bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling Warm Rain With an Eddy Diffusivity/Mass Flux Parameterization: 1. Model Description and Validation
Authors: Suselj Kay , Smalley Mark , Lebsock Matthew D. , Kurowski Marcin J. , Witte Mikael K. , Teixeira Joao 
Published: July 2022

AbstractA new version of the stochastic multiplume Jet Propulsion Laboratory Eddy‐Diffusivity/Mass‐Flux (JPL‐EDMF) parameterization which consistently couples the simplified Khairoutdinov and Kogan (2000), https://doi.org/10.1175/1520-0493(2000)128<0229:ANCPPI>2.0.CO;2, warm phase cloud microphysical parameterization with the parameterization of cloud macrophysical and subgrid scale dynamical processes is described. The new parameterization combines the EDMF approach with an assumed shape of a joint probability density function of thermodynamic and kinematic variables which provide the basis for the computation of all parameterized processes. As far as we are aware this is the first attempt to consistently couple all of these parameterized processes in the EDMF framework. This paper is part one of a two paper series. Here, the JPL‐EDMF parameterization is described and benchmark simulations of precipitating stratocumulus and cumulus convection are performed in a single‐column‐model framework. The parameterization results compare favorably to the reference large‐eddy‐simulation results. In the second part (Smalley et al., 2022, https://doi.org/10.1029/2021MS002729) the JPL‐EDMF parameterization is validated for a wide range of observation‐based scenarios covering the continuous transition from subtropical stratocumulus to cumulus convection derived from global reanalysis, and parameterization uncertainties are studied in detail.
Analytical Expressions of Drainable and Fillable Porosity for Layered Soils Under Shallow Groundwater Environments
Authors: Xiao Xue , Xu Xu , Huang Guanhua 
Published: July 2022

AbstractThis study presents the analytical expressions of drainable and fillable porosity for layered soils under shallow groundwater environments. The expressions of drainable porosity λd and fillable porosity λf for two‐layered soils are first derived with water table depth change ∆d→0 under dynamic soil moisture conditions. The expressions of λd and λf consider the dynamic soil moisture conditions through the assumption of vertical fluxes in the unsaturated zone, varying as functions of water table elevation h. The analytical expressions of λd and λf have the same formula form but different values under evapotranspiration and recharge conditions, which is also verified using the numerical calculation. The case comparisons indicate that the vertical distribution of soil layers and the fluxes have significant effects on the performance of λd and λf. Our proposed expressions could effectively characterize the effects of soil layering and vertical fluxes on λd and λf. They could improve the accuracy of the previous expressions for single‐layer soils, and complement the lack of description for layered soils under dynamic soil moisture conditions in previous expressions. Furthermore, under the hydrostatic assumption (static equilibrium of soil water pressure distribution) in the unsaturated zone, the expressions of drainable porosity λd* and fillable porosity λf* for two‐layered soils with large water table fluctuations are derived based on λd and λf (asterisks in λd* and λf* is to distinguish them from λd and λf derived based on ∆d→0). Verification with drainage experimental data indicates that the proposed expressions can be extended to well capture the λd* and λf* changes for two‐layered soils. Application scenarios suggest that our analytical expressions of drainable and fillable porosity are useful to improve the application performance of related subsurface modeling and groundwater estimation for layered soils under shallow water table environments.
Dissolved Iron Patterns Impacted by Shallow Hydrothermal Sources Along a Transect Through the Tonga‐Kermadec Arc
Authors: Tilliette C. , Taillandier V. , Bouruet‐Aubertot P. , Grima N. , Maes C. , Montanes M. , Sarthou G. , Vorrath M.‐E. , Arnone V. , Bressac M. , González‐Santana D. , Gazeau F. , Guieu C. 
Published: July 2022

