bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Advection on the Three Dimensional Distribution of Turbulent Kinetic Energy and Its Generation in Idealized Tropical Cyclone Simulations
Authors: Wadler Joshua B. , Nolan David. S. , Zhang Jun A. , Shay Lynn K. , Olson Joseph B. , Cione Joseph J. 
Published: May 2023

AbstractThe distribution of turbulent kinetic energy (TKE) and its budget terms is estimated in simulated tropical cyclones (TCs) of various intensities. Each simulated TC is subject to storm motion, wind shear, and oceanic coupling. Different storm intensities are achieved through different ocean profiles in the model initialization. For each oceanic profile, the atmospheric simulations are performed with and without TKE advection. In all simulations, the TKE is maximized at low levels (i.e., below 1 km) and ∼0.5 km radially inward of the azimuthal‐mean radius of maximum wind speed at 1‐km height. As in a previous study, the axisymmetric TKE decreases with height in the eyewall, but more abruptly in simulations without TKE advection. The largest TKE budget terms are shear generation and dissipation, though variability in vertical turbulent transport and buoyancy production affect the change in the azimuthal‐mean TKE distribution. The general relationships between the TKE budget terms are consistent across different radii, regardless of storm intensity. In terms of the asymmetric distribution in the eyewall, TKE is maximized in the front‐left quadrant where the sea surface temperature (SST) is highest and is minimized in the rear‐right quadrant where the SST is the lowest. In the category‐5 simulation, the height of the TKE maximum varies significantly in the eyewall between quadrants and is between ∼400 m in the rear‐right quadrant and ∼1,000 m in the front‐left quadrant. When TKE advection is included in the simulations, the maximum eyewall TKE values are downwind compared to the simulations without TKE advection.
Food, Energy, and Water Production Within Watersheds of the United States
Authors: Ao Yufei Zoe , Bakar Siddik Md Abu , Konar Megan , Marston Landon T. 
Published: May 2023

AbstractThe production of food, electricity, and treated water is often tracked and managed along political or infrastructure boundaries. Yet, water resources, a critical input in the production of these goods, are delineated along natural landscape features (i.e., watersheds). The boundary mismatch between water resources and the associated production of economic goods conceals hydrologic dependencies and vulnerabilities in the provisioning of Food‐Energy‐Water (FEW) resources. In this study, we pair economic, infrastructure, and hydrologic data to evaluate the production of food, electricity, and treated water within watersheds of the conterminous United States. The US FEW sectors produced 950 million tonnes of crops, 3,973 million MWh of electricity, and supplied water to 263 million people in 2017. FEW production consumed 128 km3of blue water (18%) and 583 km3of green water (82%). Watersheds in central and southern California, the Midwest, and the Southwest have the largest FEW blue water consumption and the greatest exposure to water stress. Nearly three‐fifths of FEW production occurs in regularly water‐stressed watersheds. FEW production in watersheds in the Great Plains and Midwest relies heavily on groundwater to buffer against intra‐ and inter‐annual streamflow variability, while surface reservoir storage buffers against water shortages in all watersheds. We show where FEW production may be susceptible to curtailments due to ongoing groundwater depletion or known infrastructure deficiencies. This study adds to our understanding of how a nation's water resources and associated infrastructure support economic activity, as well as areas where economic activity is exposed to hydrological and infrastructure risks.
In Situ Rb/Sr Geochronology and Stable Isotope Geochemistry Evidence for Neoproterozoic and Paleozoic Fracture‐Hosted Fluid Flow and Microbial Activity in Paleoproterozoic Basement, SW Sweden
Authors: Drake Henrik , Tillberg Mikael , Reinhardt Manuel , Whitehouse Martin J. , Kooijman Ellen 
Published: May 2023

