bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective hydrodeoxygenation of α, β-unsaturated carbonyl compounds to alkenes
Authors: Wang Tianjiao , Xin Yu , Chen Bingfeng , Zhang Bin , Luan Sen , Dong Minghua , Wu Yuxuan , Cheng Xiaomeng , Liu Ye , Liu Huizhen , Han Buxing 
Published: March 2024

AbstractAchieving selective hydrodeoxygenation of α, β-unsaturated carbonyl groups to alkenes poses a substantial challenge due to the presence of multiple functional groups. In this study, we develop a ZnNC-X catalyst (X represents the calcination temperature) that incorporates both Lewis acidic-basic sites and Zn-Nx sites to address this challenge. Among the catalyst variants, ZnNC-900 catalyst exhibits impressive selectivity for alkenes in the hydrodeoxygenation of α, β-unsaturated carbonyl compounds, achieving up to 94.8% selectivity. Through comprehensive mechanism investigations and catalyst characterization, we identify the Lewis acidic-basic sites as responsible for the selective hydrogenation of C=O bonds, while the Zn-Nx sites facilitate the subsequent selective hydrodeoxygenation step. Furthermore, ZnNC-900 catalyst displays broad applicability across a diverse range of unsaturated carbonyl compounds. These findings not only offer valuable insights into the design of effective catalysts for controlling alkene selectivity but also extend the scope of sustainable transformations in synthetic chemistry.
Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes
Authors: Feng Huijuan , Lu Xiang-Jun , Maji Suvrajit , Liu Linxi , Ustianenko Dmytro , Rudnick Noam D. , Zhang Chaolin 
Published: March 2024

AbstractUV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.
GWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle
Authors: Tang Lijing , Swedlund Benjamin , Dupont Sébastien , Harland Chad , Costa Monteiro Moreira Gabriel , Durkin Keith , Artesi Maria , Mullaart Eric , Sartelet Arnaud , Karim Latifa , Coppieters Wouter , Georges Michel , Charlier Carole 
Published: March 2024

AbstractFive to ten percent of mammalian genomes is occupied by multiple clades of endogenous retroviruses (ERVs), that may count thousands of members. New ERV clades arise by retroviral infection of the germline followed by expansion by reinfection and/or retrotransposition. ERV mobilization is a source of deleterious variation, driving the emergence of ERV silencing mechanisms, leaving “DNA fossils”. Here we show that the ERVK[2-1-LTR] clade is still active in the bovine and a source of disease-causing alleles. We develop a method to measure the rate of ERVK[2-1-LTR] mobilization, finding an average of 1 per ~150 sperm cells, with >10-fold difference between animals. We perform a genome-wide association study and identify eight loci affecting ERVK[2-1-LTR] mobilization. We provide evidence that polymorphic ERVK[2-1-LTR] elements in four of these loci cause the association. We generate a catalogue of full length ERVK[2-1-LTR] elements, and show that it comprises 15% of C-type autonomous elements, and 85% of D-type non-autonomous elements lacking functional genes. We show that >25% of the variance of mobilization rate is determined by the number of C-type elements, yet that de novo insertions are dominated by D-type elements. We propose that D-type elements act as parasite-of-parasite gene drives that may contribute to the observed demise of ERV elements.
TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells
Authors: Xu Meng , Senanayaka Dulmi , Zhao Rongwei , Chigumira Tafadzwa , Tripathi Astha , Tones Jason , Lackner Rachel M. , Wondisford Anne R. , Moneysmith Laurel N. , Hirschi Alexander , Craig Sara , Alishiri Sahar , O’Sullivan Roderick J. , Chenoweth David M. , Reiter Nicholas J. , Zhang Huaiying 
Published: March 2024