AbstractIn the Western Tropical South Pacific, a hotspot of dinitrogen‐fixing organisms has been identified. The survival of these species depends on the availability of dissolved iron (DFe); however, the source of this DFe is still unclear. DFe was measured along a transect from 175°E to 166°W near 19–21°S. The distribution of DFe showed high spatial variability: low concentrations (∼0.2 nmol kg−1) in the South Pacific gyre and high concentrations (up to 50 nmol kg−1) in the west of the Tonga arc, indicating that this arc is a clear boundary between iron‐poor and iron‐rich waters. An optimal multiparameter analysis was used to distinguish the relative importance of physical transport relative to non‐conservative processes on the observed distribution. This analysis demonstrated that the shallow hydrothermal sources present along the Tonga‐Kermadec arc are responsible for the high concentrations observed in the photic layer. Nevertheless, in contrast to what has been observed for deep hydrothermal plumes, our results highlighted the rapid decrease in DFe concentrations near shallow hydrothermal sources. This is likely due to a shorter residence time of surface water masses combined with several biogeochemical processes at play (precipitation, scavenging, biological uptake, and photoreduction). This study clearly highlights the role of shallow hydrothermal sources on the DFe cycle within the Tonga‐Kermadec arc where a strong link to biological activity in surface waters can be assessed, despite the small but significant fraction of DFe ultimately stabilized. It also emphasizes the need to consider the impact of these sources for a better understanding of the global iron cycle.
Kindlin-2 loss in condylar chondrocytes causes spontaneous osteoarthritic lesions in the temporomandibular joint in mice
Authors: Lai Yumei , Zheng Wei , Qu Minghao , Xiao Christopher C. , Chen Sheng , Yao Qing , Gong Weiyuan , Tao Chu , Yan Qinnan , Zhang Peijun , Wu Xiaohao , Xiao Guozhi 
Published: July 2022

AbstractThe progressive destruction of condylar cartilage is a hallmark of the temporomandibular joint (TMJ) osteoarthritis (OA); however, its mechanism is incompletely understood. Here, we show that Kindlin-2, a key focal adhesion protein, is strongly detected in cells of mandibular condylar cartilage in mice. We find that genetic ablation of Kindlin-2 in aggrecan-expressing condylar chondrocytes induces multiple spontaneous osteoarthritic lesions, including progressive cartilage loss and deformation, surface fissures, and ectopic cartilage and bone formation in TMJ. Kindlin-2 loss significantly downregulates the expression of aggrecan, Col2a1 and Proteoglycan 4 (Prg4), all anabolic extracellular matrix proteins, and promotes catabolic metabolism in TMJ cartilage by inducing expression of Runx2 and Mmp13 in condylar chondrocytes. Kindlin-2 loss decreases TMJ chondrocyte proliferation in condylar cartilages. Furthermore, Kindlin-2 loss promotes the release of cytochrome c as well as caspase 3 activation, and accelerates chondrocyte apoptosis in vitro and TMJ. Collectively, these findings reveal a crucial role of Kindlin-2 in condylar chondrocytes to maintain TMJ homeostasis.
Thermally-curable nanocomposite printing for the scalable manufacturing of dielectric metasurfaces
Authors: Kim Wonjoong , Yoon Gwanho , Kim Joohoon , Jeong Heonyeong , Kim Yeseul , Choi Hojung , Badloe Trevon , Rho Junsuk , Lee Heon 
Published: July 2022

AbstractMetasurfaces consisting of artificially designed meta-atoms have been popularized recently due to their advantages of amplitude and phase of light control. However, the electron beam lithography method for metasurface fabrication has high cost and low throughput, which results in a limitation for the fabrication of metasurfaces. In this study, nanocomposite printing technology is used to fabricate high-efficiency metasurfaces with low cost. To demonstrate the efficiency of the proposed fabrication method, a metahologram is designed and fabricated using a nanocomposite. The metahologram exhibits conversion efficiencies of 48% and 35% at wavelengths of 532 and 635 nm, respectively. The nanocomposite is composed of polymers with nanoparticles, so durability tests are also performed to evaluate the effects of temperature and humidity on the metasurfaces. The test verifies that at temperatures below the glass transition temperature of the base resin, the nanostructures do not collapse, so the efficiency of the metasurfaces remains almost the same. The surrounding humidity does not affect the nanostructures at all. Hence, the durability of the nanocomposite metasurfaces can be further enhanced by replacing the base resin, and this nanocomposite printing method will facilitate practical metasurface use at low cost.
Ets1 mediates sorafenib resistance by regulating mitochondrial ROS pathway in hepatocellular carcinoma
Authors: Vishnoi Kanchan , Ke Rong , Viswakarma Navin , Srivastava Piush , Kumar Sandeep , Das Subhasis , Singh Sunil Kumar , Principe Daniel R. , Rana Ajay , Rana Basabi 
Published: July 2022

