bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of CO2 Column Concentration Above Cloud Tops With a Spaceborne IPDA Lidar
Authors: Mao Zhihua , Zhang Yang , Bu Lingbing , Wang Qin , Xiao Wei , Lee Xuhui , Liang Dingyuan , Burhan Khalid Muhammad , Liu Jiqiao , Chen Weibiao , Liu Sihan , Wang Zhongting 
Published: November 2024

AbstractThe Atmospheric Environment Monitoring Satellite (AEMS), launched by China in 2022, was equipped with active remote sensing lidar for carbon monitoring. It adopts the Integrated Path Differential Absorption (IPDA) technology to monitor global CO2 column concentration (XCO2). The calculation of cloud top XCO2 requires cloud height data. A comparison between SRTM global elevation data and 1,572 nm channel elevation data reveals a coefficient of determination (R2) of 0.998, with an average deviation of 1.24 m. The cloud top XCO2 observations are consistent with the OCO‐2 and CarbonTracker trends. The ocean carbon uptake rate, assessed by the difference in CO2 concentration between cloud top and sea surface, is −0.319 mmol/m2/h, which is in good agreement with the associated carbon flux data. This demonstrates the great potential of IPDA lidar for remote sensing of cloud top CO2 and quantifying ocean carbon uptake.
A Parametric Study of Quasi‐Static Electron Acceleration by Modified Electron Acoustic Wave and Comparison to Knight Relation
Authors: Shi Run , Liang Jun , Hu Zejun , Han Desheng , Xiong Yating 
Published: November 2024

AbstractA comprehensive understanding of how a magnetic source potential is distributed in the magnetosphere‐ionosphere circuit, and the relationship between the field‐aligned current and the parallel potential, is essential for accurately interpreting the observational characteristics of a quasi‐static arc. In this study, we investigate the formation of quasi‐static electron acceleration led by kinetic Alfvén wave‐electron acoustic wave coupling, based on one‐dimensional kinetic simulations. Various controlling factors of the coupling process are considered, including the hot electron density and temperature, the cold electron density and temperature, the perpendicular wave number, and the ionospheric conductance. The ratio between the parallel potential drop and field‐aligned current is found to be approximately proportional to the square root of the hot electron temperature and inversely proportional to the hot electron density, similar to the Knight relation but with a modified slope factor that depends on the perpendicular wavelength and cold electron parameters. Meanwhile, with smaller perpendicular wavelength, lower hot electron density, higher hot electron temperature, and lower cold electron density, more potential drop is applied to the parallel electron acceleration in the transition region.
Biogeochemical Traits of a High Latitude South Pacific Ocean Calcareous Nannoplankton Community During the Oligocene
Authors: Sheward Rosie M. , Herrle Jens O. , Fuchs Julian , Gibbs Samantha J. , Bown Paul R. , Eibes Pia M. 
Published: November 2024

AbstractMarine phytoplankton community composition influences the production and export of biomass and inorganic minerals (such as calcite), contributing to core marine ecosystem processes that drive biogeochemical cycles and support marine life. Here we use morphological and assemblage data sets within a size‐trait model to investigate the mix of cellular biogeochemical traits (size, biomass, calcite) present in high latitude calcareous nannoplankton communities through the Oligocene (ca. 34–26 Ma) to better understand the biogeochemical consequences of past climate variability on this major calcifying phytoplankton group. Our record from IODP Site U1553 in the southwest Pacific reveals that nannoplankton communities were most size diverse during the earliest Oligocene, which we propose is linked to evidence for increased nutrient availability in the region across the Eocene‐Oligocene transition. In addition to driving changes in community size structure, early Oligocene extinctions of the largest Reticulofenestra species combined with an increasing dominance of heavily calcified, small‐medium‐sized cells through time also led to an overall increase in community inorganic to organic carbon ratios (PIC:POC) throughout the Oligocene. Crucially, genus‐level cellular PIC:POC diversity meant that abundance was not always the best indicator of which species were the major contributors to community biomass and calcite. As shifts in plankton size structure and calcareous nannoplankton PIC:POC have previously been highlighted as important in biological carbon pump dynamics, our results suggest that changes in community composition that are coupled to changes in community biogeochemical trait diversity have the potential to significantly alter the role of calcareous nannoplankton in marine biogeochemical processes.
A comparative analysis of transformed indolent lymphomas and de novo diffuse large B-cell lymphoma: a population-based cohort study
Authors: Vaughn John L. , Ramdhanny Angela , Munir Malak , Rimmalapudi Sravani , Epperla Narendranath 
Published: November 2024

