bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Two Parameterizations for the Restratification Effect of Mesoscale Eddies in an Isopycnal Ocean Model
Authors: Loose Nora , Marques Gustavo M. , Adcroft Alistair , Bachman Scott , Griffies Stephen M. , Grooms Ian , Hallberg Robert W. , Jansen Malte F. 
Published: December 2023

AbstractThere are two distinct parameterizations for the restratification effect of mesoscale eddies: the Greatbatch and Lamb (1990, GL90, https://journals.ametsoc.org/view/journals/phoc/20/10/1520-0485_1990_020_1634_opvmom_2_0_co_2.xml?tab_body=abstract-display) parameterization, which mixes horizontal momentum in the vertical, and the Gent and McWilliams (1990, GM90, https://journals.ametsoc.org/view/journals/phoc/20/1/1520-0485_1990_020_0150_imiocm_2_0_co_2.xml) parameterization, which flattens isopycnals adiabatically. Even though these two parameterizations are effectively equivalent under the assumption of quasi‐geostrophy, GL90 has been used much less than GM90, and exclusively in z‐coordinate models. In this paper, we compare the GL90 and GM90 parameterizations in an idealized isopycnal coordinate model, both from a theoretical and practical perspective. From a theoretical perspective, GL90 is more attractive than GM90 for isopycnal coordinate models because GL90 provides an interpretation that is fully consistent with thickness‐weighted isopycnal averaging, while GM90 cannot be entirely reconciled with any fully isopycnal averaging framework. From a practical perspective, the GL90 and GM90 parameterizations lead to extremely similar energy levels, flow and vertical structure, even though their energetic pathways are very different. The striking resemblance between the GL90 and GM90 simulations persists from non‐eddying through eddy‐permitting resolution. We conclude that GL90 is a promising alternative to GM90 for isopycnal coordinate models, where it is more consistent with theory, computationally more efficient, easier to implement, and numerically more stable. Assessing the applicability of GL90 in realistic global ocean simulations with hybrid coordinate schemes should be a priority for future work.
Geochemical Compositions of Size‐Fractioned Sediment Samples From the Yangtze and Yellow Rivers: Implications for Chemical Weathering, Fractionation Behavior of Provenance Tracers, and Sources of Radial Sand Ridges
Authors: Wu Chao , Wu Yang , Yu Xiaoxiao , Chen Yiwei , Zhang Weiguo , Liu Jie , Wei Gangjian 
Published: December 2023

AbstractRiver sediments are valuable archives of the environmental conditions within their catchments. The Yangtze and Yellow Rivers are the most active fluvial systems for sediment transport in East Asia, and they are regarded as potential sediment sources for the radial sand ridges (RSRs) in the southwestern Yellow Sea. We used the geochemical compositions of size‐fractioned sediment samples from the Yangtze and Yellow Rivers to characterize chemical weathering, the fractionation behavior of provenance tracers, and the sources of RSRs. For the Yangtze and Yellow River sediments, the (Rb + Sr)/Ti ratio is a reliable chemical weathering proxy that is grain‐size independent. The chemical indices of Chemical Index of Alteration, Rb/Sr, (Rb + Sr)/Ti, and acid‐leached elements from common grain‐size fractions together reveal that the Yangtze River basin undergoes stronger chemical weathering than the Yellow River basin, indicating that the chemical weathering is dominated by latitudinally‐dependent climatic variations. The dissolution and precipitation of amorphous Fe‐Mn oxides can result in the significant fractionation of La/Y, La/Sc, Nb/Co, La/Co, (La/Sm)N, (La/Yb)N, Ti/Sc, Zr/Y, Zr/Co, and Cr/Ta, whereas Zr/Ti and Zr/Nb are largely unaffected. Based on the robust provenance tracers of Zr/La, La/Hf, (La/Yb)N, Zr/Nb, Ti/Zr, and Hf/Ta, we conclude that the RSRs in the southwestern Yellow Sea are mainly derived from Yangtze River sediments, and that part of the clay fraction is from the Yellow River. In future research, we suggest that established geochemical indicators of chemical weathering and sediment provenance can be applied to the deposits of the Yangtze and Yellow River Deltas, the Yellow Sea, and the East China Sea.
Variation of Electron Lifetime Due To Scattering by Electrostatic Electron Cyclotron Harmonic Waves in the Inner Magnetosphere With Electron Distribution Parameters
Authors: Stoll Katja , Pick Leonie , Wang Dedong , Cao Xing , Ni Binbin , Shprits Yuri 
Published: December 2023