AbstractThe telomere repeat-containing RNA (TERRA) forms R-loops to promote homology-directed DNA synthesis in the alternative lengthening of telomere (ALT) pathway. Here we report that TERRA contributes to ALT via interacting with the lysine-specific demethylase 1A (LSD1 or KDM1A). We show that LSD1 localizes to ALT telomeres in a TERRA dependent manner and LSD1 function in ALT is largely independent of its demethylase activity. Instead, LSD1 promotes TERRA recruitment to ALT telomeres via RNA binding. In addition, LSD1 and TERRA undergo phase separation, driven by interactions between the RNA binding properties of LSD1 and the G-quadruplex structure of TERRA. Importantly, the formation of TERRA-LSD1 condensates enriches the R-loop stimulating protein Rad51AP1 and increases TERRA-containing R-loops at telomeres. Our findings suggest that LSD1-TERRA phase separation enhances the function of R-loop regulatory molecules for ALT telomere maintenance, providing a mechanism for how the biophysical properties of histone modification enzyme-RNA interactions impact chromatin function.
Room-temperature strong coupling in a single-photon emitter-metasurface system
Authors: Do T. Thu Ha , Nonahal Milad , Li Chi , Valuckas Vytautas , Tan Hark Hoe , Kuznetsov Arseniy I. , Nguyen Hai Son , Aharonovich Igor , Ha Son Tung 
Published: March 2024

AbstractSolid state single-photon sources with high brightness and long coherence time are promising qubit candidates for modern quantum technology. To prevent decoherence processes and preserve the integrity of the qubits, decoupling the emitters from their surrounding environment is essential. To this end, interfacing single photon emitters (SPEs) with high-finesse cavities is required, especially in the strong coupling regime, when the interaction between emitters can be mediated by cavity fields. However, achieving strong coupling at elevated temperatures is challenging due to competing incoherent processes. Here, we address this long-standing problem by using a quantum system, which comprises a class of SPEs in hexagonal boron nitride and a dielectric cavity based on bound states in the continuum (BIC). We experimentally demonstrate, at room temperature, strong coupling of the system with a large Rabi splitting of ~4 meV thanks to the combination of the narrow linewidth and large oscillator strength of the emitters and the efficient photon trapping of the BIC cavity. Our findings unveil opportunities to advance the fundamental understanding of quantum dynamical system in strong coupling regime and to realise scalable quantum devices capable of operating at room temperature.
Structural characterization of the oligomerization of full-length Hantaan virus polymerase into symmetric dimers and hexamers
Authors: Durieux Trouilleton Quentin , Housset Dominique , Tarillon Paco , Arragain Benoît , Malet Hélène 
Published: March 2024

AbstractHantaan virus is a dangerous human pathogen whose segmented negative-stranded RNA genome is replicated and transcribed by a virally-encoded multi-functional polymerase. Here we describe the complete cryo-electron microscopy structure of Hantaan virus polymerase in several oligomeric forms. Apo polymerase protomers can adopt two drastically different conformations, which assemble into two distinct symmetric homodimers, that can themselves gather to form hexamers. Polymerase dimerization induces the stabilization of most polymerase domains, including the C-terminal domain that contributes the most to dimer’s interface, along with a lariat region that participates to the polymerase steadying. Binding to viral RNA induces significant conformational changes resulting in symmetric oligomer disruption and polymerase activation, suggesting the possible involvement of apo multimers as protecting systems that would stabilize the otherwise flexible C-terminal domains. Overall, these results provide insights into the multimerization capability of Hantavirus polymerase and may help to define antiviral compounds to counteract these life-threatening viruses.
An isotropic zero thermal expansion alloy with super-high toughness
Authors: Yu Chengyi , Lin Kun , Zhang Qinghua , Zhu Huihui , An Ke , Chen Yan , Yu Dunji , Li Tianyi , Fu Xiaoqian , Yu Qian , You Li , Kuang Xiaojun , Cao Yili , Li Qiang , Deng Jinxia , Xing Xianran 
Published: March 2024

AbstractZero thermal expansion (ZTE) alloys with high mechanical response are crucial for their practical usage. Yet, unifying the ZTE behavior and mechanical response in one material is a grand obstacle, especially in multicomponent ZTE alloys. Herein, we report a near isotropic zero thermal expansion (αl = 1.10 × 10−6 K−1, 260–310 K) in the natural heterogeneous LaFe54Co3.5Si3.35 alloy, which exhibits a super-high toughness of 277.8 ± 14.7 J cm−3. Chemical partition, in the dual-phase structure, assumes the role of not only modulating thermal expansion through magnetic interaction but also enhancing mechanical properties via interface bonding. The comprehensive analysis reveals that the hierarchically synergistic enhancement among lattice, phase interface, and heterogeneous structure is significant for strong toughness. Our findings pave the way to tailor thermal expansion and obtain prominent mechanical properties in multicomponent alloys, which is essential to ultra-stable functional materials.
Dendritic cell-targeted therapy expands CD8 T cell responses to bona-fide neoantigens in lung tumors
Authors: López Lucía , Morosi Luciano Gastón , La Terza Federica , Bourdely Pierre , Rospo Giuseppe , Amadio Roberto , Piperno Giulia Maria , Russo Valentina , Volponi Camilla , Vodret Simone , Joshi Sonal , Giannese Francesca , Lazarevic Dejan , Germano Giovanni , Stoitzner Patrizia , Bardelli Alberto , Dalod Marc , Pace Luigia , Caronni Nicoletta , Guermonprez Pierre , Benvenuti Federica 
Published: March 2024