AbstractHistologic transformation (HT) of indolent non-Hodgkin lymphoma (iNHL) to diffuse large B-cell lymphoma (DLBCL) carries a poor prognosis. Using the Surveillance, Epidemiology, and End Results-17 database, we conducted a population-based study of adult patients with transformed follicular lymphoma (t-FL), marginal zone lymphoma (t-MZL), lymphoplasmacytic lymphoma/Waldenström macroglobulinemia (t-LPL/WM), and de novo DLBCL. Primary outcome was relative survival (RS), and secondary outcomes included overall survival (OS) and lymphoma-specific survival (LSS). Outcomes were modeled using flexible parametric survival models, while multivariable modeling was used to compare RS, OS, and LSS. The incidence of HT was highest in splenic MZL (SMZL, 6.78%) and lowest in extranodal MZL (EMZL, 1.62%). Median follow-up times were similar for patients with de novo DLBCL and transformed indolent lymphomas. The 5-year RS and OS were longer in de novo DLBCL compared to all other transformed iNHL subtypes (68 versus 59%, respectively). For t-FL, early transformation (within 2 years of diagnosis, Hazard ratio [HR] = 1.34) and prior treatment (HR = 1.89) were associated with inferior survival. This association was not observed in other transformed lymphoma subtypes. This is the first comparative study to show that the outcomes of t-LPL/WM were inferior compared to de novo DLBCL and highlights the need to incorporate early experimental therapies in patients with t-FL with early transformation and receipt of prior chemotherapy.
Spatio-temporal transcriptomics of chromothriptic SHH-medulloblastoma identifies multiple genetic clones that resist treatment and drive relapse
Authors: Kats Ilia , Simovic-Lorenz Milena , Schreiber Hannah Sophia , Sant Pooja , Mallm Jan-Philipp , Körber Verena , Li Albert , Velmurugan Pravin , Heuer Sophie , Kües Luisa , Devens Frauke , Sill Martin , Jugold Manfred , Moustafa Mahmoud , Abdollahi Amir , Winkler Frank , Korshunov Andrey , Pfister Stefan M. , Stegle Oliver , Ernst Aurélie 
Published: November 2024

AbstractPaediatric medulloblastomas with chromothripsis are characterised by high genomic instability and are among the tumours with the worst prognosis. However, the molecular makeup and the determinants of the aggressiveness of chromothriptic medulloblastoma are not well understood. Here, we apply spatial transcriptomics to profile a cohort of 13 chromothriptic and non-chromothriptic medulloblastomas from the same molecular subgroup. Our data reveal a higher extent of spatial intra-tumour heterogeneity in chromothriptic medulloblastomas compared to non-chromothripictic tumours, which is associated with increased proliferation and stemness, but lower immune infiltration and differentiation. Spatial mapping of genetic subclones of the same tumour identify a regionally distinct architecture and clone-specific phenotypic features, with distinct degrees of differentiation, proliferation and immune infiltration between clones. We conduct temporal profiling of 11 samples from patient-derived xenografts from a patient with chromothriptic medulloblastoma, covering the transition from the minimal residual disease stage to treatment-resistant regrown tumours. In chromothriptic medulloblastoma, an ecosystem of cells from multiple genetic clones resist treatment and lead to relapse. Finally, we identify tumour microtubes in chromothriptic medulloblastoma, calling for exploration of cell network communication as a putative target.
Self-organized spatial targeting of contractile actomyosin rings for synthetic cell division
Authors: Reverte-López María , Kanwa Nishu , Qutbuddin Yusuf , Belousova Viktoriia , Jasnin Marion , Schwille Petra 
Published: November 2024

