bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization
Authors: Gres Anna T. , Kirby Karen A. , McFadden William M. , Du Haijuan , Liu Dandan , Xu Chaoyi , Bryer Alexander J. , Perilla Juan R. , Shi Jiong , Aiken Christopher , Fu Xiaofeng , Zhang Peijun , Francis Ashwanth C. , Melikyan Gregory B. , Sarafianos Stefan G. 
Published: September 2023

AbstractHIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CANTD-CANTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45Aa α9-helices compared to WT, E45A/R132T, WTPF74, WTNup153, and WTCPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.
Previous immunity shapes immune responses to SARS-CoV-2 booster vaccination and Omicron breakthrough infection risk
Authors: Pérez-Alós Laura , Hansen Cecilie Bo , Almagro Armenteros Jose Juan , Madsen Johannes Roth , Heftdal Line Dam , Hasselbalch Rasmus Bo , Pries-Heje Mia Marie , Bayarri-Olmos Rafael , Jarlhelt Ida , Hamm Sebastian Rask , Møller Dina Leth , Sørensen Erik , Ostrowski Sisse Rye , Frikke-Schmidt Ruth , Hilsted Linda Maria , Bundgaard Henning , Nielsen Susanne Dam , Iversen Kasper Karmark , Garred Peter 
Published: September 2023

AbstractThe heterogeneity of the SARS-CoV-2 immune responses has become considerably more complex over time and diverse immune imprinting is observed in vaccinated individuals. Despite vaccination, following the emergence of the Omicron variant, some individuals appear more susceptible to primary infections and reinfections than others, underscoring the need to elucidate how immune responses are influenced by previous infections and vaccination. IgG, IgA, neutralizing antibodies and T-cell immune responses in 1,325 individuals (955 of which were infection-naive) were investigated before and after three doses of the BNT162b2 vaccine, examining their relation to breakthrough infections and immune imprinting in the context of Omicron. Our study shows that both humoral and cellular responses following vaccination were generally higher after SARS-CoV-2 infection compared to infection-naive. Notably, viral exposure before vaccination was crucial to achieving a robust IgA response. Individuals with lower IgG, IgA, and neutralizing antibody responses postvaccination had a significantly higher risk of reinfection and future Omicron infections. This was not observed for T-cell responses. A primary infection before Omicron and subsequent reinfection with Omicron dampened the humoral and cellular responses compared to a primary Omicron infection, consistent with immune imprinting. These results underscore the significant impact of hybrid immunity for immune responses in general, particularly for IgA responses even after revaccination, and the importance of robust humoral responses in preventing future infections.
Construction of double reaction zones for long-life quasi-solid aluminum-ion batteries by realizing maximum electron transfer
Authors: Yu Zhijing , Wang Wei , Zhu Yong , Song Wei-Li , Huang Zheng , Wang Zhe , Jiao Shuqiang 
Published: September 2023

AbstractAchieving high energy density and long cycling life simultaneously remains the most critical challenge for aluminum-ion batteries (AIBs), especially for high-capacity conversion-type positive electrodes suffering from shuttle effect in strongly acidic electrolytes. Herein, we develop a layered quasi-solid AIBs system with double reaction zones (DRZs, Zone 1 and Zone 2) to address such issues. Zone 1 is designed to accelerate reaction kinetics by improving wetting ability of quasi-solid electrolyte to active materials. A composite three-dimensional conductive framework (Zone 2) interwoven by gel network for ion conduction and carbon nanotube network as electronic conductor, can fix the active materials dissolved from Zone 1 to allow for continuing electrochemical reactions. Therefore, a maximum electron transfer is realized for the conversion-type mateials in DRZs, and an ultrahigh capacity (400 mAh g−1) and an ultralong cycling life (4000 cycles) are achieved. Such strategy provides a new perspective for constructing high-energy-density and long-life AIBs.
A Lassa virus mRNA vaccine confers protection but does not require neutralizing antibody in a guinea pig model of infection
Authors: Ronk Adam J. , Lloyd Nicole M. , Zhang Min , Atyeo Caroline , Perrett Hailee R. , Mire Chad E. , Hastie Kathryn M. , Sanders Rogier W. , Brouwer Philip J. M. , Saphire Erica Olmann , Ward Andrew B. , Ksiazek Thomas G. , Alvarez Moreno Juan Carlos , Thaker Harshwardhan M. , Alter Galit , Himansu Sunny , Carfi Andrea , Bukreyev Alexander 
Published: September 2023

