bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Improved 3D Numerical Ray‐Tracing Method for Solving the Spitze Effects Based on Poeverlein's Diagram
Authors: Song Huan , Qing Haiyin , Xu Jiyao 
Published: January 2024

AbstractThe Spitze phenomenon is closely related to the Earth's magnetic field, and characterizes high‐frequency (HF) rays propagating in the ionosphere. Specifically, when the reflection conditions are satisfied, HF rays are reflected perpendicular to the Earth's magnetic field. Studying the HF rays reflected from the Spitze region is important to indirectly learn about the ionosphere magnetic properties. The 3D numerical ray‐tracing method is a widely used HF rays inversion technique. However, the conventional 3D Haselegrove numerical ray‐tracing method can not trace the ordinary rays in the Spitze region back to the ground. Therefore, we improved the conventional ray‐tracing method based on Poeverlein's diagram. The improved method can change the ordinary rays' propagation directions when they travel very close to the Spitze reflection point. In this way, the ordinary rays' propagation interruption caused by the Spitze can be eliminated. An example showing the ordinary and extraordinary rays traced by the conventional and improved ray‐tracing methods under the quiet ionosphere is provided to validate the improvement. In addition, three disturbed ionospheric backgrounds with large‐scale, medium‐scale, and small‐scale TIDs are designed to simulate various HF rays for further validation. The simulation results show that the Spitze exists in the quiet and disturbed ionosphere, and the improved ray‐tracing method can properly solve the Spitze effects on the traced ordinary rays.
Premature Deaths Due To Heat Exposure: The Potential Effects of Neighborhood‐Level Versus City‐Level Acclimatization Within US Cities
Authors: Shindell D. , Hunter R. , Faluvegi G. , Parsons L. 
Published: January 2024

AbstractFor the population of a given US city, the risk of premature death associated with heat exposure increases as temperatures rise, but risks in hotter cities are generally lower than in cooler cities at equivalent temperatures due to factors such as acclimatization. Those living in especially hot neighborhoods within cities might therefore suffer much more than average if such adaptation is only at the city‐wide level, whereas they might not experience greatly increased risk if adjustment is at the neighborhood level. To compare these possibilities, we use high spatial resolution temperature data to evaluated heat‐related deaths assuming either adjustment at the city‐wide or at the neighborhood scale in 10 large US cities. On average, we find that if inhabitants are adjusted to their local conditions, a neighborhood that was 10°C hotter than a cooler one would experience only about 1.0–1.5 excess heat deaths per year per 100,000 persons. By contrast, if inhabitants are acclimatized to city‐wide temperatures, the hotter neighborhood would experience about 15 excess deaths per year per 100,000 persons. Using idealized analyses, we demonstrate that current city‐wide epidemiological data do not differentiate between these differing adjustments. Given the very large effects of assumptions about neighborhood‐level acclimatization found here, as well as the fact that current literature is conflicting on the spatial scale of acclimatization, more neighborhood‐level epidemiological data are urgently needed to determine the health impacts of variations in heat exposure within urban areas, better constrain projected changes, and inform mitigation efforts.
Unraveling the Tectonic History of the Tharsis Rise on Mars: Plume Migration and Critical Taper Dome
Authors: Karagoz Oguzcan , Kenkmann Thomas , Hergarten Stefan 
Published: January 2024

