bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST
Authors: Zhang Yufan , Xu Zhonghe , Xiao Yu , Jiang Haodong , Zuo Xiaobing , Li Xing , Fang Xianyang 
Published: May 2024

AbstractThe fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric “A”-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore–quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST–tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.
Active droplets through enzyme-free, dynamic phosphorylation
Authors: Poprawa Simone M. , Stasi Michele , Kriebisch Brigitte A. K. , Wenisch Monika , Sastre Judit , Boekhoven Job 
Published: May 2024

AbstractLife continuously transduces energy to perform critical functions using energy stored in reactive molecules like ATP or NADH. ATP dynamically phosphorylates active sites on proteins and thereby regulates their function. Inspired by such machinery, regulating supramolecular functions using energy stored in reactive molecules has gained traction. Enzyme-free, synthetic systems that use dynamic phosphorylation to regulate supramolecular processes have not yet been reported, to our knowledge. Here, we show an enzyme-free reaction cycle that consumes the phosphorylating agent monoamidophosphate by transiently phosphorylating histidine and histidine-containing peptides. The phosphorylated species are labile and deactivate through hydrolysis. The cycle exhibits versatility and tunability, allowing for the dynamic phosphorylation of multiple precursors with a tunable half-life. Notably, we show the resulting phosphorylated products can regulate the peptide’s phase separation, leading to active droplets that require the continuous conversion of fuel to sustain. The reaction cycle will be valuable as a model for biological phosphorylation but can also offer insights into protocell formation.
Disentangling the effects of structure and lone-pair electrons in the lattice dynamics of halide perovskites
Authors: Caicedo-Dávila Sebastián , Cohen Adi , Motti Silvia G. , Isobe Masahiko , McCall Kyle M. , Grumet Manuel , Kovalenko Maksym V. , Yaffe Omer , Herz Laura M. , Fabini Douglas H. , Egger David A. 
Published: May 2024

AbstractHalide perovskites show great optoelectronic performance, but their favorable properties are paired with unusually strong anharmonicity. It was proposed that this combination derives from the ns2 electron configuration of octahedral cations and associated pseudo-Jahn–Teller effect. We show that such cations are not a prerequisite for the strong anharmonicity and low-energy lattice dynamics encountered in these materials. We combine X-ray diffraction, infrared and Raman spectroscopies, and molecular dynamics to contrast the lattice dynamics of CsSrBr3 with those of CsPbBr3, two compounds that are structurally similar but with the former lacking ns2 cations with the propensity to form electron lone pairs. We exploit low-frequency diffusive Raman scattering, nominally symmetry-forbidden in the cubic phase, as a fingerprint of anharmonicity and reveal that low-frequency tilting occurs irrespective of octahedral cation electron configuration. This highlights the role of structure in perovskite lattice dynamics, providing design rules for the emerging class of soft perovskite semiconductors.
Long-term relapse-free survival enabled by integrating targeted antibacteria in antitumor treatment
Authors: Wang Yuanlin , Han Yaqian , Yang Chenhui , Bai Tiancheng , Zhang Chenggang , Wang Zhaotong , Sun Ye , Hu Ying , Besenbacher Flemming , Chen Chunying , Yu Miao 
Published: May 2024

AbstractThe role of tumor-resident intracellular microbiota (TRIM) in carcinogenesis has sparked enormous interest. Nevertheless, the impact of TRIM-targeted antibacteria on tumor inhibition and immune regulation in the tumor microenvironment (TME) remains unexplored. Herein, we report long-term relapse-free survival by coordinating antibacteria with antitumor treatment, addressing the aggravated immunosuppression and tumor overgrowth induced by TRIM using breast and prostate cancer models. Combining Ag+ release with a Fenton-like reaction and photothermal conversion, simultaneous bacteria killing and multimodal antitumor therapy are enabled by a single agent. Free of immune-stimulating drugs, the agent restores antitumor immune surveillance and activates immunological responses. Secondary inoculation and distal tumor analysis confirm lasting immunological memory and systemic immune responses. A relapse-free survival of >700 days is achieved. This work unravels the crucial role of TRIM-targeted antibacteria in tumor inhibition and unlocks an unconventional route for immune regulation in TME and a complete cure for cancer.
Structural mechanism of bacteriophage lambda tail’s interaction with the bacterial receptor
Authors: Ge Xiaofei , Wang Jiawei 
Published: May 2024

