bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geological Knowledge‐Guided Dual‐Branch Deep Learning Model for Identification of Geochemical Anomalies Related to Mineralization
Authors: Xu Ying , Zuo Renguang , Bai Yang 
Published: January 2025

AbstractGeochemical survey data are a type of spatial big data that play an increasingly significant role in mineral exploration. One challenge in the era of big data is how to mine geochemical data in support of mineral exploration. In this study, based on a generative adversarial network framework, we proposed an unsupervised spatial–spectrum dual‐branch deep learning method for geochemical anomaly identification, namely dual‐DL, which consists of a spatial branch and a spectrum branch. The spatial branch was constructed using the convolutional neural network and convolutional autoencoder, which can effectively capture spatial geochemical patterns and extract spatial relationships between neighboring pixels. The spectrum branch consists of a recurrent neural network that can study geochemical elemental assemblies within a single pixel. The geological knowledge was added into the model, including selecting the input order of geochemical elements and constructing the loss function of the model. A case study was conducted to recognize geochemical anomalies associated with gold polymetallic mineralization in Hubei Province, China. The results demonstrated that (a) the unsupervised dual‐DL model has superior performance in identifying mineralization related to geochemical anomalies, (b) the geological knowledge‐guided unsupervised dual‐DL model can improve the accuracy and interpretability of geochemical anomaly identification.
GRK5 is required for adipocyte differentiation through ERK activation
Authors: Seramur Mary E. , McDonald Bailey , Davis Matt , Reeves Tony E. , Solberg Woods Leah C. , Chuang Key Chia-Chi 
Published: January 2025

Abstract
Previous studies have identified G protein-coupled receptor (GPCR) kinase 5 (GRK5) as a genetic factor contributing to obesity pathogenesis, but the underlying mechanism remains unclear. We demonstrate here that Grk5 mRNA is more abundant in stromal vascular fractions of mouse white adipose tissue, the fraction that contains adipose progenitor cells, or committed preadipocytes, than in adipocyte fractions. Thus, we generated a GRK5 knockout (KO) 3T3-L1 preadipocyte to further investigate the mechanistic role of GRK5 in regulating adipocyte differentiation. During adipogenic stimulation, GRK5 KO preadipocytes had decreased lipid accumulation and delayed mature adipocyte development compared to wildtype cells coupled with suppressed adipogenic and lipogenic gene expression. Beside GPCR signaling, RNA sequencing and pathway analysis identified insulin-like growth factor 1 (IGF-1) signaling to be one of the top 5 significantly dysregulated pathways in GRK5 KO cells. GRK5 KO cells also displayed decreased insulin-stimulated ERK phosphorylation, a downstream target of insulin-stimulated IGF-1 receptor activation, suggesting that GRK5 acts through this critical pathway to impact 3T3-L1 adipocyte differentiation. To find a more translational approach, we identified a new small molecule GRK5 inhibitor that was able to reduce 3T3-L1 adipogenesis. These data suggest that GRK5 is required for adipocyte differentiation through IGF-1 receptor/ERK activation and may be a promising translational target for obesity.
Finite element-based nonlinear dynamic optimization of nanomechanical resonators
Authors: Li Zichao , Alijani Farbod , Sarafraz Ali , Xu Minxing , Norte Richard A. , Aragón Alejandro M. , Steeneken Peter G. 
Published: January 2025

Abstract
Nonlinear dynamic simulations of mechanical resonators have been facilitated by the advent of computational techniques that generate nonlinear reduced order models (ROMs) using the finite element (FE) method. However, designing devices with specific nonlinear characteristics remains inefficient since it requires manual adjustment of the design parameters and can result in suboptimal designs. Here, we integrate an FE-based nonlinear ROM technique with a derivative-free optimization algorithm to enable the design of nonlinear mechanical resonators. The resulting methodology is used to optimize the support design of high-stress nanomechanical Si3N4 string resonators, in the presence of conflicting objectives such as simultaneous enhancement of Q-factor and nonlinear Duffing constant. To that end, we generate Pareto frontiers that highlight the trade-offs between optimization objectives and validate the results both numerically and experimentally. To further demonstrate the capability of multi-objective optimization for practical design challenges, we simultaneously optimize the design of nanoresonators for three key figure-of-merits in resonant sensing: power consumption, sensitivity and response time. The presented methodology can facilitate and accelerate designing (nano) mechanical resonators with optimized performance for a wide variety of applications.
PCDH17 induces colorectal cancer metastasis by destroying the vascular endothelial barrier
Authors: Dong Fengyun , Zhou Pinghui , Kong Feifei , Cao Sijie , Pan Xiaozao , Cai Shujing , Chen Xinke , Wang Sen , Li Na , He Baoyu , Zhao Rou , Zhang Bin , Bie Qingli 
Published: January 2025