AbstractWrinkle ridges are widespread tectonic landforms that serve as paleo‐strain and paleo‐stress indicators of the compressional history and thermal evolution of Mars. To reconstruct the center of the Tharsis rise and its migration with time, we mapped wrinkle ridges in the periphery of the dome and analyzed 34,741 wrinkle ridge segments with a total length of 77,294 km. We determined the deviation of each wrinkle ridge segment from a concentric strike direction for systematically changing centers. A fitting procedure indicates that all wrinkle ridge segments can be allocated with good precision to five different stress centers (C1‐5) within the Tharsis rise: the southern edge of the Alba Mons caldera (C1), Ceraunius Fossae (C2), between Ulysses Patera and Pavonis Chasma (C3), Phoenicis Lacus (C4), and Claritas Rupes (C5). We performed a morphometric analysis of each wrinkle ridge and calculated the amount of shortening and depth of detachment, making use of methods for constructing balanced cross‐sections. The amount of horizontal shortening varies from 1.5 to 3.8 km and the range of the detachment depth was found to be between 2.9 and 8.8 km, with significant variance forming an acute wedge of 1.2°–2.2°. Based on the critical taper theory, we inferred a very low basal friction coefficient ranging from 0.077 to 0.093 across the detachments for the five centers (C1–C5). Our findings suggest that these detachments are either localized along salt or clay layers or occur where liquid water is dominant below an impermeable permafrost layer.
Detecting Paleoclimate Transitions With Laplacian Eigenmaps of Recurrence Matrices (LERM)
Authors: James Alexander , Emile‐Geay Julien , Malik Nishant , Khider Deborah 
Published: January 2024

AbstractPaleoclimate records can be considered low‐dimensional projections of the climate system that generated them. Understanding what these projections tell us about past climates, and changes in their dynamics, is a main goal of time series analysis on such records. Laplacian eigenmaps of recurrence matrices (LERM) is a novel technique using univariate paleoclimate time series data to indicate when notable shifts in dynamics have occurred. LERM leverages time delay embedding to construct a manifold that is mappable to the attractor of the climate system; this manifold can then be analyzed for significant dynamical transitions. Through numerical experiments with observed and synthetic data, LERM is applied to detect both gradual and abrupt regime transitions. Our paragon for gradual transitions is the Mid‐Pleistocene Transition (MPT). We show that LERM can robustly detect gradual MPT‐like transitions for sufficiently high signal‐to‐noise (S/N) ratios, though with a time lag related to the embedding process. Our paragon of abrupt transitions is the “8.2 ka” event; we find that LERM is generally robust at detecting 8.2 ka‐like transitions for sufficiently high S/N ratios, though edge effects become more influential. We conclude that LERM can usefully detect dynamical transitions in paleogeoscientific time series, with the caveat that false positive rates are high when dynamical transitions are not present, suggesting the importance of using multiple records to confirm the robustness of transitions. We share an open‐source Python package to facilitate the use of LERM in paleoclimatology and paleoceanography.
Hypoxia induces mitochondrial protein lactylation to limit oxidative phosphorylation
Authors: Mao Yunzi , Zhang Jiaojiao , Zhou Qian , He Xiadi , Zheng Zhifang , Wei Yun , Zhou Kaiqiang , Lin Yan , Yu Haowen , Zhang Haihui , Zhou Yineng , Lin Pengcheng , Wu Baixing , Yuan Yiyuan , Zhao Jianyuan , Xu Wei , Zhao Shimin 
Published: January 2024

AbstractOxidative phosphorylation (OXPHOS) consumes oxygen to produce ATP. However, the mechanism that balances OXPHOS activity and intracellular oxygen availability remains elusive. Here, we report that mitochondrial protein lactylation is induced by intracellular hypoxia to constrain OXPHOS. We show that mitochondrial alanyl-tRNA synthetase (AARS2) is a protein lysine lactyltransferase, whose proteasomal degradation is enhanced by proline 377 hydroxylation catalyzed by the oxygen-sensing hydroxylase PHD2. Hypoxia induces AARS2 accumulation to lactylate PDHA1 lysine 336 in the pyruvate dehydrogenase complex and carnitine palmitoyltransferase 2 (CPT2) lysine 457/8, inactivating both enzymes and inhibiting OXPHOS by limiting acetyl-CoA influx from pyruvate and fatty acid oxidation, respectively. PDHA1 and CPT2 lactylation can be reversed by SIRT3 to activate OXPHOS. In mouse muscle cells, lactylation is induced by lactate oxidation-induced intracellular hypoxia during exercise to constrain high-intensity endurance running exhaustion time, which can be increased or decreased by decreasing or increasing lactylation levels, respectively. Our results reveal that mitochondrial protein lactylation integrates intracellular hypoxia and lactate signals to regulate OXPHOS.
Efficient genomics-based ‘end-to-end’ selective tree breeding framework
Authors: El-Kassaby Yousry A. , Cappa Eduardo P. , Chen Charles , Ratcliffe Blaise , Porth Ilga M. 
Published: January 2024