AbstractRecent studies have shown that biosignatures of ancient microbial life exist in mineral coatings in deep bedrock fractures of Precambrian cratons, but such surveys have been few and far between. Here, we report results from southwestern Sweden in an area of 1.6–1.5 Ga Paleoproterozoic rocks heavily reworked by the 1.14–0.96 Ga Sveconorwegian orogeny, a terrane previously scarcely explored for ancient microbial biosignatures. Calcite‐pyrite‐adularia‐illite‐coated fractures were analyzed for stable isotopes via Secondary Ion Mass Spectrometry (δ13C, δ18O, δ34S) and in situ Rb/Sr geochronology via Laser‐ablation inductively coupled plasma mass spectrometry. The Rb/Sr ages for calcite‐adularia and calcite‐illite show that several fluid flow events can be discerned (797 ± 18–769 ± 7, 391 ± 5–387 ± 6, 356 ± 5–347 ± 4, and 301 ± 7 Ma). The δ13C, δ18O and 87Sr/86Sr values of different calcite growth zones further confirmed episodic fluid flow. Pyrite δ34S values down to −49.9‰V‐CDT, together with systematically increased δ34S from crystal core to rim, suggest formation following microbial sulfate reduction under semi‐closed conditions. Assemblages involving MSR‐related pyrite generally have Devonian to Permian Rb/Sr ages, indicating an association to extension‐related fracturing and fluid mixing during foreland‐basin formation linked to Caledonian orogeny in the northwest. An assemblage with an age of 301 ± 7 Ma is potentially related to Oslo Rift extension, whereas the Neo‐Proterozoic ages relate to post‐Sveconorwegian extensional tectonics. Remnants of short‐chained fatty acids in the youngest calcite coatings further indicate a biogenic origin, while the absence of organic molecules in older calcite is in line with thermal degradation, potentially related to heating during Caledonian foreland basin burial.
Broadband Strong Ground Motion Modeling Using Planar Dynamic Rupture With Fractal Parameters
Authors: Gallovič F. , Valentová Ľ. 
Published: May 2023

AbstractDynamic rupture modeling represents a promising physics‐based approach to strong ground motion simulations. However, its application in a broad frequency range (0–10 Hz), interesting for engineering studies, is challenging. The main reason is that widely used and relatively simple planar fault models with smooth distributions of initial stress and frictional parameters, or even self‐similar initial stress, result in ground motions depleted in high‐frequency content. Here we propose an efficient approach for the linear slip‐weakening friction model on a planar fault based on the Ide and Aochi (2005,https://doi.org/10.1029/2004jb003591) multiscale model with a small‐scale random fractal distribution of the slip‐weakening distanceDc. We propose a way to combine these variations with a large‐scale deterministic dynamic model. We illustrate the approach on an elliptical model and a smooth model of the 2016Mw6.2 Amatrice, Italy, earthquake from low‐frequency dynamic rupture inversion. To intensify the incoherence of the rupture propagation, we also include a variation of the strength and initial stress, both correlated withDc. These additions result in sustained high‐frequency radiation during the whole rupture propagation and omega‐square source time functions. The new model of the Amatrice earthquake generates synthetics that agree with the local ground motion model up to 5 Hz in terms of spectral accelerations while preserving the average and integral dynamic rupture parameters (e.g., stress drop, fracture and radiated energy). The fractal dynamic model can be easily implemented in any dynamic rupture propagation code and is thus readily applicable in broadband physics‐based ground motion predictions for earthquake scenarios in seismic hazard assessment.
UTX inactivation in germinal center B cells promotes the development of multiple myeloma with extramedullary disease
Authors: Rizq Ola , Mimura Naoya , Oshima Motohiko , Momose Shuji , Takayama Naoya , Itokawa Naoki , Koide Shuhei , Shibamiya Asuka , Miyamoto-Nagai Yurie , Rizk Mohamed , Nakajima-Takagi Yaeko , Aoyama Kazumasa , Wang Changshan , Saraya Atsunori , Ito Ryoji , Seimiya Masanori , Watanabe Mariko , Yamasaki Satoshi , Shibata Tatsuhiro , Yamaguchi Kiyoshi , Furukawa Yoichi , Chiba Tetsuhiro , Sakaida Emiko , Nakaseko Chiaki , Tamaru Jun-ichi , Tai Yu-Tzu , Anderson Kenneth C. , Honda Hiroaki , Iwama Atsushi 
Published: May 2023

AbstractUTX/KDM6A, a histone H3K27 demethylase and a key component of the COMPASS complex, is frequently lost or mutated in cancer; however, its tumor suppressor function remains largely uncharacterized in multiple myeloma (MM). Here, we show that the conditional deletion of the X-linked Utx in germinal center (GC) derived cells collaborates with the activating BrafV600E mutation and promotes induction of lethal GC/post-GC B cell malignancies with MM-like plasma cell neoplasms being the most frequent. Mice that developed MM-like neoplasms showed expansion of clonal plasma cells in the bone marrow and extramedullary organs, serum M proteins, and anemia. Add-back of either wild-type UTX or a series of mutants revealed that cIDR domain, that forms phase-separated liquid condensates, is largely responsible for the catalytic activity-independent tumor suppressor function of UTX in MM cells. Utx loss in concert with BrafV600E only slightly induced MM-like profiles of transcriptome, chromatin accessibility, and H3K27 acetylation, however, it allowed plasma cells to gradually undergo full transformation through activation of transcriptional networks specific to MM that induce high levels of Myc expression. Our results reveal a tumor suppressor function of UTX in MM and implicate its insufficiency in the transcriptional reprogramming of plasma cells in the pathogenesis of MM.
Fragile X Messenger Ribonucleoprotein 1 (FMR1), a novel inhibitor of osteoblast/osteocyte differentiation, regulates bone formation, mass, and strength in young and aged male and female mice
Authors: Deosthale Padmini , Balanta-Melo Julián , Creecy Amy , Liu Chongshan , Marcial Alejandro , Morales Laura , Cridlin Julita , Robertson Sylvia , Okpara Chiebuka , Sanchez David J. , Ayoubi Mahdi , Lugo Joaquín N. , Hernandez Christopher J. , Wallace Joseph M. , Plotkin Lilian I. 
Published: May 2023