AbstractBacteriophage infection, a pivotal process in microbiology, initiates with the phage’s tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. Although comprehensive studies on the interaction between bacteriophage lambda and its outer membrane receptor, LamB, have provided rich information about the system’s biochemical properties, the precise molecular mechanism remains undetermined. This study revealed the high-resolution cryo-electron microscopy (cryo-EM) structures of the bacteriophage lambda tail complexed with its irreversible Shigella sonnei 3070 LamB receptor and the closed central tail fiber. These structures reveal the complex processes that trigger infection and demonstrate a substantial conformational change in the phage lambda tail tip upon LamB binding. Providing detailed structures of bacteriophage lambda infection initiation, this study contributes to the expanding knowledge of lambda-bacterial interaction, which holds significance in the fields of microbiology and therapeutic development.
Short-time high-temperature oxidation behavior of nanocrystalline Ta coating at 850 °C
Authors: Niu Yunsong , Xing Lingling , Zhu Shenglong , Huang Jinfeng , Chen Minghui , Wang Fuhui , Chen Qiang 
Published: May 2024

AbstractShort-time oxidation behavior of nanocrystalline Ta coating is studied at 850 °C in comparison with that of the Ta sheet. Owing to the large PBR value and insufficient expansion space, the oxide scale on Ta sheet is dramatically cracked, delaminated and pulverized, resulting in rapid deterioration. For nanocrystalline Ta coatings with columnar structures and quantitative grain boundaries, a rapid oxygen diffusion rate causes no initial Ta2O5 to form. The gap between columns provides spaces for bulk expansion, resulting in few opening cracks and delamination. Ta oxidation experiences a crystallization course from amorphous Ta oxide, leading to in situ temperature surging and thus pulverization.
Synthesis and utilization of titanium dioxide nano particle (TiO2NPs) for photocatalytic degradation of organics
Authors: Kholief M. G. , Hesham Abd El-Latif , Hashem F. S. , Mohamed F. M. 
Published: May 2024

AbstractA green technique that emerged as a promise in the degradation of numerous organic contaminants is photocatalysis. The aim of this study concerns photocatalytic degradation of organic using titanium dioxide nano particles (TiO2 NPs) which syntheses from ilmenite by different leaching methods using different ingredients such as HCl, HNO3 and Aqua Regia. The affecting factors such as rate of addition, reaction time, ilmenite grain size, acid to ilmenite ratio and reaction temperature were conducted. Comprehensive physicochemical characterization of Ilmenite and TiO2 NPs were conducted using different analytical techniques such as XRD, XRF, SEM, TEM and FTIR. Photocatalytic degradation of organics is confirmed by studies of affecting factors on the effectiveness of TiO2 NPs such as dose, agitation forces, light intensity, initial concentration, pH, time, and temperature. The removal percentages of TSS, COD, BOD and TN of organics were explored. From the results the maximum removal percentage of TSS were 97.3 and 96.9% before and after secondary treatment conducted using ferric chloride (FC). The maximum removal percentage of TKN, BOD, and COD before secondary treatment were conducted using mixture of TiO2 NPs, FC, and chitosan, which reached 44.2, 44 and 46.3%, respectively. The maximum removal percentage of TKN, BOD, and COD after secondary treatment were conducted using mixture of TiO2 NPs, FC, and chitosan, which reached 94.9, 99.7 and 99.6%, respectively. Overall, the results derived from this investigation suggest that the TiO2 NPs/UV holds significant advanced treatment of sewage water, making it a viable choice for water reuse applications.
A sustainable green-approach for biofabrication of chitosan nanoparticles, optimization, characterization, its antifungal activity against phytopathogenic Fusarium culmorum and antitumor activity
Authors: El-Naggar Noura El-Ahmady , Shiha Alaa M. , Mahrous Hoda , Mohammed A. B. Abeer 
Published: May 2024