Abstract
Compromised vascular integrity facilitates the cancer cells extravasation and metastasis. However, the mechanisms leading to a disruption in vascular integrity in colorectal cancer (CRC) remain unclear. In this study, PCDH17 expression was higher in the vascular endothelial cells of colon cancer with distant metastasis, and the rates of PCDH17+ endothelial cells (ECs) was associated with the M stage in clinical pathological characteristics analysis and correlated with a poor survival prognosis. The liver and lung metastatic dissemination of MC-38 was significantly decreased in PCDH17–/–mice. The ubiquitination and degradation of VEGFR2 was prevented by the interaction between PCDH17 and the E3 ubiquitin ligase MARCH5, which causing the separation of internalized VE-cadherin, and increased the vascular permeability and metastasis of CRC. These results highlight the importance of PCDH17 in maintaining vascular integrity, which has emphasis for endothelial barrier function in metastatic cancer. PCDH17 has the potential to be a marker for predicting tumor metastasis as well as a viable treatment target for CRC.
Apaf-1 is an evolutionarily conserved DNA sensor that switches the cell fate between apoptosis and inflammation
Authors: Ruan Jie , Wei Xuxia , Li Suizhi , Ye Zijian , Hu Linyi , Zhuang Ru , Cao Yange , Wang Shaozhou , Wu Shengpeng , Peng Dezhi , Chen Shangwu , Yuan Shaochun , Xu Anlong 
Published: January 2025

Abstract
Apoptotic protease activating factor 1 (Apaf-1) was traditionally defined as a scaffold protein in mammalian cells for assembling a caspase activation platform known as the ‘apoptosome’ after its binding to cytochrome c. Although Apaf-1 structurally resembles animal NOD-like receptor (NLR) and plant resistance (R) proteins, whether it is directly involved in innate immunity is still largely unknown. Here, we found that Apaf-1-like molecules from lancelets, fruit flies, mice, and humans have conserved DNA sensing functionality. Mechanistically, mammalian Apaf-1 recruits receptor-interacting protein 2 (RIP2, also known as RIPK2) via its WD40 repeat domain and promotes RIP2 oligomerization to initiate NF-κB-driven inflammation upon cytoplasmic DNA recognition. Furthermore, DNA binding of Apaf-1 determines cell fate by switching the cellular processes between intrinsic stimuli-activated apoptosis and inflammation. These findings suggest that Apaf-1 is an evolutionarily conserved DNA sensor and may serve as a cell fate checkpoint, which determines whether cells initiate inflammation or undergo apoptosis by distinct ligand binding.
Generation of live mice from haploid ESCs with germline-DMR deletions or switch
Authors: Ma Yongjian , Yan Meng , Xie Zhenfei , Zhang Hongling , Li Zhoujie , Li Yuanyuan , Yang Suming , Zhang Meiling , Li Wen , Li Jinsong 
Published: January 2025

Abstract
Genomic imprinting is required for sexual reproduction and embryonic development of mammals, in which, differentially methylated regions (DMRs) regulate the parent-specific monoallelic expression of imprinted genes. Numerous studies on imprinted genes have highlighted their critical roles in development. However, what imprinting network is essential for development is still unclear. Here, we establish a stepwise system to reconstruct a development-related imprinting network, in which diploid embryonic stem cells (ESCs) are derived by fusing between parthenogenetic (PG)- and androgenetic (AG)-haploid embryonic stem cells (haESCs) with different DMR deletions (termed Ha-Ha-fusion system), followed by tetraploid complementation to produce all-haESC fetuses. Diploid ESCs fused between PG-haESCs carrying 8 maternally-derived DMR deletions and AG-haESCs with 2 paternally-derived DMR deletions give rise to live pups efficiently, among which, one lives to weaning. Strikingly, diploid ESCs derived from the fusion of PG-haESCs with 7 maternal DMR deletions and AG-haESCs with 2 paternal DMR deletions and maternal Snrpn-DMR deletion also support full-term embryonic development. Moreover, embryos reconstructed by injection of AG-haESCs with hypomethylated H19-DMR into oocytes with H19-DMR deletion develop into live mice sustaining inverted allelic gene expression. Together, our findings indicate that restoration of monoallelic expression of 10 imprinted regions is adequate for the full-term development of all-haESC pups, and it works irrespective of their parental origins. Meanwhile, Ha-Ha-fusion system provides a useful tool for deciphering imprinting regulation networks during embryonic development.
Differences between the normal and perceived appropriate portion sizes of discretionary foods
Authors: Liu Qingzhou , Allman-Farinelli Margaret , Rangan Anna 
Published: January 2025