AbstractFragile X Messenger Ribonucleoprotein 1 (FMR1) gene mutations lead to fragile X syndrome, cognitive disorders, and, in some individuals, scoliosis and craniofacial abnormalities. Four-month-old (mo) male mice with deletion of theFMR1gene exhibit a mild increase in cortical and cancellous femoral bone mass. However, consequences of absence of FMR1 in bone of young/aged male/female mice and the cellular basis of the skeletal phenotype remain unknown. We found that absence of FMR1 results in improved bone properties with higher bone mineral density in both sexes and in 2- and 9-mo mice. The cancellous bone mass is higher only in females, whereas, cortical bone mass is higher in 2- and 9-mo males, but higher in 2- and lower in 9-mo female FMR1-knockout mice. Furthermore, male bones show higher biomechanical properties at 2mo, and females at both ages. Absence of FMR1 increases osteoblast/mineralization/bone formation and osteocyte dendricity/gene expression in vivo/ex vivo/in vitro, without affecting osteoclasts in vivo/ex vivo. Thus, FMR1 is a novel osteoblast/osteocyte differentiation inhibitor, and its absence leads to age-, site- and sex-dependent higher bone mass/strength.
The EZH2–PRC2–H3K27me3 axis governs the endometrial cell cycle and differentiation for blastocyst invasion
Authors: Fukui Yamato , Hirota Yasushi , Aikawa Shizu , Sakashita Akihiko , Shimizu-Hirota Ryoko , Takeda Norihiko , Ishizawa Chihiro , Iida Rei , Kaku Tetsuaki , Hirata Tomoyuki , Hiraoka Takehiro , Akaeda Shun , Matsuo Mitsunori , Osuga Yutaka 
Published: May 2023

AbstractInfertility occurs in 15% of couples worldwide. Recurrent implantation failure (RIF) is one of the major problems in in vitro fertilization and embryo transfer (IVF–ET) programs, and how to manage patients with RIF to achieve successful pregnancy outcomes remains unresolved. Here, a uterine polycomb repressive complex 2 (PRC2)-regulated gene network was found to control embryo implantation. Our RNA-seq analyses of the human peri-implantation endometrium obtained from patients with RIF and fertile controls revealed that PRC2 components, including its core enzyme enhancer of zeste homolog 2 (EZH2)-catalyzing H3K27 trimethylation (H3K27me3) and their target genes are dysregulated in the RIF group. Although fertility of uterine epithelium-specific knockout mice ofEzh2(eKO mice) was normal,Ezh2-deleted mice in the uterine epithelium and stroma (uKO mice) exhibited severe subfertility, suggesting that stromal Ezh2 plays a key role in female fertility. The RNA-seq and ChIP-seq analyses revealed that H3K27me3-related dynamic gene silencing is canceled, and the gene expression of cell-cycle regulators is dysregulated inEzh2-deleted uteri, causing severe epithelial and stromal differentiation defects and failed embryo invasion. Thus, our findings indicate that the EZH2–PRC2–H3K27me3 axis is critical to preparing the endometrium for the blastocyst invasion into the stroma in mice and humans.
Nuclear softening mediated by Sun2 suppression delays mechanical stress-induced cellular senescence
Authors: Yue Xianlin , Cui Jie , Sun Zewei , Liu Lei , Li Ying , Shao Liwei , Feng Qi , Wang Ziyue , Hambright William S. , Cui Yan , Huard Johnny , Mu Yanling , Mu Xiaodong 
Published: May 2023