AbstractChitosan is a natural non-toxic, biocompatible, biodegradable, and mucoadhesive polymer. It also has a broad spectrum of applications such as agriculture, medical fields, cosmetics and food industries. In this investigation, chitosan nanoparticles were produced by an aqueous extract of Cympopogon citratus leaves as a reducing agent. According to the SEM and TEM micrographs, CNPs had a spherical shape, and size ranging from 8.08 to 12.01 nm. CNPs have a positively charged surface with a Zeta potential of + 26 mV. The crystalline feature of CNPs is determined by X-ray diffraction. There are many functional groups, including C꞊C, CH2-OH, C–O, C-S, N–H, CN, CH and OH were detected by FTIR analysis. As shown by the thermogravimetric study, CNPs have a high thermal stability. For the optimization of the green synthesis of CNPs, a Face centered central composite design (FCCCD) with 30 trials was used. The maximum yield of CNPs (13.99 mg CNPs/mL) was produced with chitosan concentration 1.5%, pH 4.5 at 40 °C, and incubation period of 30 min. The antifungal activity of CNPs was evaluated against phytopathogenic fungus; Fusarium culmorum. A 100% rate of mycelial growth inhibition was gained by the application of 20 mg CNPs/mL. The antitumor activity of the green synthesized CNPs was examined using 6 different cell lines, the viability of the cells reduced when the concentration of green synthesized CNPs increased, the IC50 dose of the green synthesized CNPs on the examined cell lines HePG-2, MCF-7, HCT-116, PC-3, Hela and WI-38 was 36.25 ± 2.3, 31.21 ± 2.2, 67.45 ± 3.5, 56.30 ± 3.3, 44.62 ± 2.6 and 74.90 ± 3.8; respectively.
Autonomous navigation and collision prediction of port channel based on computer vision and lidar
Authors: Zhang Zhan , Yang NanWu , Yang YiJian 
Published: May 2024

AbstractThis study aims to enhance the safety and efficiency of port navigation by reducing ship collision accidents, minimizing environmental risks, and optimizing waterways to increase port throughput. Initially, a three-dimensional map of the port’s waterway, including data on water depth, rocks, and obstacles, is generated through laser radar scanning. Visual perception technology is adopted to process and identify the data for environmental awareness. Single Shot MultiBox Detector (SSD) is utilized to position ships and obstacles, while point cloud data create a comprehensive three-dimensional map. In order to improve the optimal navigation approach of the Rapidly-Exploring Random Tree (RRT), an artificial potential field method is employed. Additionally, the collision prediction model utilizes K-Means clustering to enhance the Faster R-CNN algorithm for predicting the paths of other ships and obstacles. The results indicate that the RRT enhanced by the artificial potential field method reduces the average path length (from 500 to 430 m), average time consumption (from 30 to 22 s), and maximum collision risk (from 15 to 8%). Moreover, the accuracy, recall rate, and F1 score of the K-Means + Faster R-CNN collision prediction model reach 92%, 88%, and 90%, respectively, outperforming other models. Overall, these findings underscore the substantial advantages of the proposed enhanced algorithm in autonomous navigation and collision prediction in port waterways.
Basal forebrain volume and metabolism in carriers of the Colombian mutation for autosomal dominant Alzheimer’s disease
Authors: Teipel Stefan , Grazia Alice , Dyrba Martin , Grothe Michel J. , Pomara Nunzio 
Published: May 2024