Abstract

Background
There are limited data on the amount of discretionary foods that people normally consume and consider as appropriate at one eating occasion. This study aimed to provide an overview of the range and assess differences of the ‘normal portion size’ and ‘perceived appropriate portion size’ of energy-dense nutrient-poor discretionary foods among consumers aged 18–65 years.

Methods
To measure normal and perceived appropriate portion sizes, a validated online image-series questionnaire consisting of eight successive portion size options for 15 discretionary foods was completed at two timepoints. Quantile regression models were used to estimate the ranges (lower boundary at 17th percentile, upper boundary at 83rd percentile) of normal and perceived appropriate portion sizes selected by two thirds of the study population. Models were adjusted for the effects of potential influencing factors including biological sex, age, usual physical activity level, cooking confidence, socio-economic status, body mass index, and baseline hunger levels.

Results
A final sample of 295 participants were included in the analysis (51% females, mean age 39.5 ± 14.1 years). The normal portion sizes were significantly higher than the perceived appropriate portion sizes across all test foods, with the effects of sex, age, and BMI being significant for some foods.

Conclusion
The finding suggests that consumers would normally consume a portion size that was larger than what they perceive to be appropriate for discretionary foods. The estimated lower and upper boundaries would be valuable for the development of pragmatic public health messages to empower consumers towards better portion control.
Scaffold-enabled high-resolution cryo-EM structure determination of RNA
Authors: Haack Daniel B. , Rudolfs Boris , Jin Shouhong , Khitun Alexandra , Weeks Kevin M. , Toor Navtej 
Published: January 2025

Abstract
Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail. These difficulties are compounded for small RNAs as cryo-EM is inherently more difficult for lower molecular weight macromolecules. Here we present a strategy for fusing small RNAs to a group II intron that yields high resolution structures of the appended RNA. We demonstrate this technology by determining the structures of the 86-nucleotide (nt) thiamine pyrophosphate (TPP) riboswitch aptamer domain and the recently described 210-nt raiA bacterial non-coding RNA involved in sporulation and biofilm formation. In the case of the TPP riboswitch aptamer domain, the scaffolding approach allowed visualization of the riboswitch ligand binding pocket at 2.5 Å resolution. We also determined the structure of the ligand-free apo state and observe that the aptamer domain of the riboswitch adopts an open Y-shaped conformation in the absence of ligand. Using this scaffold approach, we determined the structure of raiA at 2.5 Å in the core. Our versatile scaffolding strategy enables efficient RNA structure determination for a broad range of small to moderate-sized RNAs, which were previously intractable for high-resolution cryo-EM studies.
Memristor-based feature learning for pattern classification
Authors: Shi Tuo , Gao Lili , Tian Yang , Tang Shuangzhu , Liu Jinchang , Li Yiqi , Zhou Ruixi , Cui Shiyu , Zhang Hui , Li Yu , Wu Zuheng , Zhang Xumeng , Li Taihao , Yan Xiaobing , Liu Qi 
Published: January 2025

Abstract
Inspired by biological processes, feature learning techniques, such as deep learning, have achieved great success in various fields. However, since biological organs may operate differently from semiconductor devices, deep models usually require dedicated hardware and are computation-complex. High energy consumption has made deep model growth unsustainable. We present an approach that directly implements feature learning using semiconductor physics to minimize disparity between model and hardware. Following this approach, a feature learning technique based on memristor drift-diffusion kinetics is proposed by leveraging the dynamic response of a single memristor to learn features. The model parameters and computational operations of the kinetics-based network are reduced by up to 2 and 4 orders of magnitude, respectively, compared with deep models. We experimentally implement the proposed network on 180 nm memristor chips for various dimensional pattern classification tasks. Compared with memristor-based deep learning hardware, the memristor kinetics-based hardware can further reduce energy and area consumption significantly. We propose that innovations in hardware physics could create an intriguing solution for intelligent models by balancing model complexity and performance.
Measurements of groundwater, hydrodynamics, and sand characteristics at a dissipative sea turtle nesting beach
Authors: Christiaanse Jakob C. , Antolínez José A. A. , van der Grinten Meye J. , Taal Falco , Figlus Jens , Dellapenna Timothy M. , Ritt Benjamin , Marshall Christopher D. , Tereszkiewicz Peter A. , Cohn Nicholas , Majzlik Edward J. , Reniers Ad J. H. M. 
Published: January 2025

