bluuebunny/crossref_metadata_2025_split huggingface dataset:
B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity
Authors: Lapuente Dennis , Winkler Thomas H. , Tenbusch Matthias 
Published: November 2023

AbstractThe emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
Extended X-ray absorption fine structure of dynamically-compressed copper up to 1 terapascal
Authors: Sio H. , Krygier A. , Braun D. G. , Rudd R. E. , Bonev S. A. , Coppari F. , Millot M. , Fratanduono D. E. , Bhandarkar N. , Bitter M. , Bradley D. K. , Efthimion P. C. , Eggert J. H. , Gao L. , Hill K. W. , Hood R. , Hsing W. , Izumi N. , Kemp G. , Kozioziemski B. , Landen O. L. , Le Galloudec K. , Lockard T. E. , Mackinnon A. , McNaney J. M. , Ose N. , Park H.-S. , Remington B. A. , Schneider M. B. , Stoupin S. , Thorn D. B. , Vonhof S. , Wu C. J. , Ping Y. 
Published: November 2023

AbstractLarge laser facilities have recently enabled material characterization at the pressures of Earth and Super-Earth cores. However, the temperature of the compressed materials has been largely unknown, or solely relied on models and simulations, due to lack of diagnostics under these challenging conditions. Here, we report on temperature, density, pressure, and local structure of copper determined from extended x-ray absorption fine structure and velocimetry up to 1 Terapascal. These results nearly double the highest pressure at which extended x-ray absorption fine structure has been reported in any material. In this work, the copper temperature is unexpectedly found to be much higher than predicted when adjacent to diamond layer(s), demonstrating the important influence of the sample environment on the thermal state of materials; this effect may introduce additional temperature uncertainties in some previous experiments using diamond and provides new guidance for future experimental design.
Unraveling the optoelectronic properties of CoSbx intrinsic selective solar absorber towards high-temperature surfaces
Authors: Taranova Anastasiia , Akbar Kamran , Yusupov Khabib , You Shujie , Polewczyk Vincent , Mauri Silvia , Balliana Eleonora , Rosen Johanna , Moras Paolo , Gradone Alessandro , Morandi Vittorio , Moretti Elisa , Vomiero Alberto 
Published: November 2023

AbstractThe combination of the ability to absorb most of the solar radiation and simultaneously suppress infrared re-radiation allows selective solar absorbers (SSAs) to maximize solar energy to heat conversion, which is critical to several advanced applications. The intrinsic spectral selective materials are rare in nature and only a few demonstrated complete solar absorption. Typically, intrinsic materials exhibit high performances when integrated into complex multilayered solar absorber systems due to their limited spectral selectivity and solar absorption. In this study, we propose CoSbx (2 < x < 3) as a new exceptionally efficient SSA. Here we demonstrate that the low bandgap nature of CoSbx endows broadband solar absorption (0.96) over the solar spectral range and simultaneous low emissivity (0.18) in the mid-infrared region, resulting in a remarkable intrinsic spectral solar selectivity of 5.3. Under 1 sun illumination, the heat concentrates on the surface of the CoSbx thin film, and an impressive temperature of 101.7 °C is reached, demonstrating the highest value among reported intrinsic SSAs. Furthermore, the CoSbx was tested for solar water evaporation achieving an evaporation rate of 1.4 kg m−2 h−1. This study could expand the use of narrow bandgap semiconductors as efficient intrinsic SSAs with high surface temperatures in solar applications.
Exploiting redundancy in large materials datasets for efficient machine learning with less data
Authors: Li Kangming , Persaud Daniel , Choudhary Kamal , DeCost Brian , Greenwood Michael , Hattrick-Simpers Jason 
Published: November 2023