AbstractWe aimed to study atrophy and glucose metabolism of the cholinergic basal forebrain in non-demented mutation carriers for autosomal dominant Alzheimer's disease (ADAD). We determined the level of evidence for or against atrophy and impaired metabolism of the basal forebrain in 167 non-demented carriers of the Colombian PSEN1 E280A mutation and 75 age- and sex-matched non-mutation carriers of the same kindred using a Bayesian analysis framework. We analyzed baseline MRI, amyloid PET, and FDG-PET scans of the Alzheimer’s Prevention Initiative ADAD Colombia Trial. We found moderate evidence against an association of carrier status with basal forebrain volume (Bayes factor (BF10) = 0.182). We found moderate evidence against a difference of basal forebrain metabolism (BF10 = 0.167). There was only inconclusive evidence for an association between basal forebrain volume and delayed memory and attention (BF10 = 0.884 and 0.184, respectively), and between basal forebrain volume and global amyloid load (BF10 = 2.1). Our results distinguish PSEN1 E280A mutation carriers from sporadic AD cases in which cholinergic involvement of the basal forebrain is already detectable in the preclinical and prodromal stages. This indicates an important difference between ADAD and sporadic AD in terms of pathogenesis and potential treatment targets.
Dietary intake, obesity, and metabolic risk factors among children and adolescents in the SEACO-CH20 cross-sectional study
Authors: Ramadas Amutha , Rizal Hussein , Rajakumar Sutha , Mariapun Jeevitha , Yasin Mohamed Shajahan , Armstrong Miranda E. G. , Su Tin Tin 
Published: May 2024

AbstractWe investigated the association between dietary intake and metabolic risk factors in children and adolescents within a semi-rural Malaysian community. Using an interviewer-led questionnaire, we surveyed 623 participants aged 7–18 from the South East Asia Community Observatory (SEACO). Anthropometric and blood pressure data were collected from all participants, while a subset (n = 162) provided blood samples for biomarker analysis, including fasting blood glucose (FBG), total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C). Metabolic syndrome was determined using the International Diabetes Federation’s Definition of Metabolic Syndrome in Children and Adolescents. Most participants were Malay (66.8%), with a median household income of MYR1,500 and a balanced sex distribution. Cereals, processed foods, beverages, fruits, and vegetables were commonly consumed. Obesity and abdominal obesity were prevalent, affecting more than a third of participants. Adherence to dietary recommendations was generally poor (ranging from 19.9 to 58.1%) and varied across age, sex, and ethnicity. Notably, some food groups displayed unexpected associations with health markers; for instance, fruit consumption was linked to abdominal obesity in children (abdominal obesity vs. normal: 2.4 servings/day vs. 1.6 servings/day). These findings emphasise the necessity of longitudinal studies to explore the complex relationship between diet and long-term health outcomes, including cardiometabolic diseases, while acknowledging the unique challenges posed by the COVID-19 pandemic on data collection and analysis.
Radiomic profiles improve prognostication and reveal targets for therapy in cervical cancer
Authors: Halle Mari Kyllesø , Hodneland Erlend , Wagner-Larsen Kari S. , Lura Njål G. , Fasmer Kristine E. , Berg Hege F. , Stokowy Tomasz , Srivastava Aashish , Forsse David , Hoivik Erling A. , Woie Kathrine , Bertelsen Bjørn I. , Krakstad Camilla , Haldorsen Ingfrid S. 
Published: May 2024

AbstractCervical cancer (CC) is a major global health problem with 570,000 new cases and 266,000 deaths annually. Prognosis is poor for advanced stage disease, and few effective treatments exist. Preoperative diagnostic imaging is common in high-income countries and MRI measured tumor size routinely guides treatment allocation of cervical cancer patients. Recently, the role of MRI radiomics has been recognized. However, its potential to independently predict survival and treatment response requires further clarification. This retrospective cohort study demonstrates how non-invasive, preoperative, MRI radiomic profiling may improve prognostication and tailoring of treatments and follow-ups for cervical cancer patients. By unsupervised clustering based on 293 radiomic features from 132 patients, we identify three distinct clusters comprising patients with significantly different risk profiles, also when adjusting for FIGO stage and age. By linking their radiomic profiles to genomic alterations, we identify putative treatment targets for the different patient clusters (e.g., immunotherapy, CDK4/6 and YAP-TEAD inhibitors and p53 pathway targeting treatments).
The threat sensitivity scale: A brief self-report measure of dispositional sensitivity toward perceiving threats to physical harm
Authors: March David S. , Hasty Connor , Olivett Vincenzo 
Published: May 2024

