bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesospheric Temperature and Circulation Response to the Hunga Tonga‐Hunga‐Ha'apai Volcanic Eruption
Authors: Yu Wandi , Garcia Rolando , Yue Jia , Smith Anne , Wang Xinyue , Randel William , Qiao Zishun , Zhu Yunqian , Harvey V. Lynn , Tilmes Simone , Mlynczak Martin 
Published: November 2023

AbstractThe Hunga Tonga Hunga‐Ha'apai (HTHH) volcanic eruption on 15 January 2022 injected water vapor and SO2 into the stratosphere. Several months after the eruption, significantly stronger westerlies, and a weaker Brewer‐Dobson circulation developed in the stratosphere of the Southern Hemisphere and were accompanied by unprecedented temperature anomalies in the stratosphere and mesosphere. In August 2022, the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) satellite instrument observed record‐breaking temperature anomalies in the stratosphere and mesosphere that alternate signs with altitude. Ensemble simulations carried out with the Whole Atmosphere Community Climate Model (WACCM6) indicate that the strengthening of the stratospheric westerlies explains the mesospheric temperature changes. The stronger westerlies cause stronger westward gravity wave drag in the mesosphere. Although the enhanced gravity wave drag is partly balanced by a weakening of planetary wave forcing, the net result is an acceleration of the mesospheric mean meridional circulation. The stronger mesospheric circulation, in turn, plays a dominant role in driving the changes in mesospheric temperatures. This study highlights the impact of large volcanic eruptions on middle atmospheric dynamics and provides insight into their long‐term effects in the mesosphere. On the other hand, we could not discern a clear mechanism for the observed changes in stratospheric circulation. In fact, an examination of the WACCM ensemble reveals that not every member reproduces the large changes observed by SABER. We conclude that there is a stochastic component to the stratospheric response to the HTHH eruption.
Spatio‐Temporal Super‐Resolution Data Assimilation (SRDA) Utilizing Deep Neural Networks With Domain Generalization
Authors: Yasuda Yuki , Onishi Ryo 
Published: November 2023

AbstractDeep learning has recently gained attention in the atmospheric and oceanic sciences for its potential to improve the accuracy of numerical simulations or to reduce computational costs. Super‐resolution is one such technique for high‐resolution inference from low‐resolution data. This paper proposes a new scheme, called four‐dimensional super‐resolution data assimilation (4D‐SRDA). This framework calculates the time evolution of a system from low‐resolution simulations using a physics‐based model, while a trained neural network simultaneously performs data assimilation and spatio‐temporal super‐resolution. The use of low‐resolution simulations without ensemble members reduces the computational cost of obtaining inferences at high spatio‐temporal resolution. In 4D‐SRDA, physics‐based simulations and neural‐network inferences are performed alternately, possibly causing a domain shift, that is, a statistical difference between the training and test data, especially in offline training. Domain shifts can reduce the accuracy of inference. To mitigate this risk, we developed super‐resolution mixup (SR‐mixup)–a data augmentation method for domain generalization. SR‐mixup creates a linear combination of randomly sampled inputs, resulting in synthetic data with a different distribution from the original data. The proposed methods were validated using an idealized barotropic ocean jet with supervised learning. The results suggest that the combination of 4D‐SRDA and SR‐mixup is effective for robust inference cycles. This study highlights the potential of super‐resolution and domain‐generalization techniques, in the field of data assimilation, especially for the integration of physics‐based and data‐driven models.
Estimating Plio‐Pleistocene North African Monsoon Runoff Into the Mediterranean Sea and Temperature Impacts
Authors: Heslop D. , Amarathunga U. , Rohling E. J. 
Published: November 2023