AbstractThrough resonant wave‐particle interactions with electrostatic electron cyclotron harmonic (ECH) waves, low‐energy plasma sheet electrons can be scattered into the atmospheric loss cone and precipitate. This process can be investigated by calculating bounce‐averaged quasi‐linear diffusion coefficients. However, the numerical calculation of ECH wave‐induced scattering rates requires the specification of several parameters, including the properties of the hot plasma sheet electrons responsible for the wave excitation. The dependence of the diffusion coefficients on these parameters and the exact contribution of scattering by ECH waves to diffuse auroral precipitation is still poorly understood and has not been carefully quantified yet. In this study, we calculate bounce‐averaged quasi‐linear scattering rates and compare the resulting lifetimes to the strong diffusion limit. We vary the temperature, plasma density, and loss cone parameters of the hot component in the electron loss cone distribution over a large range based on previous studies and observations. By adopting a new model that derives the wave normal angle from the midpoint and the angular width of the growth rate profile, our findings suggest that the electron lifetime near the loss cone is not significantly affected by the hot electron temperature and loss cone parameters. However, there is an increase in electron lifetimes with increasing plasma density. For an electric field amplitude of 1 mV/m, the electron lifetime is below or equal to the lifetime calculated using the strong diffusion limit up to E = 0.25 keV when n = 1.5 cm−3, and up to E = 0.22 keV when n = 9 cm−3.
Conditions for Energetic Electrons and Gamma Rays in Thunderstorm Ground Enhancements
Authors: Williams E. , Mailyan B. , Karapetyan G. , Mkrtchyan H. 
Published: December 2023

AbstractThe role of free passage distance (FPD: the distance between the avalanche region and surface detectors) in influencing the relative numbers of energetic electrons and gamma rays in Thunderstorm Ground Enhancements (TGEs) is reconsidered and focuses on the contrast between long (>100 m) versus short (<100 m) FPDs, respectively. Estimates of FPD are based on information from published balloon soundings of the electric field, from published profiles of radar reflectivity in TGEs, and from analyses of Japan winter storms. All these data sources support typical values of FPD >100 m. Neither the shortcomings of present particle detectors in distinguishing electrons from gamma rays, nor the dominance of gamma rays over electrons, are sufficient evidence to deny the robust presence of Compton electrons at FDP values greater than 100 m that have also been shown in earlier simulations as well as the present Comment. Problems with having sustained electric fields of breakeven magnitude within 100 m of the Earth's surface (in relatively rare TGEs) are identified. The resolution of these problems, and the prominent nocturnal presence of these rare events, may possibly be explained by the descent of a strong field region in a collapsing storm, and by a low cloud base that intercepts and immobilizes fast corona ions, thereby preserving the intense electric field.
From Outcrop to Spectrum—An Automated Approach to Modal Mineralogy of Silt‐Sized Sediment Applied to Central European Loess
Authors: Lünsdorf Nils Keno , Lünsdorf Jan Ontje , Újvári Gábor , Dunkl István , Wolfram Lukas , Hobrecht Adrian , Laake Lothar , von Eynatten Hilmar 
Published: December 2023

AbstractProvenance information from recent and ancient sedimentary archives is obscured by several factors and for disentangling these intermingled signals, analysis by multiple methods is paramount. In sedimentary provenance analysis (SPA), single‐grain methods determining mineralogy, chemical composition, or radiometric ages are of key importance but are mostly applied to sand‐sized sediments or sedimentary rocks. Finer grained sediments or sedimentary rocks are usually analyzed by whole‐rock geochemical means and seldom by single‐grain methods. Considering the abundance of fine‐grained sedimentary archives, a strong need for single‐grain, multi‐method analyses of silt‐sized sediments is obvious. Thus, we propose a workflow that is optimized for sample throughput and correlative analysis of fine‐grained sediments based on machine learning methods. The feasibility of the workflow is demonstrated by differentiating three Central European loess‐paleosol‐sequences. The increased sample throughput enables access to sedimentary archives at high spatial and/or temporal resolution, which will open up new research pathways in SPA of silt‐sized sediments.
Global Warming Weakens the Ocean Front and Phytoplankton Blooms in the Luzon Strait Over the Past 40 years
Authors: Lao Qibin , Liu Sihai , Wang Chao , Chen Fajin 
Published: December 2023