AbstractThe incidence and mortality of hepatocellular carcinoma (HCC) are on a rise in the Western countries including US, attributed mostly to late detection. Sorafenib has been the first-line FDA-approved drug for advanced unresectable HCC for almost a decade, but with limited efficacy due to the development of resistance. More recently, several other multi-kinase inhibitors (lenvatinib, cabozantinib, regorafenib), human monoclonal antibody (ramucirumab), and immune checkpoint inhibitors (nivolumab, pembrolizumab) have been approved as systemic therapies. Despite this, the median survival of patients is not significantly increased. Understanding of the molecular mechanism(s) that govern HCC resistance is critically needed to increase efficacy of current drugs and to develop more efficacious ones in the future. Our studies with sorafenib-resistant (soraR) HCC cells using transcription factor RT2 Profiler PCR Arrays revealed an increase in E26 transformation–specific-1 (Ets-1) transcription factor in all soraR cells. HCC TMA studies showed an increase in Ets-1 expression in advanced HCC compared to the normal livers. Overexpression or knocking down Ets-1 modulated sorafenib resistance-related epithelial–mesenchymal transition (EMT), migration, and cell survival. In addition, the soraR cells showed a significant reduction of mitochondrial damage and mitochondrial reactive oxygen species (mROS) generation, which were antagonized by knocking down Ets-1 expression. More in-depth analysis identified GPX-2 as a downstream mediator of Ets-1-induced sorafenib resistance, which was down-regulated by Ets-1 knockdown while other antioxidant pathway genes were not affected. Interestingly, knocking down GPX2 expression significantly increased sorafenib sensitivity in the soraR cells. Our studies indicate the activation of a novel Ets-1–GPX2 signaling axis in soraR cells, targeting which might successfully antagonize resistance and increase efficacy.
Microbial autotrophic biorefineries: Perspectives for biopolymer production
Authors: Srisawat Pisanee , Higuchi-Takeuchi Mieko , Numata Keiji 
Published: July 2022

AbstractThe use of autotrophic microorganisms to fabricate biochemical products has attracted much attention in both academia and industry. Unlike heterotrophic microorganisms that require carbohydrates and amino acids for growth, autotrophic microorganisms have evolved to utilize either light (photoautotrophs) or chemical compounds (chemolithotrophs) to fix carbon dioxide (CO2) and drive metabolic processes. Several biotechnological approaches, including synthetic biology and metabolic engineering, have been proposed to harness autotrophic microorganisms as a sustainable/green production platform for commercially essential products such as biofuels, commodity chemicals, and biopolymers. Here, we review the recent advances in natural autotrophic microorganisms (photoautotrophic and chemoautotrophic), focusing on the biopolymer production. We present current state-of-the-art technologies to engineer autotrophic microbial cell factories for efficient biopolymer production.
A-site cation influence on the conduction band of lead bromide perovskites
Authors: Man Gabriel J. , Kamal Chinnathambi , Kalinko Aleksandr , Phuyal Dibya , Acharya Joydev , Mukherjee Soham , Nayak Pabitra K. , Rensmo Håkan , Odelius Michael , Butorin Sergei M. 
Published: July 2022

AbstractHot carrier solar cells hold promise for exceeding the Shockley-Queisser limit. Slow hot carrier cooling is one of the most intriguing properties of lead halide perovskites and distinguishes this class of materials from competing materials used in solar cells. Here we use the element selectivity of high-resolution X-ray spectroscopy and density functional theory to uncover a previously hidden feature in the conduction band states, the σ-π energy splitting, and find that it is strongly influenced by the strength of electronic coupling between the A-cation and bromide-lead sublattice. Our finding provides an alternative mechanism to the commonly discussed polaronic screening and hot phonon bottleneck carrier cooling mechanisms. Our work emphasizes the optoelectronic role of the A-cation, provides a comprehensive view of A-cation effects in the crystal and electronic structures, and outlines a broadly applicable spectroscopic approach for assessing the impact of chemical alterations of the A-cation on perovskite electronic structure.
Accelerated western European heatwave trends linked to more-persistent double jets over Eurasia
Authors: Rousi Efi , Kornhuber Kai , Beobide-Arsuaga Goratz , Luo Fei , Coumou Dim 
Published: July 2022