AbstractSince their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method’s superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.
How spin relaxes and dephases in bulk halide perovskites
Authors: Xu Junqing , Li Kejun , Huynh Uyen N. , Fadel Mayada , Huang Jinsong , Sundararaman Ravishankar , Vardeny Valy , Ping Yuan 
Published: January 2024

AbstractSpintronics in halide perovskites has drawn significant attention in recent years, due to their highly tunable spin-orbit fields and intriguing interplay with lattice symmetry. Here, we perform first-principles calculations to determine the spin relaxation time (T1) and ensemble spin dephasing time ($${T}_{2}^{*}$$

T

2

*

) in a prototype halide perovskite, CsPbBr3. To accurately capture spin dephasing in external magnetic fields we determine the Landé g-factor from first principles and take it into account in our calculations. These allow us to predict intrinsic spin lifetimes as an upper bound for experiments, identify the dominant spin relaxation pathways, and evaluate the dependence on temperature, external fields, carrier density, and impurities. We find that the Fröhlich interaction that dominates carrier relaxation contributes negligibly to spin relaxation, consistent with the spin-conserving nature of this interaction. Our theoretical approach may lead to new strategies to optimize spin and carrier transport properties.
Leafhopper salivary vitellogenin mediates virus transmission to plant phloem
Authors: Wang Yanfei , Lu Chengcong , Guo Shude , Guo Yuxin , Wei Taiyun , Chen Qian 
Published: January 2024

AbstractSalivary effectors of piercing-sucking insects can suppress plant defense to promote insect feeding, but it remains largely elusive how they facilitate plant virus transmission. Leafhopper Nephotettix cincticeps transmits important rice reovirus via virus-packaging exosomes released from salivary glands and then entering the rice phloem. Here, we report that intact salivary vitellogenin of N. cincticeps (NcVg) is associated with the GTPase Rab5 of N. cincticeps (NcRab5) for release from salivary glands. In virus-infected salivary glands, NcVg is upregulated and packaged into exosomes mediated by virus-induced NcRab5, subsequently entering the rice phloem. The released NcVg inherently suppresses H2O2 burst of rice plants by interacting with rice glutathione S-transferase F12, an enzyme catalyzing glutathione-dependent oxidation, thus facilitating leafhoppers feeding. When leafhoppers transmit virus, virus-upregulated NcVg thus promotes leafhoppers feeding and enhances viral transmission. Taken together, the findings provide evidence that viruses exploit insect exosomes to deliver virus-hijacked effectors for efficient transmission.
Selective blockade of Cav1.2 (α1C) versus Cav1.3 (α1D) L-type calcium channels by the black mamba toxin calciseptine
Authors: Mesirca Pietro , Chemin Jean , Barrère Christian , Torre Eleonora , Gallot Laura , Monteil Arnaud , Bidaud Isabelle , Diochot Sylvie , Lazdunski Michel , Soong Tuck Wah , Barrère-Lemaire Stéphanie , Mangoni Matteo E. , Nargeot Joël 
Published: January 2024