AbstractLassa virus is a member of the Arenaviridae family, which causes human infections ranging from asymptomatic to severe hemorrhagic disease with a high case fatality rate. We have designed and generated lipid nanoparticle encapsulated, modified mRNA vaccines that encode for the wild-type Lassa virus strain Josiah glycoprotein complex or the prefusion stabilized conformation of the Lassa virus glycoprotein complex. Hartley guinea pigs were vaccinated with two 10 µg doses, 28 days apart, of either construct. Vaccination induced strong binding antibody responses, specific to the prefusion conformation of glycoprotein complex, which were significantly higher in the prefusion stabilized glycoprotein complex construct group and displayed strong Fc-mediated effects. However, Lassa virus-neutralizing antibody activity was detected in some but not all animals. Following the challenge with a lethal dose of the Lassa virus, all vaccinated animals were protected from death and severe disease. Although the definitive mechanism of protection is still unknown, and assessment of the cell-mediated immune response was not investigated in this study, these data demonstrate the promise of mRNA as a vaccine platform against the Lassa virus and that protection against Lassa virus can be achieved in the absence of virus-neutralizing antibodies.
Unexpected doping effects on phonon transport in quasi-one-dimensional van der Waals crystal TiS3 nanoribbons
Authors: Liu Chenhan , Wu Chao , Tan Xian Yi , Tao Yi , Zhang Yin , Li Deyu , Yang Juekuan , Yan Qingyu , Chen Yunfei 
Published: September 2023

AbstractDoping usually reduces lattice thermal conductivity because of enhanced phonon-impurity scattering. Here, we report unexpected doping effects on the lattice thermal conductivity of quasi-one-dimensional (quasi-1D) van der Waals (vdW) TiS3 nanoribbons. As the nanoribbon thickness reduces from ~80 to ~19 nm, the concentration of oxygen atoms has a monotonic increase along with a 7.4-fold enhancement in the thermal conductivity at room temperature. Through material characterizations and atomistic modellings, we find oxygen atoms diffuse more readily into thinner nanoribbons and more sulfur atoms are substituted. The doped oxygen atoms induce significant lattice contraction and coupling strength enhancement along the molecular chain direction while have little effect on vdW interactions, different from that doping atoms induce potential and structural distortions along all three-dimensional directions in 3D materials. With the enhancement of coupling strength, Young’s modulus is enhanced while phonon-impurity scattering strength is suppressed, significantly improving the phonon thermal transport.
SiGra: single-cell spatial elucidation through an image-augmented graph transformer
Authors: Tang Ziyang , Li Zuotian , Hou Tieying , Zhang Tonglin , Yang Baijian , Su Jing , Song Qianqian 
Published: September 2023

AbstractRecent advances in high-throughput molecular imaging have pushed spatial transcriptomics technologies to subcellular resolution, which surpasses the limitations of both single-cell RNA-seq and array-based spatial profiling. The multichannel immunohistochemistry images in such data provide rich information on the cell types, functions, and morphologies of cellular compartments. In this work, we developed a method, single-cell spatial elucidation through image-augmented Graph transformer (SiGra), to leverage such imaging information for revealing spatial domains and enhancing substantially sparse and noisy transcriptomics data. SiGra applies hybrid graph transformers over a single-cell spatial graph. SiGra outperforms state-of-the-art methods on both single-cell and spot-level spatial transcriptomics data from complex tissues. The inclusion of immunohistochemistry images improves the model performance by 37% (95% CI: 27–50%). SiGra improves the characterization of intratumor heterogeneity and intercellular communication and recovers the known microscopic anatomy. Overall, SiGra effectively integrates different spatial modality data to gain deep insights into spatial cellular ecosystems.
Single nucleus transcriptomics of ventral midbrain identifies glial activation associated with chronic opioid use disorder
Authors: Wei Julong , Lambert Tova Y. , Valada Aditi , Patel Nikhil , Walker Kellie , Lenders Jayna , Schmidt Carl J. , Iskhakova Marina , Alazizi Adnan , Mair-Meijers Henriette , Mash Deborah C. , Luca Francesca , Pique-Regi Roger , Bannon Michael J. , Akbarian Schahram 
Published: September 2023