AbstractExtensive efforts to gather materials data have largely overlooked potential data redundancy. In this study, we present evidence of a significant degree of redundancy across multiple large datasets for various material properties, by revealing that up to 95% of data can be safely removed from machine learning training with little impact on in-distribution prediction performance. The redundant data is related to over-represented material types and does not mitigate the severe performance degradation on out-of-distribution samples. In addition, we show that uncertainty-based active learning algorithms can construct much smaller but equally informative datasets. We discuss the effectiveness of informative data in improving prediction performance and robustness and provide insights into efficient data acquisition and machine learning training. This work challenges the “bigger is better” mentality and calls for attention to the information richness of materials data rather than a narrow emphasis on data volume.
Observational evidence of accelerating electron holes and their effects on passing ions
Authors: Dong Yue , Yuan Zhigang , Huang Shiyong , Xue Zuxiang , Yu Xiongdong , Pollock C. J. , Torbert R. B. , Burch J. L. 
Published: November 2023

AbstractAs a universal structure in space plasma, electron holes represent an obvious signature of nonlinear process. Although the theory has a 60-year history, whether electron hole can finally accelerate ambient electrons (or ions) is quite controversial. Previous theory for one-dimensional holes predicts that net velocity change of passing electrons (or ions) occurs only if the holes have non-zero acceleration. However, the prediction has not yet been demonstrated in observations. Here, we report four electron holes whose acceleration/deceleration is obtained by fitting the spatial separations and detection time delays between different Magnetospheric Multiscale spacecraft. We find that electron hole acceleration/deceleration is related to the ion velocity distribution gradient at the hole’s velocity. We observe net velocity changes of ions passing through the accelerating/decelerating holes, in accordance with theoretical predictions. Therefore, we show that electron holes with non-zero acceleration can cause the velocity of passing ions to increase in the acceleration direction.
Bifunctionality of dirhodium tetracarboxylates in metallaphotocatalysis
Authors: Shi Taoda , Zhang Tianyuan , Yang Jiying , Li Yukai , Shu Jirong , Zhao Jingyu , Zhang Mengchu , Zhang Dan , Hu Wenhao 
Published: November 2023

AbstractMetallaphotocatalysis has been recognized as a pivotal catalysis enabling new reactivities. Traditional metallaphotocatalysis often requires two or more separate catalysts and exhibits flaw in cost and substrate-tolerance, thus representing an await-to-solve issue in catalysis. We herein realize metallaphotocatalysis with a bifunctional dirhodium tetracarboxylate ([Rh2]) alone. The [Rh2] shows an photocatalytic activity of promoting singlet oxygen (1O2) oxidation. By harnessing its photocatalytic activity, the [Rh2] catalyzes a photochemical cascade reaction (PCR) via combination of carbenoid chemistry and 1O2 chemistry. The PCR is characterized by high atom-efficiency, excellent stereoselectivities, mild conditions, scalable synthesis, and pharmaceutically interesting products. DFT calculations-aided mechanistic study rationalizes the reaction pathway and interprets the origin of stereoselectivities of the PCR. The products show inhibitory activity against PTP1B, being promising in the treatment of type II diabetes and cancers. Overall, here we show the bifunctional [Rh2] merges Rh-carbenoid chemistry and 1O2 chemistry.
Thermo-responsive chiral micelles as recyclable organocatalyst for asymmetric Rauhut-Currier reaction in water
Authors: Xu Lei , Zhou Li , Li Yan-Xiang , Gao Run-Tan , Chen Zheng , Liu Na , Wu Zong-Quan 
Published: November 2023

AbstractDeveloping eco-friendly chiral organocatalysts with the combined advantages of homogeneous catalysis and heterogeneous processes is greatly desired. In this work, a family of amphiphilic one-handed helical polyisocyanides bearing phosphine pendants is prepared, which self-assembles into well-defined chiral micelles in water and showed thermo-responsiveness with a cloud point of approximately 38.4 °C. The micelles with abundant phosphine moieties at the interior efficiently catalyze asymmetric cross Rauhut-Currier reaction in water. Various water-insoluble substrates are transferred to target products in high yield with excellent enantioselectivity. The yield and enantiomeric excess (ee) of the product generated in water are up to 90% and 96%, respectively. Meanwhile, the yields of the same R-C reaction catalyzed by the polymer itself in organic solvents is <16%, with an ee < 72%. The homogeneous reaction of the chiral micelles in water turns to heterogeneous at temperatures higher than the cloud point, and the catalyst precipitation facilitates product isolation and catalyst recovery. The polymer catalyst is recycled 10 times while maintaining activity and enantioselectivity.
Precursor region with full phonon softening above the charge-density-wave phase transition in 2H-TaSe2
Authors: Shen Xingchen , Heid Rolf , Hott Roland , Haghighirad Amir-Abbas , Salzmann Björn , dos Reis Cantarino Marli , Monney Claude , Said Ayman H. , Frachet Mehdi , Murphy Bridget , Rossnagel Kai , Rosenkranz Stephan , Weber Frank 
Published: November 2023