Abstract
Beach groundwater and nearshore hydrodynamic data were collected during a field experiment along two dissipative beach transects on Galveston Island, Texas, in the fall of 2023. The monitored beaches serve as nesting habitat for the critically endangered Kemp’s ridley sea turtle. Conditions ranged from calm to stormy, with two storms occurring during the experiment, inundating the entire beach up to the dune toe. Collected hydrodynamic data include readings from pressure loggers submerged in the foreshore and mounted in groundwater wells in the backshore, data from two wave buoys about 1.5 km offshore, and GoPro timestacks of the instantaneous waterline (wave runup). Other collected data include bathymetry and topography surveys, subsurface temperature and moisture content readings, and sediment characteristics. This comprehensive dataset can be used to (1) study relevant beach inundation and groundwater processes, including their effect on the local ecosystem (e.g., repeated flooding of sea turtle nests), (2) study the propagation of nearshore hydrodynamic processes into the beach matrix and groundwater table, and (3) validate existing beach groundwater models.
Developmental defects in ectodermal appendages caused by missense mutation in edaradd gene in the nfr mangrove killifish kryptolebias marmoratus
Authors: Saud Hussein A. , O’Neill Paul A. , Ring Brian C. , Kudoh Tetsuhiro 
Published: January 2025

Abstract
The mangrove killifish, Kryptolebias marmoratus, can reproduce with self-fertilisation, offering a unique and useful genetic tool for generation of genetic mutants and quick identification of mutated genes. From an ENU-mutated mangrove killifish line R228, we have isolated a novel mutant line, no-fin-ray/nfr in which homozygous mutant of adult fish fin ray development is largely reduced. Illumina RNAseq with 3 embryos each from mutants, siblings and the parental WT strain Hon9 (only 9 embryos as total) identified a mutation in the edaradd in a highly conserved C-terminal death domain. Edaradd is known as a cytoplasmic accessory protein for the Ectodysplasin A (EDA) signalling pathway. To confirm the crucial role of edaradd during fin development, CRISPR RNAs were designed to suppress the gene in another killifish species, Arabian killifish. Indeed, Arabian killifish edaradd crispants showed a potent reduction of the fin development with 100% frequency. Furthermore, EDA crispants also showed identical phenotypes to that of edaradd crispants, confirming the fin defect in the mutants/crispants is caused by the signalling pathway of the EDA in the killifish species. These data demonstrate a powerful genetic approach using isogenic self-fertilising mangrove killifish as a tool for identifying mutants and their mutations, and revealed the crucial role of edaradd for the first time in the fish fin development.
Experimental study of different oxides in B2O3–ZnO–BaO glass system for gamma-ray shielding
Authors: Elsafi Mohamed , Sayyed M. I. , Hanafy Taha A. 
Published: January 2025

Abstract
Glass system of 45B2O3–20ZnO–30BaO–5X, (where X represents CaO, MgO, Al2O3, TiO2, CuO and Fe2O3) in mole percentage was investigated for gamma ray radiation shielding experimentally. Six glass composites were fabricated and the density was measured experimentally and the BZBCa glass sample has the least density with a value of 3.932 g cm−3 and this is due to the presence of CaO in it, and the sample BZBFe has the highest density with a value of 4.031 g cm−3. Through comparing the linear attenuation coefficient (LAC) data (experimental and Phy-X) for the BZBX glass samples, the LAC values for glass samples obtained experimentally and using Phy-X are in a very close range. All the glass samples have the greatest LAC values at 0.0595 MeV, the lowest energy value. Sample BZBCu has a LAC value of 16.203 1/cm, which is also the highest LAC value among all the studied glasses, this is as a result of the high density of this glass and due to the high atomic number of Cu. The glasses’ transmission factor (TF) at 1 cm thickness against energy was determined. The TF values of all the glasses were almost zero. The TF values increased significantly for all the glasses when the energy was increased to 0.662 MeV, and for sample BZBCa its TF value increases 74.08%, which was the highest TF value increase. The half-value layer and other shielding parameters have been determined experimentally.
Evaluation of hesperidin as a potential larvicide against Culex pipiens with computational prediction of its mode of action via molecular docking
Authors: Haikal Abdullah , Kamal Mahmoud , Hosni Eslam M. , Amen Yhiya 
Published: January 2025