AbstractThe Luzon Strait is a channel where warmer Kuroshio water from the Pacific Ocean intrudes into the South China Sea (SCS). Under climate change impact, the temperature in marginal seas, including the SCS, rises faster than in open oceans. We speculated that the variation of frontal intensity and its eco‐environmental impact in the Luzon Strait may be different from coastal waters, whose frontal intensity is increasing, thus stimulating phytoplankton growth. To confirm this speculation, 40‐year satellite, and multiple data sources were analyzed in the Luzon Strait. The results showed that strong frontal intensity (front coverage of over 60%) and higher Chlorophyll a content occurred simultaneously in the Luzon Strait during the winter monsoon period. Phytoplankton blooms were enhanced during El Niño years because the stronger Kuroshio intrusion generated stronger fronts and intensified local upwelling in the Luzon Strait. On an interannual scale, the frontal intensity and phytoplankton growth exhibited a significantly decreasing trend in the Luzon Strait over the past 40 years, since the faster warming in the SCS reduced the temperature difference between the Pacific Ocean and the SCS. Warming and weakening fronts reduced the mixed layer depth to the oligotrophic layer, thus limiting the phytoplankton growth. This study confirmed that faster temperature rises in marginal seas reduced the frontal intensity and phytoplankton growth in the strait between oceans and marginal seas.
A Warming Southern Gulf of Mexico: Reconstruction of Anthropogenic Environmental Changes From a Siderastrea siderea Coral on the Northern Coast of Cuba
Authors: Harbott M. , Wu H. C. , Kuhnert H. , Jimenez C. , González‐Díaz P. , Rixen T. 
Published: December 2023

AbstractThe Gulf of Mexico is a vital region for the Atlantic Meridional Overturning Circulation (AMOC), that fuels the exchange of heat between the tropics and the polar regions. A weakening of the AMOC would have dire consequences for the planet. First observations and ocean models show that this process has already started. Very limited knowledge of the components that are part of the AMOC such as the Loop Current (LC) make it difficult to understand its dynamics as well as changes in strength or temperature since the onset of the Industrial Revolution. Currently, there are no continuous in situ sea surface temperature or salinity measurements for the southeastern Gulf of Mexico or reconstruction attempts for this region, showing the necessity for high‐resolution climate archives. A Siderastrea siderea coral core was retrieved from the northwestern Cuban coast and used as a sub‐seasonally resolved sea surface temperature and hydroclimate archive. The approach is based on skeletal δ18O, and trace and minor element contents show an increase in temperature over 160 years since 1845 of 2.6–3.3°C. A possible stagnation of the warming trend set in after the 1980s, indicating a potential weakening of the Loop Current. Impacts in sea surface salinity such as El Niño events in the Pacific region can still be detected in the Gulf of Mexico as decreases in salinity in 1998 from the reconstructed δ18OSW coral record. In situ measurements remain crucial to understand the dynamics in the LC and its influence on the AMOC.
Astronomically‐Paced Changes in Paleoproductivity, Winnowing, and Mineral Flux Over Broken Ridge (Indian Ocean) Since the Early Miocene
Authors: Lyu J. , Auer G. , Bialik O. M. , Christensen B. , Yamaoka R. , De Vleeschouwer D. 
Published: December 2023