AbstractResearch on charge-density-wave (CDW) ordered transition-metal dichalcogenides continues to unravel new states of quantum matter correlated to the intertwined lattice and electronic degrees of freedom. Here, we report an inelastic x-ray scattering investigation of the lattice dynamics of the canonical CDW compound 2H-TaSe2 complemented by angle-resolved photoemission spectroscopy and density functional perturbation theory. Our results rule out the formation of a central-peak without full phonon softening for the CDW transition in 2H-TaSe2 and provide evidence for a novel precursor region above the CDW transition temperature TCDW, which is characterized by an overdamped phonon mode and not detectable in our photoemission experiments. Thus, 2H-TaSe2 exhibits structural before electronic static order and emphasizes the important lattice contribution to CDW transitions. Our ab-initio calculations explain the interplay of electron-phonon coupling and Fermi surface topology triggering the CDW phase transition and predict that the CDW soft phonon mode promotes emergent superconductivity near the pressure-driven CDW quantum critical point.
Tau forms synaptic nano-biomolecular condensates controlling the dynamic clustering of recycling synaptic vesicles
Authors: Longfield Shanley F. , Mollazade Mahdie , Wallis Tristan P. , Gormal Rachel S. , Joensuu Merja , Wark Jesse R. , van Waardenberg Ashley J. , Small Christopher , Graham Mark E. , Meunier Frédéric A. , Martínez-Mármol Ramón 
Published: November 2023

AbstractNeuronal communication relies on the release of neurotransmitters from various populations of synaptic vesicles. Despite displaying vastly different release probabilities and mobilities, the reserve and recycling pool of vesicles co-exist within a single cluster suggesting that small synaptic biomolecular condensates could regulate their nanoscale distribution. Here, we performed a large-scale activity-dependent phosphoproteome analysis of hippocampal neurons in vitro and identified Tau as a highly phosphorylated and disordered candidate protein. Single-molecule super-resolution microscopy revealed that Tau undergoes liquid-liquid phase separation to generate presynaptic nanoclusters whose density and number are regulated by activity. This activity-dependent diffusion process allows Tau to translocate into the presynapse where it forms biomolecular condensates, to selectively control the mobility of recycling vesicles. Tau, therefore, forms presynaptic nano-biomolecular condensates that regulate the nanoscale organization of synaptic vesicles in an activity-dependent manner.
Enhancement and contextual modulation of visuospatial processing by thalamocollicular projections from ventral lateral geniculate nucleus
Authors: Li Zhong , Peng Bo , Huang Junxiang J. , Zhang Yuan , Seo Michelle B. , Fang Qi , Zhang Guang-Wei , Zhang Xiaohui , Zhang Li I. , Tao Huizhong Whit 
Published: November 2023

AbstractIn the mammalian visual system, the ventral lateral geniculate nucleus (vLGN) of the thalamus receives salient visual input from the retina and sends prominent GABAergic axons to the superior colliculus (SC). However, whether and how vLGN contributes to fundamental visual information processing remains largely unclear. Here, we report in mice that vLGN facilitates visually-guided approaching behavior mediated by the lateral SC and enhances the sensitivity of visual object detection. This can be attributed to the extremely broad spatial integration of vLGN neurons, as reflected in their much lower preferred spatial frequencies and broader spatial receptive fields than SC neurons. Through GABAergic thalamocollicular projections, vLGN specifically exerts prominent surround suppression of visuospatial processing in SC, leading to a fine tuning of SC preferences to higher spatial frequencies and smaller objects in a context-dependent manner. Thus, as an essential component of the central visual processing pathway, vLGN serves to refine and contextually modulate visuospatial processing in SC-mediated visuomotor behaviors via visually-driven long-range feedforward inhibition.
High-density EMG, IMU, kinetic, and kinematic open-source data for comprehensive locomotion activities
Authors: Dimitrov Hristo , Bull Anthony M. J. , Farina Dario 
Published: November 2023