AbstractA key challenge for bottom-up synthetic biology is engineering a minimal module for self-division of synthetic cells. Actin-based cytokinetic rings are considered a promising structure to produce the forces required for the controlled excision of cell-like compartments such as giant unilamellar vesicles (GUVs). Despite prior demonstrations of actin ring targeting to GUV membranes and myosin-induced constriction, large-scale vesicle deformation has been precluded due to the lacking spatial control of these contractile structures. Here we show the combined reconstitution of actomyosin rings and the bacterial MinDE protein system within GUVs. Incorporating this spatial positioning tool, able to induce active transport of membrane-attached diffusible molecules, yields self-organized equatorial assembly of actomyosin rings in vesicles. Remarkably, the synergistic effect of Min oscillations and the contractility of actomyosin bundles induces mid-vesicle deformations and vesicle blebbing. Our system showcases how functional machineries from various organisms may be combined in vitro, leading to the emergence of functionalities towards a synthetic division system.
Moiré magnetism in CrBr3 multilayers emerging from differential strain
Authors: Yao Fengrui , Rossi Dario , Gabrovski Ivo A. , Multian Volodymyr , Hua Nelson , Watanabe Kenji , Taniguchi Takashi , Gibertini Marco , Gutiérrez-Lezama Ignacio , Rademaker Louk , Morpurgo Alberto F. 
Published: November 2024

AbstractInterfaces between twisted 2D materials host a wealth of physical phenomena originating from the long-scale periodicity associated with the resulting moiré structure. Besides twisting, an alternative route to create structures with comparably long—or even longer—periodicities is inducing a differential strain between adjacent layers in a van der Waals (vdW) material. Despite recent theoretical efforts analyzing its benefits, this route has not yet been implemented experimentally. Here we report evidence for the simultaneous presence of ferromagnetic and antiferromagnetic regions in CrBr3—a hallmark of moiré magnetism—from the observation of an unexpected magnetoconductance in CrBr3 tunnel barriers with ferromagnetic Fe3GeTe2 and graphene electrodes. The observed magnetoconductance evolves with temperature and magnetic field as the magnetoconductance measured in small-angle CrBr3 twisted junctions, in which moiré magnetism occurs. Consistent with Raman measurements and theoretical modeling, we attribute the phenomenon to the presence of a differential strain in the CrBr3 multilayer, which locally modifies the stacking and the interlayer exchange between adjacent CrBr3 layers, resulting in spatially modulated spin textures. Our conclusions indicate that inducing differential strain in vdW multilayers is a viable strategy to create moiré-like superlattices, which in the future may offer in-situ continuous tunability even at low temperatures.
An integrated single-cell atlas of blood immune cells in aging
Authors: Filippov Igor , Schauser Leif , Peterson Pärt 
Published: November 2024

AbstractRecent advances in single-cell technologies have facilitated studies on age-related alterations in the immune system. However, previous studies have often employed different marker genes to annotate immune cell populations, making it challenging to compare results. In this study, we combined seven single-cell transcriptomic datasets, comprising more than a million cells from one hundred and three donors, to create a unified atlas of human peripheral blood mononuclear cells (PBMC) from both young and old individuals. Using a consistent set of marker genes for immune cell annotation, we standardized the classification of immune cells and assessed their prevalence in both age groups. The integrated dataset revealed several consistent trends related to aging, including a decline in CD8+ naive T cells and MAIT cells and an expansion of non-classical monocyte compartments. However, we observed significant variability in other cell types. Our analysis of the long non-coding RNA MALAT1hi T cell population, previously implicated in age-related T cell exhaustion, showed that this population is highly heterogeneous with a mixture of naïve-like and memory-like cells. Despite substantial variation among the datasets when comparing gene expression between age groups, we identified a high-confidence signature of CD8+ naive T cell aging marked by an increased expression of pro-inflammatory genes. In conclusion, our study emphasizes the importance of standardizing existing single-cell datasets to enable the comprehensive examination of age-related cellular changes across multiple datasets.
Phase separation and ageing of glycine-rich protein from tick adhesive
Authors: Ganar Ketan A. , Nandy Manali , Turbina Polina , Chen Chang , Suylen Dennis , Nihoul Elisa , Pascoe Emily Louise , van der Beelen Stan , Plaum Maarten , van den Bos Leendert , Koenraadt Constantianus J. M. , Dijkgraaf Ingrid , Deshpande Siddharth 
Published: November 2024

