurological disease control. The accuracy of the classifiers was greater than 83% and 77% for the training set and the unseen test set, respectively. The classifiers contained 114 genes. Among them, 41 genes have been reported in previous ALS studies, and others are novel in this field. These genes are involved in mitochondrial respiration, lipid metabolism, endosomal trafficking, and iron metabolism, which may promote the progression of ALS pathology.
A high-throughput ResNet CNN approach for automated grapevine leaf hair quantification
Authors: Malagol Nagarjun , Rao Tanuj , Werner Anna , Töpfer Reinhard , Hausmann Ludger 
Published: January 2025

AbstractThe hairiness of the leaves is an essential morphological feature within the genus Vitis that can serve as a physical barrier. A high leaf hair density present on the abaxial surface of the grapevine leaves influences their wettability by repelling forces, thus preventing pathogen attack such as downy mildew and anthracnose. Moreover, leaf hairs as a favorable habitat may considerably affect the abundance of biological control agents. The unavailability of accurate and efficient objective tools for quantifying leaf hair density makes the study intricate and challenging. Therefore, a validated high-throughput phenotyping tool was developed and established in order to detect and quantify leaf hair using images of single grapevine leaf discs and convolution neural networks (CNN). We trained modified ResNet CNNs with a minimalistic number of images to efficiently classify the area covered by leaf hairs. This approach achieved an overall model prediction accuracy of 95.41%. As final validation, 10,120 input images from a segregating F1 biparental population were used to evaluate the algorithm performance. ResNet CNN-based phenotypic results compared to ground truth data received by two experts revealed a strong correlation with R values of 0.98 and 0.92 and root-mean-square error values of 8.20% and 14.18%, indicating that the model performance is consistent with expert evaluations and outperforms the traditional manual rating. Additional validation between expert vs. non-expert on six varieties showed that non-experts contributed to over- and underestimation of the trait, with an absolute error of 0% to 30% and -5% to -60%, respectively. Furthermore, a panel of 16 novice evaluators produced significant bias on set of varieties. Our results provide clear evidence of the need for an objective and accurate tool to quantify leaf hairiness.
Increasing temporal stability of global tropical cyclone precipitation
Authors: Deng E , Xiang Qian , Chan Johnny C. L. , Dong Yue , Tu Shifei , Chan Pak-Wai , Ni Yi-Qing 
Published: January 2025

AbstractTropical cyclone (TC) precipitation has led to escalating urban flooding and transportation disruptions in recent years. The volatility of the TC rain rate (RR) over short periods complicates accurate forecasting. Here, we use satellite-based observational rainfall datasets from 1998 to 2019 to calculate changes in TC 24-h RR and quantify the temporal stability of TC precipitation. We demonstrate a significant global increase in the annual temporal stability of TC RR across the total rainfall area, inner-core, and rainband areas. Specifically, the probabilities of rapid RR increase and decrease events in the TC total rainfall area decreased at rates of –1.74 ± 0.57% per decade and –2.23 ± 0.55% per decade, respectively. Based on the reanalysis dataset, we propose that the synergistic effects of increased atmospheric stability and total column water vapor—both resulting from anthropogenic warming at low latitudes—are potentially associated with this trend.
Third-party evaluators perceive AI as more compassionate than expert humans
Authors: Ovsyannikova Dariya , de Mello Victoria Oldemburgo , Inzlicht Michael 
Published: January 2025

AbstractEmpathy connects us but strains under demanding settings. This study explored how third parties evaluated AI-generated empathetic responses versus human responses in terms of compassion, responsiveness, and overall preference across four preregistered experiments. Participants (N = 556) read empathy prompts describing valenced personal experiences and compared the AI responses to select non-expert or expert humans. Results revealed that AI responses were preferred and rated as more compassionate compared to select human responders (Study 1). This pattern of results remained when author identity was made transparent (Study 2), when AI was compared to expert crisis responders (Study 3), and when author identity was disclosed to all participants (Study 4). Third parties perceived AI as being more responsive—conveying understanding, validation, and care—which partially explained AI’s higher compassion ratings in Study 4. These findings suggest that AI has robust utility in contexts requiring empathetic interaction, with the potential to address the increasing need for empathy in supportive communication contexts.
Female sex is linked to a stronger association between sTREM2 and CSF p-tau in Alzheimer’s disease
Authors: Biel Davina , Suárez-Calvet Marc , Dewenter Anna , Steward Anna , Roemer Sebastian N , Dehsarvi Amir , Zhu Zeyu , Pescoller Julia , Frontzkowski Lukas , Kreuzer Annika , Haass Christian , Schöll Michael , Brendel Matthias , Franzmeier Nicolai 
Published: January 2025