AbstractNovel sensor technology enables new insights in the neuromechanics of human locomotion that were previously not possible. Here, we provide a dataset of high-density surface electromyography (HDsEMG) and high-resolution inertial measurement unit (IMU) signals, along with motion capture and force data for the lower limb of 10 healthy adults during multiple locomotion modes. The participants performed level-ground and slope walking, as well as stairs ascent/descent, side stepping gait, and stand-to-walk and sit-to-stand-to-walk, at multiple walking speeds. These data can be used for the development and validation of locomotion mode recognition and control algorithms for prosthetics, exoskeletons, and bipedal robots, and for motor control investigations.
A chromosome-level genome assembly of Korean mint (Agastache rugosa)
Authors: Park Hyun-Seung , Jo Ick Hyun , Raveendar Sebastin , Kim Nam-Hoon , Gil Jinsu , Shim Donghwan , Kim Changsoo , Yu Ju-Kyung , So Yoon-Sup , Chung Jong-Wook 
Published: November 2023

AbstractAgastache rugosa, also known as Korean mint, is a perennial plant from the Lamiaceae family that is traditionally used for various ailments and contains antioxidant and antibacterial phenolic compounds. Molecular breeding of A. rugosa can enhance secondary metabolite production and improve agricultural traits, but progress in this field has been delayed due to the lack of chromosome-scale genome information. Herein, we constructed a chromosome-level reference genome using Nanopore sequencing and Hi-C technology, resulting in a final genome assembly with a scaffold N50 of 52.15 Mbp and a total size of 410.67 Mbp. Nine pseudochromosomes accounted for 89.1% of the predicted genome. The BUSCO analysis indicated a high level of completeness in the assembly. Repeat annotation revealed 561,061 repeat elements, accounting for 61.65% of the genome, with Copia and Gypsy long terminal repeats being the most abundant. A total of 26,430 protein-coding genes were predicted, with an average length of 1,184 bp. The availability of this chromosome-scale genome will advance our understanding of A. rugosa’s genetic makeup and its potential applications in various industries.
Tumor microenvironment heterogeneity in bladder cancer identifies biologically distinct subtypes predicting prognosis and anti-PD-L1 responses
Authors: Li YaFei , Liu Yi , Kang Zhengjun , Guo Jianhua , Liu Nan 
Published: November 2023

AbstractBladder cancer (BCa) is heterogeneous in the tumour microenvironment (TME). However, the role of the TME in BCa in modulating the response to immunotherapy has not been fully explored. We therefore analysed fractions of immune cells using CIBERSORTx and clustered BCa into subtypes. We also analyzed weighted correlation networks to generate immunotherapy-related hub genes that we used to construct a prediction model using multivariate Cox and LASSO regression analyses. We found that BCa comprised three subtypes (C1‒C3). The prognosis of the patients was the most favourable and the response rate to anti-programmed death ligand 1 (PD-L1) was the highest in C1 among the three subtypes. Immune cells, including CD8+, CD4+ memory activated, and follicular helper T cells, activated NK cells, and M1 macrophages infiltrated the C1 subtype. The C2 subtype was enriched in M0 macrophages and activated mast cells, and the C3 subtype was enriched in B and resting immune cells. Mechanistically, the enhanced immunogenicity of subtypes C1 and C2 correlated positively with a higher response rate, whereas the dysregulated ECM-related pathways in the C2 subtype and glycolytic and fatty acid metabolic pathways in the C3 subtype impaired the responses of patients to anti-PD-L1 therapy. We also constructed a TME-related signature based on 18 genes that performed well in terms of overall survival. In conclusion, we determined prognoses and anti-PD-L1 responses by analysing TME heterogeneity in BCa.
Emergence of behavioral phenomena and adaptation effects in human numerosity decoder using recurrent neural networks
Authors: Verma Bhavesh K , Sengupta Rakesh 
Published: November 2023