Abstract
Hard ticks feed on their host for multiple days. To ensure firm attachment, they secrete a protein-rich saliva that eventually forms a solid cement cone. The underlying mechanism of this liquid-to-solid transition is currently not understood. This study focuses on the phase transitions of a disordered glycine-rich protein (GRP) found in tick saliva. We show that GRP undergoes liquid–liquid phase separation via simple coacervation to form biomolecular condensates in salty environments. Cation–π and π–π interactions mediated by periodically placed arginine and aromatic amino-acid residues are the primary driving forces that promote phase separation. Interestingly, GRP condensates exhibit ageing by undergoing liquid-to-gel transition over time and exhibit adhesive properties, similar to the naturally occurring cement cone. Finally, we provide evidence for protein-rich condensates in natural tick saliva. Our findings provide a starting point to gain further insights into the bioadhesion of ticks, to develop novel tick control strategies, and towards achieving biomedical applications such as tissue sealants.
Light-based gamma entrainment with novel invisible spectral flicker stimuli
Authors: Hansen Luna S. , Carstensen Marcus H. , Henney Mark A. , Nguyen N. Mai , Thorning-Schmidt Martin W. , Broeng Jes , Petersen Paul Michael , Andersen Tobias S. 
Published: November 2024

AbstractLight-based gamma entrainment using sensory stimuli (GENUS) shows considerable potential for the treatment of Alzheimer’s disease (AD) in both animal and human models. While the clinical efficacy of GENUS for AD is paramount, its effectiveness will eventually also rely on the barrier to treatment adherence imposed by the discomfort of gazing at luminance flickering (LF) light. Currently, there have been few attempts to improve the comfort of GENUS. Here we investigate if Invisible spectral flicker (ISF), a novel type of light-based 40 Hz GENUS for which the flicker is almost imperceptible, can be used as a more comfortable option. We found that whereas ISF, LF, and chromatic flicker (CF) all produce a 40 Hz steady-state visually evoked potential (SSVEP), ISF scores significantly better on measures of comfort and perceived flicker. We also demonstrate that, while there is a trend towards a lower SSVEP response, reducing the stimulation brightness has no significant effect on the 40 Hz SSVEP or perceived flicker, though it significantly improves comfort. Finally, there is a slight decrease in the 40 Hz SSVEP response when stimulating with ISF from increasingly peripheral angles. This may ease the discomfort of GENUS treatment by freeing patients from gazing directly at the light.
Face mask identification with enhanced cuckoo optimization and deep learning-based faster regional neural network
Authors: Pandey Binay Kumar , Pandey Digvijay , Lelisho Mesfin Esayas 
Published: November 2024