AbstractNuclear decoupling and softening are the main cellular mechanisms to resist mechanical stress-induced nuclear/DNA damage, however, its molecular mechanisms remain much unknown. Our recent study of Hutchinson-Gilford progeria syndrome (HGPS) disease revealed the role of nuclear membrane protein Sun2 in mediating nuclear damages and cellular senescence in progeria cells. However, the potential role of Sun2 in mechanical stress-induced nuclear damage and its correlation with nuclear decoupling and softening is still not clear. By applying cyclic mechanical stretch to mesenchymal stromal cells (MSCs) of WT and Zmpset24−/− mice (Z24−/−, a model for HGPS), we observed much increased nuclear damage in Z24−/− MSCs, which also featured elevated Sun2 expression, RhoA activation, F-actin polymerization and nuclear stiffness, indicating the compromised nuclear decoupling capacity. Suppression of Sun2 with siRNA effectively reduced nuclear/DNA damages caused by mechanical stretch, which was mediated by increased nuclear decoupling and softening, and consequently improved nuclear deformability. Our results reveal that Sun2 is greatly involved in mediating mechanical stress-induced nuclear damage by regulating nuclear mechanical properties, and Sun2 suppression can be a novel therapeutic target for treating progeria aging or aging-related diseases.
Tracing the introduction of the invasive common myna using population genomics
Authors: Atsawawaranunt Kamolphat , Ewart Kyle M. , Major Richard E. , Johnson Rebecca N. , Santure Anna W. , Whibley Annabel 
Published: May 2023

AbstractThe common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand’s North Island’s axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.
High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays
Authors: Díaz-Perlas Cristina , Ricken Benjamin , Farrera-Soler Lluc , Guschin Dmitrii , Pojer Florence , Lau Kelvin , Gerhold Christian-Benedikt , Heinis Christian 
Published: May 2023

AbstractCommon inflammatory disorders such as ulcerative colitis and Crohn’s disease are non-invasively diagnosed or monitored by the biomarker calprotectin. However, current quantitative tests for calprotectin are antibody-based and vary depending on the type of antibody and assay used. Additionally, the binding epitopes of applied antibodies are not characterized by structures and for most antibodies it is unclear if they detect calprotectin dimer, tetramer, or both. Herein, we develop calprotectin ligands based on peptides, that offer advantages such as homogenous chemical composition, heat-stability, site-directed immobilization, and chemical synthesis at high purity and at low cost. By screening a 100-billion peptide phage display library against calprotectin, we identified a high-affinity peptide (Kd = 26 ± 3 nM) that binds to a large surface region (951 Å2) as shown by X-ray structure analysis. The peptide uniquely binds the calprotectin tetramer, which enabled robust and sensitive quantification of a defined species of calprotectin by ELISA and lateral flow assays in patient samples, and thus offers an ideal affinity reagent for next-generation inflammatory disease diagnostic assays.
Wood xerogel for fabrication of high-performance transparent wood
Authors: Wang Shennan , Li Lengwan , Zha Li , Koskela Salla , Berglund Lars A. , Zhou Qi 
Published: May 2023

AbstractOptically transparent wood has been fabricated by structure-retaining delignification of wood and subsequent infiltration of thermo- or photocurable polymer resins but still limited by the intrinsic low mesopore volume of the delignified wood. Here we report a facile approach to fabricate strong transparent wood composites using the wood xerogel which allows solvent-free infiltration of resin monomers into the wood cell wall under ambient conditions. The wood xerogel with high specific surface area (260 m2 g–1) and high mesopore volume (0.37 cm3 g–1) is prepared by evaporative drying of delignified wood comprising fibrillated cell walls at ambient pressure. The mesoporous wood xerogel is compressible in the transverse direction and provides precise control of the microstructure, wood volume fraction, and mechanical properties for the transparent wood composites without compromising the optical transmittance. Transparent wood composites of large size and high wood volume fraction (50%) are successfully prepared, demonstrating potential scalability of the method.
Ancient gene linkages support ctenophores as sister to other animals
Authors: Schultz Darrin T. , Haddock Steven H. D. , Bredeson Jessen V. , Green Richard E. , Simakov Oleg , Rokhsar Daniel S. 
Published: May 2023

AbstractA central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits1–6. Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question7–11. Here we develop chromosome-scale gene linkage, also known as synteny, as a phylogenetic character for resolving this question12. We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve as outgroups for phylogenetic analysis. We find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of ctenophores, placing ctenophores as the sister group to all other animals. The patterns of synteny shared by sponges, bilaterians, and cnidarians are the result of rare and irreversible chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These findings provide a new framework for resolving deep, recalcitrant phylogenetic problems and have implications for our understanding of animal evolution.
Structural basis of NINJ1-mediated plasma membrane rupture in cell death
Authors: Degen Morris , Santos José Carlos , Pluhackova Kristyna , Cebrero Gonzalo , Ramos Saray , Jankevicius Gytis , Hartenian Ella , Guillerm Undina , Mari Stefania A. , Kohl Bastian , Müller Daniel J. , Schanda Paul , Maier Timm , Perez Camilo , Sieben Christian , Broz Petr , Hiller Sebastian 
Published: May 2023

AbstractEukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1–7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.