AbstractHumans possess an innate ability to visually perceive numerosities, which refers to the cardinality of a set. Numerous studies indicate that the lateral intraparietal cortex (LIP) and other intraparietal sulcus (IPS) regions (region) of the brain contain the neurological substrates responsible for number processing. Existing computational models of number perception often focus on a limited range of numbers and fail to account for important behavioral characteristics like adaptation effects, despite simulating fundamental aspects such as size and distance effects. To address these limitations, our study develops (introduces) a novel computational model of number perception utilizing a network of neurons with self-excitatory and mutual inhibitory properties. Our approach assumes that the mean activation of the network at steady state can encode numerosity by exhibiting a monotonically increasing relationship with the input variable set size. By optimizing the total number of inhibition strengths required, we achieve coverage of the full range of numbers through three distinct intervals: 1 to 4, 5 to 17, and 21 to 50. Remarkably, this division aligns closely with the breakpoints in numerosity perception identified in behavioral studies. Furthermore, our study develops a method for decoding the mean activation into a continuous scale of numbers spanning from 1 to 50. Additionally, we propose a mechanism for dynamically selecting the inhibition strength based on current inputs, enabling the network to operate effectively across an extended (entire) range of numerosities. Our model not only sheds new light on the generation of diverse behavioral phenomena in the brain but also elucidates how continuous visual attributes and adaptation effects influence perceived numerosity.
Genotoxicity and oxidative stress induction by calcium hydroxide, calcium titanate or/and yttrium oxide nanoparticles in mice
Authors: Mohamed Hanan R. H. , Farouk Ahmed H. , Elbasiouni Salma H. , Nasif Kirolls A. , Safwat Gehan , Diab Ayman 
Published: November 2023

AbstractIntensive uses of Calcium hydroxide (Ca(OH)2NPs), calcium titanate (CaTiO3NPs) and yttrium oxide (Y2O3NPs) nanoparticles increase their environmental release and human exposure separately or together through contaminated air, water and food. However, too limited data are available on their genotoxicity. Therefore, this study explored the effect of Ca(OH)2NPs, CaTiO3NPs or/and Y2O3NPs administration on the genotoxicityand oxidative stress induction in mice hepatic tissue. Mice were orally administered Ca(OH)2NPs, CaTiO3NPs and Y2O3NPs separately or simultaneously together at a dose level of 50 mg/kg b.w. for two successive weeks (3 days per week). Marked induction of DNA damage noticed after oral administration of Ca(OH)2NPs or CaTiO3NPs alone together with high Ca(OH)2NPs induced reactive oxygen species (ROS) generation and a slight CaTiO3NPs induced ROS production were highly decreased after simultaneous coadministration of administration of Y2O3NPs with Ca(OH)2NPs and CaTiO3NPs up to the negative control level. Oral administration of Y2O3NPs alone also did not cause observable changes in the genomic DNA integrity and the ROS generation level compared to the negative control levels. Similarly, significant elevations in P53 gene expression and high reductions in Kras and HSP-70 genes expression were observed only after administration of Ca(OH)2NPs alone, while, remarkable increases in the Kras and HSP-70 genes expression and non-significant changes in p53 gene expression were noticed after administration of CaTiO3NPs and Y2O3NPs separately or simultaneously together with Ca(OH)2NPs. Conclusion: Ca(OH)2NPs exhibited the highest genotoxic effect through oxidative stress induction and disruption of apoptotic (p53 and Kras) and protective (HSP-70) genes expression. Slight DNA damage was noticed after CaTiO3NPs administration. However, administration of Y2O3NPs alone was non-genotoxic and coadministration of Y2O3NPs with Ca(OH)2NPs and CaTiO3NPs restored genomic DNA integrity and normal expression of apoptotic p53 and protective HSP-70 genes disrupted by Ca(OH)2NPs and CaTiO3NPs. Thus co-administration of Y2O3NPs with Ca(OH)2NPs and CaTiO3NPs is recommended to counter Ca(OH)2NPs and CaTiO3NPs induced genotoxicity and oxidative stress.