AbstractA mask identification and social distance monitoring system using Unmanned Aerial Vehicles (UAV) in the outdoors has been proposed for a health establishment. The above approach performed surveillance of the surrounding area using cameras installed in UAVs and internet of things technologies, and the captured images seem useful for tracking the entire environment. However, innate images from unmanned aerial vehicles show an adaptable visual effect in an uncontrolled environment, making face-mask detection and recognition harder. The UAV picture first had to be converted to grayscale, then its contrast was amplified. Image contrast was improved using Optimum Wavelet-Based Masking and the Enhanced Cuckoo Methodology (ECM). According to the contrast-enhanced image, Gabor-Transform (GT) and Stroke Width Transform (SWT) methods are used to derive attributes that help categorise mask-wearers and non-mask-wearers. Using the retrieved attributes, a Weighted Naive Bayes Classification (WNBC) detected masks in the images. Additionally, a deep neural network-based, the faster Region-Based Convolutional Neural Networks (R-CNN) algorithm combined with Adaptive Galactic Swarm Optimization (AGSO) is being used to identify appropriate and incorrect face mask wear in images, as well as to monitor social distancing among individuals in crowded areas. When the system recognises unmasked individuals, it sends their information to the doctor and the nearby police station. One unmanned aerial vehicle’s automated system alert people via speakers, ensuring social spacing. The problem involves a large percentage of appropriate and incorrect face mask wear using data from GitHub and Kaggle, including a training repository of 16,000 images and a testing data set of 12,751 images. To enhance the performance of the model’s learning, the methodology of 10-fold cross-validation will be used. Precision, recall, F1-score, and speed are then measured to determine the efficacy of the suggested approach.
Mechanical characteristics and antibacterial activity against Staphylococcus aureus of sustainable cellulosic paper coated with Ag and Cu modified ZnO nanoparticles
Authors: Geioushy Ramadan A. , El-Sherbiny Samya , Mohamed Eslam T. , Fouad Osama A. , Samir Marwa 
Published: November 2024

AbstractIn this study, zinc oxide (ZnO) nanoparticles were prepared and modified using a wet chemical method with different concentrations of Ag and Cu nanoparticles. The objective was to improve the mechanical, optical, and antibacterial properties of the coated paper by using the prepared pigments. The long-term antimicrobial effects of the coated paper were evaluated over 25 years. The successful synthesis of a hexagonal structure of ZnO nanoparticles decorated with spherical Ag and Cu nanoparticles ranging from 20 to 50 nm was confirmed using X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and transmission electron microscopy (TEM). By increasing the concentrations of Ag and Cu from 0.01% to 1.0%, the mechanical properties of the coated paper were enhanced. The tensile strength reached a maximum of 6.77 kN/m and 7.03 kN/m, elongation increased to 1.69% and 1.70%, tensile energy absorption improved to approximately 77 and 80 J/m2, and burst strength rose to 218 and 219 kPa, respectively. The use of Ag-modified ZnO maintains the optical properties, while Cu-modified ZnO reduces brightness and whiteness without affecting opacity. The antimicrobial inhibition activity was improved with higher silver (Ag) and copper (Cu) content. The formulations containing 1% Ag/ZnO and 1%Cu/ZnO showed long-lasting antibacterial effects against gram-positive Staphylococcus aureus bacteria. Even after 25 years of aging, they maintained inhibition rates of 92.2% and 62.2%, respectively. The molecular docking and GeneMANIA analysis revealed the potential of ZnO, Ag-modified ZnO, and Cu-modified ZnO nanoparticles to disrupt the S. aureus cell wall biosynthesis pathway by targeting the MurA enzyme and associated cell wall synthesis genes.
De-identification is not enough: a comparison between de-identified and synthetic clinical notes
Authors: Sarkar Atiquer Rahman , Chuang Yao-Shun , Mohammed Noman , Jiang Xiaoqian 
Published: November 2024

AbstractFor sharing privacy-sensitive data, de-identification is commonly regarded as adequate for safeguarding privacy. Synthetic data is also being considered as a privacy-preserving alternative. Recent successes with numerical and tabular data generative models and the breakthroughs in large generative language models raise the question of whether synthetically generated clinical notes could be a viable alternative to real notes for research purposes. In this work, we demonstrated that (i) de-identification of real clinical notes does not protect records against a membership inference attack, (ii) proposed a novel approach to generate synthetic clinical notes using the current state-of-the-art large language models, (iii) evaluated the performance of the synthetically generated notes in a clinical domain task, and (iv) proposed a way to mount a membership inference attack where the target model is trained with synthetic data. We observed that when synthetically generated notes closely match the performance of real data, they also exhibit similar privacy concerns to the real data. Whether other approaches to synthetically generated clinical notes could offer better trade-offs and become a better alternative to sensitive real notes warrants further investigation.