AbstractPersistent heat extremes can have severe impacts on ecosystems and societies, including excess mortality, wildfires, and harvest failures. Here we identify Europe as a heatwave hotspot, exhibiting upward trends that are three-to-four times faster compared to the rest of the northern midlatitudes over the past 42 years. This accelerated trend is linked to atmospheric dynamical changes via an increase in the frequency and persistence of double jet stream states over Eurasia. We find that double jet occurrences are particularly important for western European heatwaves, explaining up to 35% of temperature variability. The upward trend in the persistence of double jet events explains almost all of the accelerated heatwave trend in western Europe, and about 30% of it over the extended European region. Those findings provide evidence that in addition to thermodynamical drivers, atmospheric dynamical changes have contributed to the increased rate of European heatwaves, with implications for risk management and potential adaptation strategies.
Neutralization capacity of antibodies elicited through homologous or heterologous infection or vaccination against SARS-CoV-2 VOCs
Authors: Bekliz Meriem , Adea Kenneth , Vetter Pauline , Eberhardt Christiane S. , Hosszu-Fellous Krisztina , Vu Diem-Lan , Puhach Olha , Essaidi-Laziosi Manel , Waldvogel-Abramowski Sophie , Stephan Caroline , L’Huillier Arnaud G. , Siegrist Claire-Anne , Didierlaurent Arnaud M. , Kaiser Laurent , Meyer Benjamin , Eckerle Isabella 
Published: July 2022

AbstractEmerging SARS-CoV-2 variants raise questions about escape from previous immunity. As the population immunity to SARS-CoV-2 has become more complex due to prior infections with different variants, vaccinations or the combination of both, understanding the antigenic relationship between variants is needed. Here, we have assessed neutralizing capacity of 120 blood specimens from convalescent individuals infected with ancestral SARS-CoV-2, Alpha, Beta, Gamma or Delta, double vaccinated individuals and patients after breakthrough infections with Delta or Omicron-BA.1. Neutralization against seven authentic SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta and Omicron-BA.1) determined by plaque-reduction neutralization assay allowed us to map the antigenic relationship of SARS-CoV-2 variants. Highest neutralization titers were observed against the homologous variant. Antigenic cartography identified Zeta and Omicron-BA.1 as separate antigenic clusters. Substantial immune escape in vaccinated individuals was detected for Omicron-BA.1 but not Zeta. Combined infection/vaccination derived immunity results in less Omicron-BA.1 immune escape. Last, breakthrough infections with Omicron-BA.1 lead to broadly neutralizing sera.
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm
Authors: Blanco-Cabra Núria , Movellan Julie , Marradi Marco , Gracia Raquel , Salvador Cristian , Dupin Damien , Loinaz Iraida , Torrents Eduard 
Published: July 2022

AbstractThe extracellular matrix protects biofilm cells by reducing diffusion of antimicrobials. Tobramycin is an antibiotic used extensively to treatP. aeruginosabiofilms, but it is sequestered in the biofilm periphery by the extracellular negative charge matrix and loses its efficacy significantly. Dispersal of the biofilm extracellular matrix with enzymes such as DNase I is another promising therapy that enhances antibiotic diffusion into the biofilm. Here, we combine the charge neutralization of tobramycin provided by dextran-based single-chain polymer nanoparticles (SCPNs) together with DNase I to break the biofilm matrix. Our study demonstrates that the SCPNs improve the activity of tobramycin and DNase I by neutralizing the ionic interactions that keep this antibiotic in the biofilm periphery. Moreover, the detailed effects and interactions of nanoformulations with extracellular matrix components were revealed through time-lapse imaging of theP. aeruginosabiofilms by laser scanning confocal microscopy with specific labeling of the different biofilm components.
A multiplex implantable microdevice assay identifies synergistic combinations of cancer immunotherapies and conventional drugs
Authors: Tatarova Zuzana , Blumberg Dylan C. , Korkola James E. , Heiser Laura M. , Muschler John L. , Schedin Pepper J. , Ahn Sebastian W. , Mills Gordon B. , Coussens Lisa M. , Jonas Oliver , Gray Joe W. 
Published: July 2022