AbstractA significant shift in Earth's climate characterizes the Neogene, transitioning from a single‐ice‐sheet planet to the current bipolar configuration. This climate evolution is closely linked to changing ocean currents, but globally‐distributed continuous high‐resolution sedimentary records are needed to fully capture this interaction. The Ocean Drilling Program (ODP) Site 752, located on Broken Ridge in the Indian Ocean, provides such a Miocene‐to‐recent archive. We use X‐ray fluorescence (XRF) core scanning to build an eccentricity‐tuned age‐depth model and reconstruct paleoceanographic changes since 23 Ma. We find two intervals of enhanced productivity, during the early and middle Miocene (18.5–13.7 Ma) and late Pliocene/early Pleistocene (3–1 Ma). We also report a mixed eccentricity‐obliquity imprint in the XRF‐derived paleoproductivity proxy. In terms of grain size, three coarsening steps occur between 19.2–16 Ma, 10.8–8 Ma, and since 2.6 Ma. The steps respectively indicate stronger current winnowing in response to vigorous Antarctic Intermediate Water flow over Broken Ridge in the early Miocene, the first transient onset of Tasman Leakage in the Late Miocene, and the intensification of global oceanic circulation at the Plio‐Pleistocene transition. High‐resolution iron and manganese series provide a detailed Neogene dust record. This study utilized a single hole from an ODP legacy‐site. Nevertheless, we managed to provide novel perspectives on past Indian Ocean responses to astronomical forcing. We conclude that Neogene sediments from Broken Ridge harbor the potential for even more comprehensive reconstructions. Realizing this potential necessitates re‐drilling of these sedimentary archives utilizing modern drilling strategies.
The development of a hiPSC-based platform to identify tissue-dependencies of IDH1 R132H
Authors: Mehjardi N. Z. , Kessler J. , Sanin A. Y. , Picard D. , Westhoff P. , Nickel Ann-Christin , Uhlmann C. , Shi W. , Steiger H. J. , Remke M. , Fischer I. , Vordermark D. , Croner R. S. , Kahlert U. D. 
Published: December 2023

AbstractThe application of patient-derived (PD) in vitro tumor models represents the classical strategy for clinical translational oncology research. Using these cellular heterogeneous cultures for the isolation of cancer stem cells (CSCs), suggested to be the main driver for disease malignancy, relies on the use of surrogate biomarkers or is based on CSC-enriching culture conditions. However, the ability of those strategies to exclusively and efficiently enrich for CSC pool has been questioned. Here we present an alternative in vitro CSC model based on the oncogenic transformation of single clone-derived human induced pluripotent stem cells (hiPSC). Hotspot mutations in the DNA encoding for the R132 codon of the enzyme isocitrate dehydrogenase 1 (IDH1) and codon R175 of p53 are commonly occurring molecular features of different tumors and were selected for our transformation strategy. By choosing p53 mutant glial tumors as our model disease, we show that in vitro therapy discovery tests on IDH1-engineered synthetic CSCs (sCSCs) can identify kinases-targeting chemotherapeutics that preferentially target tumor cells expressing corresponding genetic alteration. In contrast, neural stem cells (NSCs) derived from the IDH1R132H overexpressing hiPSCs increase their resistance to the tested interventions indicating glial–to-neural tissue-dependent differences of IDH1R132H. Taken together, we provide proof for the potential of our sCSC technology as a potent addition to biomarker-driven drug development projects or studies on tumor therapy resistance. Moreover, follow-up projects such as comparing in vitro drug sensitivity profiles of hiPSC-derived tissue progenitors of different lineages, might help to understand a variety of tissue-related functions of IDH1 mutations.
Programmed cell death in hepatic fibrosis: current and perspectives
Authors: Lu Ju-Lu , Yu Chuan-Xin , Song Li-Jun 
Published: December 2023

AbstractThe initiation, development and resolution of hepatic fibrosis are influenced by various cytokines, chemokines, damage-associated molecular patterns (DAMPs) and signaling pathways. A significant number of studies in recent years have indicated that the progression of hepatic fibrosis is closely linked to programmed cell death processes such as apoptosis, autophagy, pyroptosis, necroptosis, ferroptosis, cuproptosis, and PANoptosis. Inducement of hepatic stellate cells (HSCs) death or preventing death in other liver cells can delay or even reverse hepatic fibrosis. Nevertheless, the roles of programmed cell death in hepatic fibrosis have not been reviewed. Therefore, this review summarizes the characteristics of various of hepatic fibrosis and programmed cell death, focuses on the latest progress of programmed cell death in the promotion and regression of hepatic fibrosis, and highlights the different roles of the programmed cell death of HSCs and other liver cells in hepatic fibrosis. In the end, the possible therapeutic approaches targeting programmed cell death for treating hepatic fibrosis are discussed and prospected.
Population-level variation in gut bifidobacterial composition and association with geography, age, ethnicity, and staple food
Authors: Lu Jing , Zhang Li , Zhang Hao , Chen Yutao , Zhao Jianxin , Chen Wei , Lu Wenwei , Li Mingkun 
Published: December 2023

