bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal Equations of State of Magnesite: Implication for the Complex Mid‐Lower Mantle Seismic Scatterers
Authors: Yu Yingxin , Sun Ningyu , Mao Zhu , Li Luo , Prakapenka Vitali B. , Lin Jung‐Fu 
Published: February 2024

AbstractMagnesite (MgCO3) entering the lower mantle together with the subducted oceanic crust is an important carbon carrier. The reaction between magnesite and mantle minerals has been documented, but its influence on the density and velocity profiles of lower mantle remains unexplored. To decipher the deep carbon transportation and its associated effect, here we determined the thermal equations of state of magnesite up to 120 GPa and 2600 K using X‐ray diffraction in laser‐heated diamond anvil cells. The obtained thermal elastic parameters of magnesite facilitated a comprehensive understanding on the influence of magnesite‐SiO2 reaction, variation of carbon and SiO2 content, and temperature on the origin of lower‐mantle scatterers at 1,000–1,800 km depth. Our modeling revealed that the depth of the lower‐mantle VS scatterers is mainly controlled by the Al2O3 content in SiO2, while its magnitude depends on the SiO2 content. Along normal geotherm, the magnesite‐SiO2 reaction would occur before the post‐stishovite transition, consuming substantial SiO2 in the subducted oceanic crust. Depending on the amount of residual SiO2, the post‐stishovite transition can produce a 2.5–5.2 (2)% VS reduction, compatible with the observed seismic scatterers in Izu‐Bonin and Mariana subduction zones. Along slab geotherm, this reaction occurs after the post‐stishovite transition, generating a greater VS reduction of 4.4–6.4 (4)%. We thus propose that the reaction between sinking MgCO3 and SiO2 in the slab is one of the potential factors influencing the magnitude of the lower‐Vs scatterers at 1,000–1,900 km depth. Our results provide new insights into the deep‐mantle carbonate transportation influencing regional geophysics.
Regulation of autophagy by perilysosomal calcium: a new player in β-cell lipotoxicity
Authors: Nguyen Ha Thu , Wiederkehr Andreas , Wollheim Claes B. , Park Kyu-Sang 
Published: February 2024

AbstractAutophagy is an essential quality control mechanism for maintaining organellar functions in eukaryotic cells. Defective autophagy in pancreatic beta cells has been shown to be involved in the progression of diabetes through impaired insulin secretion under glucolipotoxic stress. The underlying mechanism reveals the pathologic role of the hyperactivation of mechanistic target of rapamycin (mTOR), which inhibits lysosomal biogenesis and autophagic processes. Moreover, accumulating evidence suggests that oxidative stress induces Ca2+ depletion in the endoplasmic reticulum (ER) and cytosolic Ca2+ overload, which may contribute to mTOR activation in perilysosomal microdomains, leading to autophagic defects and β-cell failure due to lipotoxicity. This review delineates the antagonistic regulation of autophagic flux by mTOR and AMP-dependent protein kinase (AMPK) at the lysosomal membrane, and both of these molecules could be activated by perilysosomal calcium signaling. However, aberrant and persistent Ca2+ elevation upon lipotoxic stress increases mTOR activity and suppresses autophagy. Therefore, normalization of autophagy is an attractive therapeutic strategy for patients with β-cell failure and diabetes.
Motion of charged particles in bright squeezed vacuum
Authors: Even Tzur Matan , Cohen Oren 
Published: February 2024

AbstractThe motion of laser-driven electrons quivers with an average energy termed pondermotive energy. We explore electron dynamics driven by bright squeezed vacuum (BSV), finding that BSV induces width oscillations, akin to electron quivering in laser light, with an equivalent ponderomotive energy. We identify closed and open trajectories of the electronic width that are associated with high harmonic generation and above-threshold ionization, respectively, similarly to trajectories of the electron position when its motion is driven by coherent light. In the case of bound electrons, the width oscillations may lead to ionization with noisy sub-cycle structure. Our results are foundational for strong-field and free-electron quantum optics, as they shed light on ionization, high harmonic generation, and nonlinear Compton scattering in BSV.
Pivotal role of IL-8 derived from the interaction between osteosarcoma and tumor-associated macrophages in osteosarcoma growth and metastasis via the FAK pathway
Authors: Tatsuno Rikito , Ichikawa Jiro , Komohara Yoshihiro , Pan Cheng , Kawasaki Tomonori , Enomoto Atsushi , Aoki Kaoru , Hayakawa Keiko , Iwata Shintaro , Jubashi Takahiro , Haro Hirotaka 
Published: February 2024