Abstract
In Alzheimer’s disease (AD), Aβ triggers p-tau secretion, which drives tau aggregation. Therefore, it is critical to characterize modulators of Aβ-related p-tau increases which may alter AD trajectories. Here, we assessed whether factors known to alter tau levels in AD modulate the association between fibrillar Aβ and secreted p-tau181 determined in the cerebrospinal fluid (CSF). To assess potentially modulating effects of female sex, younger age, and ApoE4, we included 322 ADNI participants with cross-sectional/longitudinal p-tau181. To determine effects of microglial activation on p-tau181, we included 454 subjects with cross-sectional CSF sTREM2. Running ANCOVAs for nominal and linear regressions for metric variables, we found that women had higher Aβ-related p-tau181 levels. Higher sTREM2 was associated with elevated p-tau181, with stronger associations in women. Similarly, ApoE4 was related to higher p-tau181 levels and faster p-tau181 increases, with stronger effects in female ApoE4 carriers. Our results show that sex alone modulates the Aβ to p-tau axis, where women show higher Aβ-dependent p-tau secretion, potentially driven by elevated sTREM2-related microglial activation and stronger effects of ApoE4 carriership in women.
Dielectric properties depend on the crystal structure of perovskite-type RbTaO3 synthesized at high pressure
Authors: Murase Kimitoshi , Yamaura Jun-ichi , Hamasaki Yousuke , Kato Takeharu , Sagayama Hajime , Yamamoto Ayako 
Published: January 2025

We prepared perovskite-type RbTaO3 at 1173 K and 4 GPa. It was cubic cell at 300 K, and showed phase transitions at 270 K with tetragonal and 80 K with orthorhombic. The relative permittivity was varied corresponding to the phase transitions.
Learning optical flow from spiking camera with direction disassembly
Authors: Zhai Mingliang , Jiang Mingming , Xiang Xuezhi , Ni Kang , Gao Hao 
Published: January 2025

AbstractConventional optical flow estimation methods typically recover two‐dimensional motion from RGB image sequences. Recently, due to the rise and widespread use of spike cameras, learning optical flow from spiking cameras has become a hot topic in the field of two‐dimensional motion estimation. Although existing methods have been designed to learn optical flow by designing feature processing methods for spike streams, there is still insufficient consideration for flow field post‐processing, resulting in limited accuracy of optical flow estimation. To address this problem, an optical flow estimation method based on directional disassembly is proposed. Specifically, the estimated flow fields along the horizontal and vertical directions are disassembled and the motion vectors along the two directions are denoised separately to reduce the burden of post‐processing for complex two‐dimensional motion information. In addition, contextual information is introduced in the post‐processing so that the scene information can effectively contribute to the results of the flow post‐processing. Experimental results show that this proposed method is capable of achieving comparable performance on spike‐based public datasets.
A reinforcement learning‐based reverse‐parking system for autonomous vehicles
Authors: Al‐Mousa Amjed , Arrabi Ahmad , Daoud Hamza 
Published: January 2025

AbstractThis work presents the design and implementation of a reinforcement learning‐based autonomous parking system where an agent is trained to reverse‐park in a selected parking spot. The parking procedure is divided into three stages, and each stage has its corresponding surrogate objective that contributes to the overall parking process. The model solely depends on features extracted from a top‐view image of the parking space. It has the advantage of potential deployment in smart parking buildings without refitting non‐autonomous cars with modern sensors. The training was conducted offline on a simulation utilizing the proximal policy optimization algorithm. The model was then transferred and tested on a hardware prototype of the parking space. The results of the system were successful as the successful parking rate reached 100% with no collisions with any objects, and the fastest parking time reached 10 s. The testing was conducted on multiple samples and scenarios of the parking setup.