AbstractDynamic interactions of neurons and glia in the ventral midbrain mediate reward and addiction behavior. We studied gene expression in 212,713 ventral midbrain single nuclei from 95 individuals with history of opioid misuse, and individuals without drug exposure. Chronic exposure to opioids was not associated with change in proportions of glial and neuronal subtypes, however glial transcriptomes were broadly altered, involving 9.5 − 6.2% of expressed genes within microglia, oligodendrocytes, and astrocytes. Genes associated with activation of the immune response including interferon, NFkB signaling, and cell motility pathways were upregulated, contrasting with down-regulated expression of synaptic signaling and plasticity genes in ventral midbrain non-dopaminergic neurons. Ventral midbrain transcriptomic reprogramming in the context of chronic opioid exposure included 325 genes that previous genome-wide studies had linked to risk of substance use traits in the broader population, thereby pointing to heritable risk architectures in the genomic organization of the brain’s reward circuitry.
Scalable electrosynthesis of commodity chemicals from biomass by suppressing non-Faradaic transformations
Authors: Zhou Hua , Ren Yue , Yao Bingxin , Li Zhenhua , Xu Ming , Ma Lina , Kong Xianggui , Zheng Lirong , Shao Mingfei , Duan Haohong 
Published: September 2023

AbstractElectrooxidation of biomass platforms provides a sustainable route to produce valuable oxygenates, but the practical implementation is hampered by the severe carbon loss stemming from inherent instability of substrates and/or intermediates in alkaline electrolyte, especially under high concentration. Herein, based on the understanding of non-Faradaic degradation, we develop a single-pass continuous flow reactor (SPCFR) system with high ratio of electrode-area/electrolyte-volume, short duration time of substrates in the reactor, and separate feeding of substrate and alkaline solution, thus largely suppressing non-Faradaic degradation. By constructing a nine-stacked-modules SPCFR system, we achieve electrooxidation of glucose-to-formate and 5-hydroxymethylfurfural (HMF)-to-2,5-furandicarboxylic acid (FDCA) with high single-pass conversion efficiency (SPCE; 81.8% and 95.8%, respectively) and high selectivity (formate: 76.5%, FDCA: 96.9%) at high concentrations (formate: 562.8 mM, FDCA: 556.9 mM). Furthermore, we demonstrate continuous and kilogram-scale electrosynthesis of potassium diformate (0.7 kg) from wood and soybean oil, and FDCA (1.17 kg) from HMF. This work highlights the importance of understanding and suppressing non-Faradaic degradation, providing opportunities for scalable biomass upgrading using electrochemical technology.
Vanquishing the computational cost of passive gamma emission tomography simulations leveraging physics-aware reduced order modeling
Authors: Cavallini Nicola , Ferretti Riccardo , Bostrom Gunnar , Croft Stephen , Fassi Aurora , Mercurio Giovanni , Nonneman Stefan , Favalli Andrea 
Published: September 2023