AbstractThe possibility of experiencing physical harm caused by an object, animal, or person is an omnipresent risk in almost any situation. People show variability in their in the propensity to perceive the possibility of harm from any ostensibly innocuous object or situation—a so-called threat bias. Despite the important psychological and societal consequences resulting from individual differences in physical threat bias, there does not currently exist an easily administered means to capture this disposition. We therefore endeavored to create a brief reliable self-report index of threat sensitivity for use by the many fields interested in the role of threat processing. We present here a physical threat sensitivity scale (TSS) that captures the dispositional tendency to perceive the possibility of physical harm in ostensibly innocuous situations or objects. We detail the development and validation of the TSS as a reliable index of individual threat bias (Studies 1a and 1b) and provide strong convergent evidence of the relationship between TS and both relevant individual differences (Study 2) and behavioral and perceptual indicates of threat bias (Study 3 and Study 4).
Function of MYB8 in larch under PEG simulated drought stress
Authors: Zhao Qingrong , Xiong Huanhuan , Yu Hongying , Wang Chen , Zhang Sufang , Hao Junfei , Wang Junhui , Zhang Hanguo , Zhang Lei 
Published: May 2024

AbstractLarch, a prominent afforestation, and timber species in northeastern China, faces growth limitations due to drought. To further investigate the mechanism of larch’s drought resistance, we conducted full-length sequencing on embryonic callus subjected to PEG-simulated drought stress. The sequencing results revealed that the differentially expressed genes (DEGs) primarily played roles in cellular activities and cell components, with molecular functions such as binding, catalytic activity, and transport activity. Furthermore, the DEGs showed significant enrichment in pathways related to protein processing, starch and sucrose metabolism, benzose-glucuronic acid interconversion, phenylpropyl biology, flavonoid biosynthesis, as well as nitrogen metabolism and alanine, aspartic acid, and glutamic acid metabolism. Consequently, the transcription factor T_transcript_77027, which is involved in multiple pathways, was selected as a candidate gene for subsequent drought stress resistance tests. Under PEG-simulated drought stress, the LoMYB8 gene was induced and showed significantly upregulated expression compared to the control. Physiological indices demonstrated an improved drought resistance in the transgenic plants. After 48 h of PEG stress, the transcriptome sequencing results of the transiently transformed LoMYB8 plants and control plants exhibited that genes were significantly enriched in biological process, cellular component and molecular function. Function analyses indicated for the enrichment of multiple KEGG pathways, including energy synthesis, metabolic pathways, antioxidant pathways, and other relevant processes. The pathways annotated by the differential metabolites mainly encompassed signal transduction, carbohydrate metabolism, amino acid metabolism, and flavonoid metabolism.
Global intracranial arterial tortuosity is associated with intracranial atherosclerotic burden
Authors: Eun Mi-Yeon , Song Ha‑Na , Choi Jong‑Un , Cho Hwan‑Ho , Kim Hyung Jun , Chung Jong-Won , Song Tae-Jin , Jung Jin-Man , Bang Oh‑Young , Kim Gyeong‑Moon , Park Hyunjin , Liebeskind David S. , Seo Woo-Keun 
Published: May 2024

AbstractThe effect of arterial tortuosity on intracranial atherosclerosis (ICAS) is not well understood. This study aimed to evaluate the effect of global intracranial arterial tortuosity on intracranial atherosclerotic burden in patients with ischemic stroke. We included patients with acute ischemic stroke who underwent magnetic resonance angiography (MRA) and classified them into three groups according to the ICAS burden. Global tortuosity index (GTI) was defined as the standardized mean curvature of the entire intracranial arteries, measured by in-house vessel analysis software. Of the 516 patients included, 274 patients had no ICAS, 140 patients had a low ICAS burden, and 102 patients had a high ICAS burden. GTI increased with higher ICAS burden. After adjustment for age, sex, vascular risk factors, and standardized mean arterial area, GTI was independently associated with ICAS burden (adjusted odds ratio [adjusted OR] 1.33; 95% confidence interval [CI] 1.09–1.62). The degree of association increased when the arterial tortuosity was analyzed limited to the basal arteries (adjusted OR 1.48; 95% CI 1.22–1.81). We demonstrated that GTI is associated with ICAS burden in patients with ischemic stroke, suggesting a role for global arterial tortuosity in ICAS.