AbstractSystematically identifying synergistic combinations of targeted agents and immunotherapies for cancer treatments remains difficult. In this study, we integrated high-throughput and high-content techniques—an implantable microdevice to administer multiple drugs into different sites in tumors at nanodoses and multiplexed imaging of tumor microenvironmental states—to investigate the tumor cell and immunological response signatures to different treatment regimens. Using a mouse model of breast cancer, we identified effective combinations from among numerous agents within days. In vivo studies in three immunocompetent mammary carcinoma models demonstrated that the predicted combinations synergistically increased therapeutic efficacy. We identified at least five promising treatment strategies, of which the panobinostat, venetoclax and anti-CD40 triple therapy was the most effective in inducing complete tumor remission across models. Successful drug combinations increased spatial association of cancer stem cells with dendritic cells during immunogenic cell death, suggesting this as an important mechanism of action in long-term breast cancer control.
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
Authors: Baranasic Damir , Hörtenhuber Matthias , Balwierz Piotr J. , Zehnder Tobias , Mukarram Abdul Kadir , Nepal Chirag , Várnai Csilla , Hadzhiev Yavor , Jimenez-Gonzalez Ada , Li Nan , Wragg Joseph , D’Orazio Fabio M. , Relic Dorde , Pachkov Mikhail , Díaz Noelia , Hernández-Rodríguez Benjamín , Chen Zelin , Stoiber Marcus , Dong Michaël , Stevens Irene , Ross Samuel E. , Eagle Anne , Martin Ryan , Obasaju Oluwapelumi , Rastegar Sepand , McGarvey Alison C. , Kopp Wolfgang , Chambers Emily , Wang Dennis , Kim Hyejeong R. , Acemel Rafael D. , Naranjo Silvia , Łapiński Maciej , Chong Vanessa , Mathavan Sinnakaruppan , Peers Bernard , Sauka-Spengler Tatjana , Vingron Martin , Carninci Piero , Ohler Uwe , Lacadie Scott Allen , Burgess Shawn M. , Winata Cecilia , van Eeden Freek , Vaquerizas Juan M. , Gómez-Skarmeta José Luis , Onichtchouk Daria , Brown Ben James , Bogdanovic Ozren , van Nimwegen Erik , Westerfield Monte , Wardle Fiona C. , Daub Carsten O. , Lenhard Boris , Müller Ferenc 
Published: July 2022

AbstractZebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects
Authors: Robertson Neil A. , Latorre-Crespo Eric , Terradas-Terradas Maria , Lemos-Portela Jorge , Purcell Alison C. , Livesey Benjamin J. , Hillary Robert F. , Murphy Lee , Fawkes Angie , MacGillivray Louise , Copland Mhairi , Marioni Riccardo E. , Marsh Joseph A. , Harris Sarah E. , Cox Simon R. , Deary Ian J. , Schumacher Linus J. , Kirschner Kristina , Chandra Tamir 
Published: July 2022

AbstractClonal hematopoiesis of indeterminate potential (CHIP) increases rapidly in prevalence beyond age 60 and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in hematopoietic stem and progenitor cells (HSPCs). Because mutations in HSPCs often drive leukemia, we hypothesized that HSPC fitness substantially contributes to transformation from CHIP to leukemia. HSPC fitness is defined as the proliferative advantage over cells carrying no or only neutral mutations. If mutations in different genes lead to distinct fitness advantages, this could enable patient stratification. We quantified the fitness effects of mutations over 12 years in older age using longitudinal sequencing and developed a filtering method that considers individual mutational context alongside mutation co-occurrence to quantify the growth potential of variants within individuals. We found that gene-specific fitness differences can outweigh inter-individual variation and, therefore, could form the basis for personalized clinical management.