AbstractPassive Gamma Emission Tomography (PGET) has been developed by the International Atomic Energy Agency to directly image the spatial distribution of individual fuel pins in a spent nuclear fuel assembly and determine potential diversion. The analysis and interpretation of PGET measurements rely on the availability of comprehensive datasets. Experimental data are expensive and limited, so Monte Carlo simulations are used to augment them. However, Monte Carlo simulations have a high computational cost to simulate the 360 angular views of the tomography. Similar challenges pervade numerical science. With the aim to create a large dataset of PGET simulated scenarios, we addressed the computational cost of Monte Carlo simulations by developing a physics-aware reduced order modeling approach. This approach combines a small subset of the 360 angular views (limited views approach) with a computationally inexpensive proxy solution (real-time forward model) that brings the essence of the physics to obtain a real-time high-fidelity solution at all angular views but at a fraction of the computational cost. The method’s ability to reconstruct 360 views with accuracy from a limited set of angular views is demonstrated by testing its performance for different types of reactor fuel assemblies.
Investigation of composed charged particles with suspension of ternary hybrid nanoparticles in 3D-power law model computed by Galerkin algorithm
Authors: Nazir Umar , Mukdasai Kanit , Sohail Muhammad , Singh Abha , Alosaimi Mohammed Theeb , Alanazi Mashael , Tulu Ayele 
Published: September 2023

AbstractTransport of heat visualizes a vital role in many industrial developments. Current study is discussing the role of Joule heating, solar thermal radiation, heat generation/absorption, reactions (homogeneous and heterogeneous) with variable thermal conductivity on partially ionized power law material past over a three-dimensional heated stretched surface. The power law model is assumed to have the thermal characteristics of ethylene glycol material. The phenomenon of momentum and energy balance is derived in Cartesian coordinates and developed PD (partial differential)-equations. Swimming pools, solar collectors, food processing, electronic gadgets, cooling systems, magnetic field measurement, computer chips, thermal enhancement, semiconductor characterization, nuclear fusion research and other physical applications are examples of ongoing research. The principle of boundary layer simplified the governing problem. The complex coupled PD (partial differential)-equations have been converted into ordinary differential equations OD (ordinary differential)-equations by using appropriate similarity transformation. The converted boundary value problem is complex and highly nonlinear which does not have the exact solution. The approximate solution is computed numerically via finite element scheme (FES) which is coded in MAPLE 18.0 symbolic package. The convergence of the scheme is established through grid independent survey and the solution is plotted against numerous involved parameters. Thermal performance produced by $$Si{O}_{2}$$

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Hyperspectral signature-band extraction and learning: an example of sugar content prediction of Syzygium samarangense
Authors: Yan Yung-Jhe , Wong Weng-Keong , Chen Chih-Jung , Huang Chi-Cho , Chien Jen‑Tzung , Ou-Yang Mang 
Published: September 2023

AbstractThis study proposes a method to extract the signature bands from the deep learning models of multispectral data converted from the hyperspectral data. The signature bands with two deep-learning models were further used to predict the sugar content of the Syzygium samarangense. Firstly, the hyperspectral data with the bandwidths lower than 2.5 nm were converted to the spectral data with multiple bandwidths higher than 2.5 nm to simulate the multispectral data. The convolution neural network (CNN) and the feedforward neural network (FNN) used these spectral data to predict the sugar content of the Syzygium samarangense and obtained the lowest mean absolute error (MAE) of 0.400° Brix and 0.408° Brix, respectively. Secondly, the absolute mean of the integrated gradient method was used to extract multiple signature bands from the CNN and FNN models for sugariness prediction. A total of thirty sets of six signature bands were selected from the CNN and FNN models, which were trained by using the spectral data with five bandwidths in the visible (VIS), visible to near-infrared (VISNIR), and visible to short-waved infrared (VISWIR) wavelengths ranging from 400 to 700 nm, 400 to 1000 nm, and 400 to 1700 nm. Lastly, these signature-band data were used to train the CNN and FNN models for sugar content prediction. The FNN model using VISWIR signature bands with a bandwidth of ± 12.5 nm had a minimum MAE of 0.390°Brix compared to the others. The CNN model using VISWIR signature bands with a bandwidth of ± 10 nm had the lowest MAE of 0.549° Brix compared to the other CNN models. The MAEs of the models with only six spectral bands were even better than those with tens or hundreds of spectral bands. These results reveal that six signature bands have the potential to be used in a small and compact multispectral device to predict the sugar content of the Syzygium samarangense.
The measurement of true initial rates is not always absolutely necessary to estimate enzyme kinetic parameters
Authors: Frère Jean-Marie , Verlaine Olivier , Matagne André 
Published: September 2023