AbstractThe prognosis of osteosarcoma (OS) has remained stagnant over the past two decades, requiring the exploration of new therapeutic targets. Cytokines, arising from tumor-associated macrophages (TAMs), a major component of the tumor microenvironment (TME), have garnered attention owing to their impact on tumor growth, invasion, metastasis, and resistance to chemotherapy. Nonetheless, the precise functional role of TAMs in OS progression requires further investigation. In this study, we investigated the interaction between OS and TAMs, as well as the contribution of TAM-produced cytokines to OS advancement. TAMs were observed to be more prevalent in lung metastases compared with that in primary tumors, suggesting their potential support for OS progression. To simulate the TME, OS and TAMs were co-cultured, and the cytokines resulting from this co-culture could stimulate OS proliferation, migration, and invasion. A detailed investigation of cytokines in the co-culture conditioned medium (CM) revealed a substantial increase in IL-8, establishing it as a pivotal cytokine in the process of enhancing OS proliferation, migration, and invasion through the focal adhesion kinase (FAK) pathway. In an in vivo model, co-culture CM promoted OS proliferation and lung metastasis, effects that were mitigated by anti-IL-8 antibodies. Collectively, IL-8, generated within the TME formed by OS and TAMs, accelerates OS proliferation and metastasis via the FAK pathway, thereby positioning IL-8 as a potential novel therapeutic target in OS.
Roles of exosomes in immunotherapy for solid cancers
Authors: Lyu Cong , Sun Haifeng , Sun Zhenqiang , Liu Yang , Wang Qiming 
Published: February 2024

AbstractAlthough immunotherapy has made breakthrough progress, its efficacy in solid tumours remains unsatisfactory. Exosomes are the main type of extracellular vesicles that can deliver various intracellular molecules to adjacent or distant cells and organs, mediating various biological functions. Studies have found that exosomes can both activate the immune system and inhibit the immune system. The antigen and major histocompatibility complex (MHC) carried in exosomes make it possible to develop them as anticancer vaccines. Exosomes derived from blood, urine, saliva and cerebrospinal fluid can be used as ideal biomarkers in cancer diagnosis and prognosis. In recent years, exosome-based therapy has made great progress in the fields of drug transportation and immunotherapy. Here, we review the composition and sources of exosomes in the solid cancer immune microenvironment and further elaborate on the potential mechanisms and pathways by which exosomes influence immunotherapy for solid cancers. Moreover, we summarize the potential clinical application prospects of engineered exosomes and exosome vaccines in immunotherapy for solid cancers. Eventually, these findings may open up avenues for determining the potential of exosomes for diagnosis, treatment, and prognosis in solid cancer immunotherapy.
Environment geometry alters subiculum boundary vector cell receptive fields in adulthood and early development
Authors: Muessig Laurenz , Ribeiro Rodrigues Fabio , Bjerknes Tale L. , Towse Benjamin W. , Barry Caswell , Burgess Neil , Moser Edvard I. , Moser May-Britt , Cacucci Francesca , Wills Thomas J. 
Published: February 2024