AbstractCross-presentation by type 1 DCs (cDC1) is critical to induce and sustain antitumoral CD8 T cell responses to model antigens, in various tumor settings. However, the impact of cross-presenting cDC1 and the potential of DC-based therapies in tumors carrying varied levels of bona-fide neoantigens (neoAgs) remain unclear. Here we develop a hypermutated model of non-small cell lung cancer in female mice, encoding genuine MHC-I neoepitopes to study neoAgs-specific CD8 T cell responses in spontaneous settings and upon Flt3L + αCD40 (DC-therapy). We find that cDC1 are required to generate broad CD8 responses against a range of diverse neoAgs. DC-therapy promotes immunogenicity of weaker neoAgs and strongly inhibits the growth of high tumor-mutational burden (TMB) tumors. In contrast, low TMB tumors respond poorly to DC-therapy, generating mild CD8 T cell responses that are not sufficient to block progression. scRNA transcriptional analysis, immune profiling and functional assays unveil the changes induced by DC-therapy in lung tissues, which comprise accumulation of cDC1 with increased immunostimulatory properties and less exhausted effector CD8 T cells. We conclude that boosting cDC1 activity is critical to broaden the diversity of anti-tumoral CD8 T cell responses and to leverage neoAgs content for therapeutic advantage.
MINSTED tracking of single biomolecules
Authors: Scheiderer Lukas , von der Emde Henrik , Hesselink Mira , Weber Michael , Hell Stefan W. 
Published: March 2024

AbstractHere we show that MINSTED localization, a method whereby the position of a fluorophore is identified with precisely controlled beams of a STED microscope, tracks fluorophores and hence labeled biomolecules with nanometer/millisecond spatiotemporal precision. By updating the position for each detected photon, MINSTED recognizes fluorophore steps of 16 nm within <250 μs using about 13 photons. The power of MINSTED tracking is demonstrated by resolving the stepping of the motor protein kinesin-1 walking on microtubules and switching protofilaments.
Super-resolution deep neural network (SRDNN) based multi-image steganography for highly secured lossless image transmission
Authors: Priya S. , Abirami S. P. , Arunkumar B. , Mishachandar B. 
Published: March 2024

AbstractInformation exchange and communication through the Internet are one of the most crucial aspects of today’s information technology world. The security of information transmitted online has grown to be a critical concern, particularly in the transfer of medical data. To overcome this, the data must be delivered securely without being altered or lost. This can be possibly done by combining the principles of cryptography and steganography. In the recent past, steganography is used with simpler methods like the least significant bit manipulation technique, in order to encode a lower-resolution image into a higher-resolution image. Here, we attempt to use deep neural networks to combine many two-dimensional colour images of the same resolution into a single cover image with the same resolution. In this technique, many secret images are concealed inside a single cover image using deep neural networks. The embedded cover image is then encrypted using a 3D chaotic map for diffusion and elliptic curve cryptography (ECC) for confusion to increase security.Supporting the fact that neural networks experience losses, the proposed system recovers up to 93% of the hidden image concealed in the original image. As the secret image features are identified and combined along with the cover image, the time complexity involved in the security process is minimized by 78% compared to securing the original data.
Voltage-controlled two-dimensional Fresnel diffraction pattern in quantum dot molecules
Authors: Mehrabzadeh Hamed , Khoshdel Hamid , Mahmoudi Mohammad , Amini Sabegh Zahra , Rasouli Saifollah 
Published: March 2024