AbstractIn the chapters dealing with enzyme reactions, the authors of all Biochemistry textbooks and of even more specialized texts consider that the characteristic parameters (kcat and Km) must be determined under initial or steady-state rate conditions. This implies the transformation of a very limited proportion of substrate (at most 10–20%) or a continuous recording of the product or substrate concentration vs. time. Both options can present practical difficulties. Is it possible to get around these very stringent conditions? Here we show that in the most favourable cases up to 70% of the substrate can be converted resulting in systematic errors on the parameters (that can easily be taken account of) if the simple Henri-Michaelis–Menten equation is utilised. Alternatively, the integrated form of the same equation directly yields excellent estimates of the same parameters. Our observations should greatly facilitate the task of researchers who study systems in which measurements of the reaction progress are painstaking or when substrate concentrations close to the detection limit must be used. The general conclusion is that it is not always absolutely necessary to determine initial or steady-state rates to obtain reliable estimations of the enzyme kinetic parameters..
Construction practice of water conveyance tunnel among complex geotechnical conditions: a case study
Authors: Duan Kaimin , Zhang Guofeng , Sun Hui 
Published: September 2023

AbstractThe construction practice of water conveyance tunnels often encounters various complex geotechnical engineering conditions, which bring huge challenges to the design and construction of water conveyance tunnels. Based on the theory of rock elastic–plastic mechanics and finite element analysis technology, this article carried out investigations of engineering geological features, geological formations and hydrological conditions establishes a calculation model for the 3# water conveyance tunnel of the Fenhe River Diversion Project, and analyzes the variation law of surrounding rock stress and displacement during TBM excavation of the tunnel. The results indicate that the dominant direction of the rock mass principal stress measured by the hydraulic fracturing method is NE84°, and the maximum horizontal principal stress, minimum horizontal principal stress, and vertical stress decrease sequentially, analyzing the characteristics of shield TBM construction technology, it is applied to the construction of water transfer tunnels. The numerical simulation of TBM construction using FLAC3D software shows that as the excavation surface advances, the subsidence value of the tunnel roof first slowly increases, then rapidly increases, and then tends to stabilize. The horizontal displacement of the surrounding rock is increasing. The maximum principal stress of the surrounding rock gradually increases. The final surrounding rock stress is 35 MPa. The TBM shield machine with mud water balance driven by indirectly controlled frequency conversion motor is selected for TBM construction of the tunnel. The study offers statistical information to support tunneling technology for water conveyance in the geotechnical engineering practice.
Linking governance with environmental quality: a global perspective
Authors: Azimi Mohammad Naim , Rahman Mohammad Mafizur , Nghiem Son 
Published: September 2023

AbstractSustainable environmental quality is a global concern, and a concrete remedy to overcome this challenge is a policy priority. Therefore, this study delves into the subject and examines the effects of governance on environmental quality in 180 countries from 1999 to 2021. To maintain comparability and precision, we first classify countries into full and income-level panels and then, innovatively, construct a composite governance index (CGI) to capture the extensive effects of governance on CO2 emissions. Complementing the stationarity properties of the variables, we employ the cross-sectionally augmented autoregressive distributed lags model to analyze the data. Our survey yields four key findings. First, a long-run nexus between CGI, CO2 emissions, and other control variables is confirmed. Second, the findings indicate that CGI is crucial to improving environmental quality by reducing CO2 emissions across all panels. Third, we find that while CGI maintains a similar magnitude, the size of its effects substantially varies according to the income level of the underlying countries. Fourth, the findings reveal that energy consumption, population growth rate, trade openness, and urbanization contribute to environmental degradation, while financial development and the human development index are significant in reducing CO2 emissions. Our findings suggest specific policy implications, summing up that one common policy is not a good fit for all environmental quality measures.