AbstractBoundaries to movement form a specific class of landmark information used for navigation: Boundary Vector Cells (BVCs) are neurons which encode an animal’s location as a vector displacement from boundaries. Here we characterise the prevalence and spatial tuning of subiculum BVCs in adult and developing male rats, and investigate the relationship between BVC spatial firing and boundary geometry. BVC directional tunings align with environment walls in squares, but are uniformly distributed in circles, demonstrating that environmental geometry alters BVC receptive fields. Inserted barriers uncover both excitatory and inhibitory components to BVC receptive fields, demonstrating that inhibitory inputs contribute to BVC field formation. During post-natal development, subiculum BVCs mature slowly, contrasting with the earlier maturation of boundary-responsive cells in upstream Entorhinal Cortex. However, Subiculum and Entorhinal BVC receptive fields are altered by boundary geometry as early as tested, suggesting this is an inherent feature of the hippocampal representation of space.
The chromatin-associated lncREST ensures effective replication stress response by promoting the assembly of fork signaling factors
Authors: Statello Luisa , Fernandez-Justel José Miguel , González Jovanna , Montes Marta , Ranieri Alessia , Goñi Enrique , Mas Aina M. , Huarte Maite 
Published: February 2024

ABSTRACTBesides the well-characterized protein network involved in the replication stress response, several regulatory RNAs have been shown to play a role in this critical process. However, it has remained elusive whether they act locally at the stressed forks. Here, by investigating the RNAs localizing on chromatin upon replication stress induced by hydroxyurea, we identified a set of lncRNAs upregulated in S-phase and controlled by stress transcription factors. Among them, we demonstrate that the previously uncharacterized lncRNA lncREST (long non-coding RNA REplication STress) is transcriptionally controlled by p53 and localizes at stressed replication forks. LncREST-depleted cells experience sustained replication fork progression and accumulate un-signaled DNA damage. Under replication stress, lncREST interacts with the protein NCL and assists in engaging its interaction with RPA. The loss of lncREST is associated with a reduced NCL-RPA interaction and decreased RPA on chromatin, leading to defective replication stress signaling and accumulation of mitotic defects, resulting in apoptosis and a reduction in tumorigenic potential of cancer cells. These findings uncover the function of a lncRNA in favoring the recruitment of replication proteins to sites of DNA replication.
Tissue-specific profiling of age-dependent miRNAomic changes in Caenorhabditis elegans
Authors: Wang Xueqing , Jiang Quanlong , Zhang Hongdao , He Zhidong , Song Yuanyuan , Chen Yifan , Tang Na , Zhou Yifei , Li Yiping , Antebi Adam , Wu Ligang , Han Jing-Dong J. , Shen Yidong 
Published: February 2024

AbstractAgeing exhibits common and distinct features in various tissues, making it critical to decipher the tissue-specific ageing mechanisms. MiRNAs are essential regulators in ageing and are recently highlighted as a class of intercellular messengers. However, little is known about the tissue-specific transcriptomic changes of miRNAs during ageing. C. elegans is a well-established model organism in ageing research. Here, we profile the age-dependent miRNAomic changes in five isolated worm tissues. Besides the diverse ageing-regulated miRNA expression across tissues, we discover numerous miRNAs in the tissues without their transcription. We further profile miRNAs in the extracellular vesicles and find that worm miRNAs undergo inter-tissue trafficking via these vesicles in an age-dependent manner. Using these datasets, we uncover the interaction between body wall muscle-derived mir-1 and DAF-16/FOXO in the intestine, suggesting mir-1 as a messenger in inter-tissue signalling. Taken together, we systematically investigate worm miRNAs in the somatic tissues and extracellular vesicles during ageing, providing a valuable resource to study tissue-autonomous and nonautonomous functions of miRNAs in ageing.
Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos
Authors: Kiyomitsu Ai , Nishimura Toshiya , Hwang Shiang Jyi , Ansai Satoshi , Kanemaki Masato T. , Tanaka Minoru , Kiyomitsu Tomomi 
Published: February 2024

AbstractDespite drastic cellular changes during cleavage, a mitotic spindle assembles in each blastomere to accurately segregate duplicated chromosomes. Mechanisms of mitotic spindle assembly have been extensively studied using small somatic cells. However, mechanisms of spindle assembly in large vertebrate embryos remain little understood. Here, we establish functional assay systems in medaka (Oryzias latipes) embryos by combining CRISPR knock-in with auxin-inducible degron technology. Live imaging reveals several unexpected features of microtubule organization and centrosome positioning that achieve rapid, accurate cleavage. Importantly, Ran-GTP assembles a dense microtubule network at the metaphase spindle center that is essential for chromosome segregation in early embryos. This unique spindle structure is remodeled into a typical short, somatic-like spindle after blastula stages, when Ran-GTP becomes dispensable for chromosome segregation. We propose that despite the presence of centrosomes, the chromosome-derived Ran-GTP pathway has essential roles in functional spindle assembly in large, rapidly dividing vertebrate early embryos, similar to acentrosomal spindle assembly in oocytes.
Clocked dynamics in artificial spin ice
Authors: Jensen Johannes H. , Strømberg Anders , Breivik Ida , Penty Arthur , Niño Miguel Angel , Khaliq Muhammad Waqas , Foerster Michael , Tufte Gunnar , Folven Erik 
Published: February 2024