AbstractBifidobacteria are key gut commensals that confer various health benefits and are commonly used as probiotics. However, little is known about the population-level variation in gut bifidobacterial composition and its affecting factors. Therefore, we analyzedBifidobacteriumspecies with amplicon sequencing of thegroELgene on fecal samples of 1674 healthy individuals, who belonged to eight ethnic groups and resided in 60 counties/cities of 28 provinces across China. We found that the composition of the bifidobacterial community was associated with geographical factors, demographic characteristics, staple food type, and urbanization. First, geography, which reflects a mixed effect of other variables, explained the largest variation in the bifidobacterial profile. Second, middle adolescence (age 14–17) and age 30 were two key change points in the bifidobacterial community development, and a bifidobacterial community resembling that of adults occurred in middle adolescence, which is much later than the maturation of the whole gut microbial community at approximately age 3. Third, each ethnicity showed a distinct bifidobacterial profile, and the remarkable amount of unknownBifidobacteriumspecies in the Tibetan gut suggested undiscovered biodiversity. Fourth, wheat as the main staple food promoted the flourish ofB. adolescentisandB. longum. Fifth, alpha diversity of the bifidobacterial community decreased with urbanization. Collectively, our findings provide insight into the environmental and host factors that shape the human gut bifidobacterial community, which is fundamental for precision probiotics.
Harnessing bioengineered myeloid progenitors for precision immunotherapies
Authors: Buys Willem , Zambidis Elias T. 
Published: December 2023

AbstractGranulocytes and macrophages are the frontline defenders of the innate immune system. These myeloid cells play a crucial role in not only eliminating pathogens and tumor cells, but also regulating adaptive immune responses. In neonatal sepsis and post-chemotherapy agranulocytosis, the absence of these cells leaves the host highly vulnerable to infections. Beyond replacement to prevent or control neutropenic sepsis, engineered myeloid cells may offer distinct opportunities for cell therapies. For example, the mobility and specific homing capacities of neutrophils to sites of inflammation could be exploited to deliver biocidal agents, or anti-inflammatory healing signals during sepsis, autoimmunity, and organ transplantation. Additionally, myeloid cells can be engineered to express chimeric antigen receptors (CAR), carry chemotherapeutics, or enhance lymphoid tumor killing. However, traditional methods of cell isolation are incapable of providing sufficient cell numbers of these short-lived cells; their propensity for premature activation further complicates their cell engineering. Here, we review current and future biotherapeutic innovations that employ engineered multipotent myeloid progenitors derived from either self-renewing human induced pluripotent stem cells (hiPSC) or primary CD34+hematopoietic stem-progenitors. We provide a roadmap for solving the challenges of sourcing, cost, and production of engineered myeloid cell therapies.
Pfs230 Domain 7 is targeted by a potent malaria transmission-blocking monoclonal antibody
Authors: Inklaar Maartje R. , de Jong Roos M. , Bekkering Ezra T. , Nagaoka Hikaru , Fennemann Felix L. , Teelen Karina , van de Vegte-Bolmer Marga , van Gemert Geert-Jan , Stoter Rianne , King C. Richter , Proellochs Nicholas I. , Bousema Teun , Takashima Eizo , Tsuboi Takafumi , Jore Matthijs M. 
Published: December 2023

AbstractMalaria transmission-blocking vaccines (TBVs) aim to induce antibodies that block Plasmodium parasite development in the mosquito midgut, thus preventing mosquitoes from becoming infectious. While the Pro-domain and first of fourteen 6-Cysteine domains (Pro-D1) of the Plasmodium gamete surface protein Pfs230 are known targets of transmission-blocking antibodies, no studies to date have discovered other Pfs230 domains that are functional targets. Here, we show that a murine monoclonal antibody (mAb), 18F25.1, targets Pfs230 Domain 7. We generated a subclass-switched complement-fixing variant, mAb 18F25.2a, using a CRISPR/Cas9-based hybridoma engineering method. This subclass-switched mAb 18F25.2a induced lysis of female gametes in vitro. Importantly, mAb 18F25.2a potently reduced P. falciparum infection of Anopheles stephensi mosquitoes in a complement-dependent manner, as assessed by standard membrane feeding assays. Together, our data identify Pfs230 Domain 7 as target for transmission-blocking antibodies and provide a strong incentive to study domains outside Pfs230Pro-D1 as TBV candidates.