Abstract
Hesperidin, a natural flavanone glycoside predominantly found in citrus fruits, has gained attention for its wide-ranging biological activities, including potential insecticidal properties. Culex pipiens, commonly known as the northern house mosquito, is a major vector of several human pathogens, such as the West Nile virus and filariasis, making it a key target in the fight against vector-borne diseases. In this study, we evaluated the larvicidal activity of Hesperidin against Culex pipiens larvae, assessing its potential as an alternative to chemical insecticides. Hesperidin demonstrated potent larvicidal effects, with a lethal concentration 50 (LC50) of 570.3 ± 0.04 µg/mL, outperforming the conventional insecticide Chlorpyrifos 588.3 ± 0.28 µg/mL in efficacy. Molecular docking simulations revealed a strong binding affinity between Hesperidin and crucial neuroreceptors in Culex pipiens, particularly acetylcholinesterase (AChE), a key enzyme involved in nerve signal transmission. The interaction between Hesperidin’s hydroxyl groups and the AChE enzyme’s active site suggests that AChE inhibition is the primary mechanism driving Hesperidin’s insecticidal action. These findings position Hesperidin as a promising, environmentally friendly alternative to synthetic insecticides. However, further research is needed to assess its toxicity to non-target organisms and optimize its formulation for broader application in mosquito control.
Impact of 17-alpha ethinyl estradiol (EE2) and diethyl phthalate (DEP) exposure on microRNAs expression and their target genes in differentiated SH-SY5Y cells
Authors: Graziosi Agnese , Corrieri Camilla , Sita Giulia , Ghelli Luca , Angelini Sabrina , di Villa Bianca Roberta d’Emmanuele , Mitidieri Emma , Sorrentino Raffaella , Hrelia Patrizia , Morroni Fabiana 
Published: January 2025

Abstract
Environmental endocrine disruptor chemicals (EDCs) have raised significant concerns due to their potential adverse effects on human health, particularly on the central nervous system (CNS). This study provides a comparative analysis of the effects of 17-alpha ethinyl estradiol (EE2) and diethyl phthalate (DEP) on neuronal cell proliferation and neurotoxicity. Using differentiated SH-SY5Y human neuronal cells, we evaluated cell viability, microRNA (miRNA) regulation, and RNA expression following exposure to subtoxic concentrations of EE2 and DEP. Our results show that both EDCs downregulated specific miRNAs—miR-18b-5p, miR-200a-3p, and miR-653-5p—affecting key processes such as cell proliferation, survival, and apoptosis. Gene expression analysis revealed the upregulation of EGFR, IGF1R, BTG2, and SH3BP4, implicating these miRNAs in the regulation of the Ras and PI3K/Akt/mTOR pathways. Our findings highlight distinct cellular responses: DEP disrupts PTEN activity, while EE2 enhances phosphorylation within the PI3K/Akt/mTOR pathway, promoting pro-survival and anti-apoptotic signals. This study emphasizes the urgent need for regulatory measures to mitigate the neurotoxic effects of EDCs and offers valuable insights into their molecular impacts on brain health.
Engineering of acyl ligase domain in non-ribosomal peptide synthetases to change fatty acid moieties of lipopeptides
Authors: Aoki Rina , Kumagawa Eri , Kamata Kazuaki , Ago Hideo , Sakai Naoki , Hasunuma Tomohisa , Taoka Naoaki , Ohta Yukari , Kobayashi Shingo 
Published: January 2025

Abstract
Cyclic lipopeptides (CLPs) produced by the genus Bacillus are amphiphiles composed of hydrophilic amino acid and hydrophobic fatty acid moieties and are biosynthesised by non-ribosomal peptide synthetases (NRPSs). CLPs are produced as a mixture of homologues with different fatty acid moieties, whose length affects CLP activity. Iturin family lipopeptides are a family of CLPs comprising cyclic heptapeptides and β-amino fatty acids and have antimicrobial activity. There is little research on how the length of the fatty acid moiety of iturin family lipopeptides is determined. Here, we demonstrated that the acyl ligase (AL) domain determines the length of the fatty acid moiety in vivo. In addition, enzyme assays revealed how mutations in the substrate-binding pocket of the AL domain affected substrate specificity in vitro. Our findings have implications for the design of fatty acyl moieties for CLP synthesis using NRPS.