AbstractArtificial spin ice (ASI) are nanomagnetic metamaterials with a wide range of emergent properties. Through local interactions, the magnetization of the nanomagnets self-organize into extended magnetic domains. However, controlling when, where and how domains change has proven difficult, yet is crucial for technological applications. Here, we introduce astroid clocking, which offers significant control of ASI dynamics in both time and space. Astroid clocking unlocks a discrete, step-wise and gradual dynamical process within the metamaterial. Notably, our method employs global fields to selectively manipulate local features within the ASI. Sequences of these clock fields drive domain dynamics. We demonstrate, experimentally and in simulations, how astroid clocking of pinwheel ASI enables ferromagnetic domains to be gradually grown or reversed at will. Richer dynamics arise when the clock protocol allows both growth and reversal to occur simultaneously. With astroid clocking, complex spatio-temporal behaviors of magnetic metamaterials become easily controllable with high fidelity.
Mechanical forces across compartments coordinate cell shape and fate transitions to generate tissue architecture
Authors: Villeneuve Clémentine , Hashmi Ali , Ylivinkka Irene , Lawson-Keister Elizabeth , Miroshnikova Yekaterina A. , Pérez-González Carlos , Myllymäki Satu-Marja , Bertillot Fabien , Yadav Bhagwan , Zhang Tao , Matic Vignjevic Danijela , Mikkola Marja L. , Manning M. Lisa , Wickström Sara A. 
Published: February 2024

AbstractMorphogenesis and cell state transitions must be coordinated in time and space to produce a functional tissue. An excellent paradigm to understand the coupling of these processes is mammalian hair follicle development, which is initiated by the formation of an epithelial invagination—termed placode—that coincides with the emergence of a designated hair follicle stem cell population. The mechanisms directing the deformation of the epithelium, cell state transitions and physical compartmentalization of the placode are unknown. Here we identify a key role for coordinated mechanical forces stemming from contractile, proliferative and proteolytic activities across the epithelial and mesenchymal compartments in generating the placode structure. A ring of fibroblast cells gradually wraps around the placode cells to generate centripetal contractile forces, which, in collaboration with polarized epithelial myosin activity, promote elongation and local tissue thickening. These mechanical stresses further enhance compartmentalization of Sox9 expression to promote stem cell positioning. Subsequently, proteolytic remodelling locally softens the basement membrane to facilitate a release of pressure on the placode, enabling localized cell divisions, tissue fluidification and epithelial invagination into the underlying mesenchyme. Together, our experiments and modelling identify dynamic cell shape transformations and tissue-scale mechanical cooperation as key factors for orchestrating organ formation.
An fMRI Dataset on Social Reward Processing and Decision Making in Younger and Older Adults
Authors: Smith David V. , Ludwig Rita M. , Dennison Jeffrey B. , Reeck Crystal , Fareri Dominic S. 
Published: February 2024