AbstractL-type voltage-gated calcium channels are involved in multiple physiological functions. Currently available antagonists do not discriminate between L-type channel isoforms. Importantly, no selective blocker is available to dissect the role of L-type isoforms Cav1.2 and Cav1.3 that are concomitantly co-expressed in the heart, neuroendocrine and neuronal cells. Here we show that calciseptine, a snake toxin purified from mamba venom, selectively blocks Cav1.2 -mediated L-type calcium currents (ICaL) at concentrations leaving Cav1.3-mediated ICaL unaffected in both native cardiac myocytes and HEK-293T cells expressing recombinant Cav1.2 and Cav1.3 channels. Functionally, calciseptine potently inhibits cardiac contraction without altering the pacemaker activity in sino-atrial node cells, underscoring differential roles of Cav1.2− and Cav1.3 in cardiac contractility and automaticity. In summary, calciseptine is a selective L-type Cav1.2 Ca2+ channel blocker and should be a valuable tool to dissect the role of these L-channel isoforms.
Midbrain node for context-specific vocalisation in fish
Authors: Schuppe Eric R. , Ballagh Irene , Akbari Najva , Fang Wenxuan , Perelmuter Jonathan T. , Radtke Caleb H. , Marchaterre Margaret A. , Bass Andrew H. 
Published: January 2024

AbstractVocalizations communicate information indicative of behavioural state across divergent social contexts. Yet, how brain regions actively pattern the acoustic features of context-specific vocal signals remains largely unexplored. The midbrain periaqueductal gray (PAG) is a major site for initiating vocalization among mammals, including primates. We show that PAG neurons in a highly vocal fish species (Porichthys notatus) are activated in distinct patterns during agonistic versus courtship calling by males, with few co-activated during a non-vocal behaviour, foraging. Pharmacological manipulations within vocally active PAG, but not hindbrain, sites evoke vocal network output to sonic muscles matching the temporal features of courtship and agonistic calls, showing that a balance of inhibitory and excitatory dynamics is likely necessary for patterning different call types. Collectively, these findings support the hypothesis that vocal species of fish and mammals share functionally comparable PAG nodes that in some species can influence the acoustic structure of social context-specific vocal signals.
Derivation of human primordial germ cell-like cells in an embryonic-like culture
Authors: Esfahani Sajedeh Nasr , Zheng Yi , Arabpour Auriana , Irizarry Agnes M. Resto , Kobayashi Norio , Xue Xufeng , Shao Yue , Zhao Cheng , Agranonik Nicole L. , Sparrow Megan , Hunt Timothy J. , Faith Jared , Lara Mary Jasmine , Wu Qiu Ya , Silber Sherman , Petropoulos Sophie , Yang Ran , Chien Kenneth R. , Clark Amander T. , Fu Jianping 
Published: January 2024

AbstractPrimordial germ cells (PGCs) are the embryonic precursors of sperm and eggs. They transmit genetic and epigenetic information across generations. Given the prominent role of germline defects in diseases such as infertility, detailed understanding of human PGC (hPGC) development has important implications in reproductive medicine and studying human evolution. Yet, hPGC specification remains an elusive process. Here, we report the induction of hPGC-like cells (hPGCLCs) in a bioengineered human pluripotent stem cell (hPSC) culture that mimics peri-implantation human development. In this culture, amniotic ectoderm-like cells (AMLCs), derived from hPSCs, induce hPGCLC specification from hPSCs through paracrine signaling downstream of ISL1. Our data further show functional roles of NODAL, WNT, and BMP signaling in hPGCLC induction. hPGCLCs are successfully derived from eight non-obstructive azoospermia (NOA) participant-derived hPSC lines using this biomimetic platform, demonstrating its promise for screening applications.
Metallopolymer strategy to explore hypoxic active narrow-bandgap photosensitizers for effective cancer photodynamic therapy
Authors: Zhang Zhao , Wei Zixiang , Guo Jintong , Lyu Jinxiao , Wang Bingzhe , Wang Gang , Wang Chunfei , Zhou Liqiang , Yuan Zhen , Xing Guichuan , Wu Changfeng , Zhang Xuanjun 
Published: January 2024