AbstractThis study explores the influence of inter-dot tunneling effects within a quantum dot molecule on the Fresnel diffraction phenomenon. Our findings indicate that the Fresnel diffraction of the output probe Gaussian field can be manipulated by adjusting the inter-dot tunneling parameter’s strength and the characteristics of the coupling field. The inter-dot tunneling effect establishes a closed-loop system, setting conditions for the interference of the applied fields. We specifically examine a Laguerre–Gaussian (LG) coupling field, investigating how its properties-such as strength, value, and sign of the orbital angular momentum (OAM)-impact the Fresnel diffraction of the output probe field. Increasing the inter-dot tunneling parameter and the coupling LG field’s strength allows for control over the spatial distribution of the Fresnel diffraction pattern. Notably, the inter-dot tunneling parameter can disturb the symmetry of the diffraction patterns. Additionally, considering a negative OAM for the coupling LG field transforms the diffraction pattern into its inverse shape. This suggests that, in the presence of the inter-dot tunneling effect, the Fresnel diffraction pattern is contingent on the direction of rotation of the helical phase front of the coupling LG field. Our results offer insights into quantum control of Fresnel diffraction patterns and the identification of OAM in LG beams, presenting potential applications in quantum technologies.
Analyzing the effects of physical activity levels on aggressive behavior in college students using a chain-mediated model
Authors: Yu Haohan , Ma Qiaochu , Sun Yao , Jiang Shan , Hu Songhan , Wang Xin 
Published: March 2024

AbstractThis study aims to examine the mediating role of self-efficacy (SE) and self-control (SC) in the relationship between physical activity (PA) and aggressive behaviors (AB) among college students. It provides a basis for the prevention and control of AB among college students. This study employed a survey research methodology, including the PA Level Scale, the General Self-efficacy Scale, the Self-control Scale, and the Chinese Aggressive Behaviors Scale on 950 college students. The chain mediating effect test and Bootstrap analysis were applied. The results were as follows: (1) There was a main effect of PA on SE, SC, and AB as well as all sub-indicators (physical aggression, verbal aggression, anger, hostility, self-directed aggression), i.e., PA had a direct effect on the control of all three; (2) PA level was significantly negatively correlated with AB and significantly positively correlated with SE and SC. That is, the higher the level of PA, the better the SE and SC, and the lower the probability of AB; (3) The three pathways had mediating effects: PA → SE → AB, PA → SC → AB, PA → SE → SC → AB, with effect sizes of 8.78%, 28.63%, and 19.08%, respectively. It is concluded that regular PA is a potent method for decreasing aggressive behavior and psychological issues in university students while additionally promoting self-efficacy and self-control. Increasing the intensity of PA may enhance the effectiveness of these chain benefits.
The analysis on groundwater storage variations from GRACE/GRACE-FO in recent 20 years driven by influencing factors and prediction in Shandong Province, China
Authors: Li Wanqiu , Bao Lifeng , Yao Guobiao , Wang Fengwei , Guo Qiuying , Zhu Jie , Zhu Jinjie , Wang Zhiwei , Bi Jingxue , Zhu Chengcheng , Zhong Yulong , Lu Shanbo 
Published: March 2024