AbstractBehavioural and neuroimaging research has shown that older adults are less sensitive to financial losses compared to younger adults. Yet relatively less is known about age-related differences in social decisions and social reward processing. As part of a pilot study, we collected behavioural and functional magnetic resonance imaging (fMRI) data from 50 participants (Younger: N = 26, ages 18–34 years; Older: N = 24, ages 63–80 years) who completed three tasks in the scanner: an economic trust game as the investor with three partners (computer, stranger, friend) as the investee; a card-guessing task with monetary gains and losses shared with three partners (computer, stranger, friend); and an ultimatum game as responder to three anonymous proposers (computer, age-similar adults, age-dissimilar adults). We also collected B0 field maps and high-resolution structural images (T1-weighted and T2-weighted images). These data could be reused to answer questions about moment-to-moment variability in fMRI signal, representational similarity between tasks, and brain structure.
Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition
Authors: Sánchez Pablo , Coutinho Felipe H. , Sebastián Marta , Pernice Massimo C. , Rodríguez-Martínez Raquel , Salazar Guillem , Cornejo-Castillo Francisco Miguel , Pesant Stéphane , López-Alforja Xabier , López-García Ester María , Agustí Susana , Gojobori Takashi , Logares Ramiro , Sala Maria Montserrat , Vaqué Dolors , Massana Ramon , Duarte Carlos M. , Acinas Silvia G. , Gasol Josep M. 
Published: February 2024

AbstractThe Ocean microbiome has a crucial role in Earth’s biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2–3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome.
DEBBIES Dataset to study Life Histories across Ectotherms
Authors: Smallegange Isabel M. , Lucas Sol 
Published: February 2024

AbstractDemographic models are used to explore how life history traits structure life history strategies across species. This study presents the DEBBIES dataset that contains estimates of eight life history traits (length at birth, puberty and maximum length, maximum reproduction rate, fraction energy allocated to respiration versus reproduction, von Bertalanffy growth rate, mortality rates) for 185 ectotherm species. The dataset can be used to parameterise dynamic energy budget integral projection models (DEB-IPMs) to calculate key demographic quantities like population growth rate and demographic resilience, but also link to conservation status or biogeographical characteristics. Our technical validation shows a satisfactory agreement between observed and predicted longevity, generation time, age at maturity across all species. Compared to existing datasets, DEBBIES accommodates (i) easy cross-taxonomical comparisons, (ii) many data-deficient species, and (iii) population forecasts to novel conditions because DEB-IPMs include a mechanistic description of the trade-off between growth and reproduction. This dataset has the potential for biologists to unlock general predictions on ectotherm population responses from only a few key life history traits.
Survey of selected viral agents (herpesvirus, adenovirus and hepatitis E virus) in liver and lung samples of cetaceans, Brazil
Authors: Sacristán C. , Ewbank A. C. , Duarte-Benvenuto A. , Sacristán I. , Zamana-Ramblas R. , Costa-Silva S. , Lanes Ribeiro V. , Bertozzi C. P. , del Rio do Valle R. , Castilho P. V. , Colosio A. C. , Marcondes M. C. C. , Lailson-Brito J. , de Freitas Azevedo A. , Carvalho V. L. , Pessi C. F. , Cremer M. , Esperón F. , Catão-Dias J. L. 
Published: February 2024

AbstractHepatic and pulmonary lesions are common in cetaceans, despite their poorly understood viral etiology. Herpesviruses (HV), adenoviruses (AdV) and hepatitis E virus (HEV) are emerging agents in cetaceans, associated with liver and/or pulmonary damage in mammals. We isolated and molecularly tested DNA for HV and AdV (n = 218 individuals; 187 liver and 108 lung samples) and RNA for HEV (n = 147 animals; 147 liver samples) from six cetacean families. All animals stranded or were bycaught in Brazil between 2001 and 2021. Positive-animals were analyzed by histopathology. Statistical analyses assessed if the prevalence of viral infection could be associated with the variables: species, family, habitat, region, sex, and age group. All samples were negative for AdV and HEV. Overall, 8.7% (19/218) of the cetaceans were HV-positive (4.8% [9/187] liver and 11.1% [12/108] lung), without HV-associated lesions. HV-prevalence was statistically significant higher in Pontoporiidae (19.2%, 10/52) when compared to Delphinidae (4.1%, 5/121), and in southeastern (17.1%, 13/76)—the most industrialized Brazilian region—when compared to the northeastern region (2.4%, 3/126). This study broadens the herpesvirus host range in cetaceans, including its description in pygmy sperm whales (Kogia breviceps) and humpback whales (Megaptera novaeangliae). Further studies must elucidate herpesvirus drivers in cetaceans.