AbstractPractical photodynamic therapy calls for high-performance, less O2-dependent, long-wavelength-light-activated photosensitizers to suit the hypoxic tumor microenvironment. Iridium-based photosensitizers exhibit excellent photocatalytic performance, but the in vivo applications are hindered by conventional O2-dependent Type-II photochemistry and poor absorption. Here we show a general metallopolymerization strategy for engineering iridium complexes exhibiting Type-I photochemistry and enhancing absorption intensity in the blue to near-infrared region. Reactive oxygen species generation of metallopolymer Ir-P1, where the iridium atom is covalently coupled to the polymer backbone, is over 80 times higher than that of its mother polymer without iridium under 680 nm irradiation. This strategy also works effectively when the iridium atom is directly included (Ir-P2) in the polymer backbones, exhibiting wide generality. The metallopolymer nanoparticles exhibiting efficient O2•− generation are conjugated with integrin αvβ3 binding cRGD to achieve targeted photodynamic therapy.
A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand
Authors: Power Jean F. , Carere Carlo R. , Welford Holly E. , Hudson Daniel T. , Lee Kevin C. , Moreau John W. , Ettema Thijs J. G. , Reysenbach Anna-Louise , Lee Charles K. , Colman Daniel R. , Boyd Eric S. , Morgan Xochitl C. , McDonald Ian R. , Craig Cary S. , Stott Matthew B. 
Published: January 2024

AbstractAllopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
Anomalous temperature dependence of elastic limit in metallic glasses
Authors: Wang Yifan , Liu Jing , Jiang Jian-Zhong , Cai Wei 
Published: January 2024

AbstractUnderstanding the atomistic mechanisms of inelastic deformation in metallic glasses (MGs) remains challenging due to their amorphous structure, where local carriers of plasticity cannot be easily defined. Using molecular dynamics (MD) simulations, we analyzed the onset of inelastic deformation in CuZr MGs, specifically the temperature dependence of the elastic limit, in terms of localized shear transformation (ST) events. We find that although the ST events initiate at lower strain with increasing temperature, the elastic limit increases with temperature in certain temperature ranges. We explain this anomalous behavior through the framework of an energy-strain landscape (ESL) constructed from high-throughput strain-dependent energy barrier calculations for the ST events identified in the MD simulations. The ESL reveals that the anomalous behavior is caused by the transition of ST events from irreversible to reversible with increasing temperature. An analytical formulation is developed to predict this transition and the temperature dependence of the elastic limit.
Mic19 depletion impairs endoplasmic reticulum-mitochondrial contacts and mitochondrial lipid metabolism and triggers liver disease
Authors: Dong Jun , Chen Li , Ye Fei , Tang Junhui , Liu Bing , Lin Jiacheng , Zhou Pang-Hu , Lu Bin , Wu Min , Lu Jia-Hong , He Jing-Jing , Engelender Simone , Meng Qingtao , Song Zhiyin , He He 
Published: January 2024

AbstractEndoplasmic reticulum (ER)-mitochondria contacts are critical for the regulation of lipid transport, synthesis, and metabolism. However, the molecular mechanism and physiological function of endoplasmic reticulum-mitochondrial contacts remain unclear. Here, we show that Mic19, a key subunit of MICOS (mitochondrial contact site and cristae organizing system) complex, regulates ER-mitochondria contacts by the EMC2-SLC25A46-Mic19 axis. Mic19 liver specific knockout (LKO) leads to the reduction of ER-mitochondrial contacts, mitochondrial lipid metabolism disorder, disorganization of mitochondrial cristae and mitochondrial unfolded protein stress response in mouse hepatocytes, impairing liver mitochondrial fatty acid β-oxidation and lipid metabolism, which may spontaneously trigger nonalcoholic steatohepatitis (NASH) and liver fibrosis in mice. Whereas, the re-expression of Mic19 in Mic19 LKO hepatocytes blocks the development of liver disease in mice. In addition, Mic19 overexpression suppresses MCD-induced fatty liver disease. Thus, our findings uncover the EMC2-SLC25A46-Mic19 axis as a pathway regulating ER-mitochondria contacts, and reveal that impairment of ER-mitochondria contacts may be a mechanism associated with the development of NASH and liver fibrosis.