AbstractMonitoring and predicting the regional groundwater storage (GWS) fluctuation is an essential support for effectively managing water resources. Therefore, taking Shandong Province as an example, the data from Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow-On (GRACE-FO) is used to invert GWS fluctuation from January 2003 to December 2022 together with Watergap Global Hydrological Model (WGHM), in-situ groundwater volume and level data. The spatio-temporal characteristics are decomposed using Independent Components Analysis (ICA), and the impact factors, such as precipitation and human activities, which are also analyzed. To predict the short-time changes of GWS, the Support Vector Machines (SVM) is adopted together with three commonly used methods Long Short-Term Memory (LSTM), Singular Spectrum Analysis (SSA), Auto-Regressive Moving Average Model (ARMA), as the comparison. The results show that: (1) The loss intensity of western GWS is significantly greater than those in coastal areas. From 2003 to 2006, GWS increased sharply; during 2007 to 2014, there exists a loss rate − 5.80 ± 2.28 mm/a of GWS; the linear trend of GWS change is − 5.39 ± 3.65 mm/a from 2015 to 2022, may be mainly due to the effect of South-to-North Water Diversion Project. The correlation coefficient between GRACE and WGHM is 0.67, which is consistent with in-situ groundwater volume and level. (2) The GWS has higher positive correlation with monthly Global Precipitation Climatology Project (GPCP) considering time delay after moving average, which has the similar energy spectrum depending on Continuous Wavelet Transform (CWT) method. In addition, the influencing facotrs on annual GWS fluctuation are analyzed, the correlation coefficient between GWS and in-situ data including the consumption of groundwater mining, farmland irrigation is 0.80, 0.71, respectively. (3) For the GWS prediction, SVM method is adopted to analyze, three training samples with 180, 204 and 228 months are established with the goodness-of-fit all higher than 0.97. The correlation coefficients are 0.56, 0.75, 0.68; RMSE is 5.26, 4.42, 5.65 mm; NSE is 0.28, 0.43, 0.36, respectively. The performance of SVM model is better than the other methods for the short-term prediction.
Machine learning developed a CD8+ exhausted T cells signature for predicting prognosis, immune infiltration and drug sensitivity in ovarian cancer
Authors: Chen Rujun , Zheng Yicai , Fei Chen , Ye Jun , Fei He 
Published: March 2024

AbstractCD8+exhausted T cells (CD8+Tex) played a vital role in the progression and therapeutic response of cancer. However, few studies have fully clarified the characters of CD8+Texrelated genes in ovarian cancer (OC). The CD8+Texrelated prognostic signature (TRPS) was constructed with integrative machine learning procedure including 10 methods using TCGA, GSE14764, GSE26193, GSE26712, GSE63885 and GSE140082 dataset. Several immunotherapy benefits indicators, including Tumor Immune Dysfunction and Exclusion (TIDE) score, immunophenoscore (IPS), TMB score and tumor escape score, were used to explore performance of TRPS in predicting immunotherapy benefits of OC. The TRPS constructed by Enet (alpha = 0.3) method acted as an independent risk factor for OC and showed stable and powerful performance in predicting clinical outcome of patients. The C-index of the TRPS was higher than that of tumor grade, clinical stage, and many developed signatures. Low TRPS score indicated a higher level of CD8+T cell, B cell, macrophage M1, and NK cells, representing a relative immunoactivated ecosystem in OC. OC patients with low risk score had a higher PD1&CTLA4 immunophenoscore, higher TMB score, lower TIDE score and lower tumor escape score, suggesting a better immunotherapy response. Moreover, higher TRPS score indicated a higher score of cancer-related hallmarks, including angiogenesis, EMT, hypoxia, glycolysis, and notch signaling. Vitro experiment showed that ARL6IP5 was downregulated in OC tissues and inhibited tumor cell proliferation. The current study constructed a novel TRPS for OC, which could serve as an indicator for predicting the prognosis, immune infiltration and immunotherapy benefits for OC patients.
Research on dynamic characteristics of cutter breaking frozen soil and optimal drum rotation speed of the new shaft tunneling machine
Authors: Chen Xin-ming , Yang Zhi , Jiao Hua-zhe , Zhang Jiang-ling , Wang Jie , Sun Jin-yu 
Published: March 2024

AbstractTo improve the efficiency of frozen soil excavation, the new shaft tunneling machine was developed. The new shaft tunneling machine exerts pressure on the frozen soil through the cutter under the joint action of its own gravity, the drum rotational force and the inertia force, and the frozen soil is damaged. By unique way of breaking frozen soil to improve the efficiency of frozen soil excavation, the drum rotation speed is one of the factors affecting the performance of frozen soil excavation. This article applies SolidWorks software to establish the model of cutter breaking frozen soil, takes advantage of Hyper Mesh finite element software coupled with LS-DYNA solver to acquire the regular pattern of change in the force change, frozen soil stress–strain and specific energy of cutter crushing frozen soil, etc., which analyzes the destruction of frozen soil when the drum of the new shaft tunneling machine is rotating at the speed of 25–40 rpm. Combine with field test to investigate the mechanism of cutter breaking frozen soil under the optimal drum rotation speed. The investigation results demonstrate that: when frozen soil's self-bearing capacity is lower than the force of cutter, it breaks up and detaches from the soil body, and frozen soil undergoes tensile, compressive and shear damages. For this research, it is instructive for practical engineering.