AbstractSapropels are dark, organic‐rich layers found in Mediterranean sediments that formed during periods of bottom water anoxia. While various mechanisms have been proposed to have caused anoxic conditions, a primary factor is considered to be water column stratification induced by freshwater runoff related to intensified North African monsoon precipitation during precession minima. Monsoon intensification also induced Green Sahara Periods that may have impacted North African hominin dispersal. In this study, we present a novel regression‐based deconvolution of a high‐resolution planktonic foraminiferal oxygen isotope record to estimate the combination of freshwater runoff reaching the eastern Mediterranean and associated surface warming of the water column over the past 5 million years. Sapropels are known to occur in clusters associated with periods of high orbital eccentricity. Our analysis reveals a consistent influence of orbital eccentricity in modulating the North African monsoon, and a possible shift in runoff source area induced by the initiation of Northern Hemisphere ice sheets. Our findings provide important insights into the role of the North African monsoon in shaping Mediterranean environmental changes over the past 5 million years.
Structural adaptation of fungal cell wall in hypersaline environment
Authors: Fernando Liyanage D. , Pérez-Llano Yordanis , Dickwella Widanage Malitha C. , Jacob Anand , Martínez-Ávila Liliana , Lipton Andrew S. , Gunde-Cimerman Nina , Latgé Jean-Paul , Batista-García Ramón Alberto , Wang Tuo 
Published: November 2023

AbstractHalophilic fungi thrive in hypersaline habitats and face a range of extreme conditions. These fungal species have gained considerable attention due to their potential applications in harsh industrial processes, such as bioremediation and fermentation under unfavorable conditions of hypersalinity, low water activity, and extreme pH. However, the role of the cell wall in surviving these environmental conditions remains unclear. Here we employ solid-state NMR spectroscopy to compare the cell wall architecture of Aspergillus sydowii across salinity gradients. Analyses of intact cells reveal that A. sydowii cell walls contain a rigid core comprising chitin, β-glucan, and chitosan, shielded by a surface shell composed of galactomannan and galactosaminogalactan. When exposed to hypersaline conditions, A. sydowii enhances chitin biosynthesis and incorporates α-glucan to create thick, stiff, and hydrophobic cell walls. Such structural rearrangements enable the fungus to adapt to both hypersaline and salt-deprived conditions, providing a robust mechanism for withstanding external stress. These molecular principles can aid in the optimization of halophilic strains for biotechnology applications.
Daily rhythm in cortical chloride homeostasis underpins functional changes in visual cortex excitability
Authors: Pracucci Enrico , Graham Robert T. , Alberio Laura , Nardi Gabriele , Cozzolino Olga , Pillai Vinoshene , Pasquini Giacomo , Saieva Luciano , Walsh Darren , Landi Silvia , Zhang Jinwei , Trevelyan Andrew J. , Ratto Gian-Michele 
Published: November 2023

AbstractCortical activity patterns are strongly modulated by fast synaptic inhibition mediated through ionotropic, chloride-conducting receptors. Consequently, chloride homeostasis is ideally placed to regulate activity. We therefore investigated the stability of baseline [Cl-]i in adult mouse neocortex, using in vivo two-photon imaging. We found a two-fold increase in baseline [Cl-]i in layer 2/3 pyramidal neurons, from day to night, with marked effects upon both physiological cortical processing and seizure susceptibility. Importantly, the night-time activity can be converted to the day-time pattern by local inhibition of NKCC1, while inhibition of KCC2 converts day-time [Cl-]i towards night-time levels. Changes in the surface expression and phosphorylation of the cation-chloride cotransporters, NKCC1 and KCC2, matched these pharmacological effects. When we extended the dark period by 4 h, mice remained active, but [Cl-]i was modulated as for animals in normal light cycles. Our data thus demonstrate a daily [Cl-]i modulation with complex effects on cortical excitability.
Rational design of a JAK1-selective siRNA inhibitor for the modulation of autoimmunity in the skin
Authors: Tang Qi , Fakih Hassan H. , Zain UI Abideen Mohammad , Hildebrand Samuel R. , Afshari Khashayar , Gross Katherine Y. , Sousa Jacquelyn , Maebius Allison S. , Bartholdy Christina , Søgaard Pia Pernille , Jackerott Malene , Hariharan Vignesh , Summers Ashley , Fan Xueli , Okamura Ken , Monopoli Kathryn R. , Cooper David A. , Echeverria Dimas , Bramato Brianna , McHugh Nicholas , Furgal Raymond C. , Dresser Karen , Winter Sarah J. , Biscans Annabelle , Chuprin Jane , Haddadi Nazgol-Sadat , Sherman Shany , Yıldız-Altay Ümmügülsüm , Rashighi Mehdi , Richmond Jillian M. , Bouix-Peter Claire , Blanchard Carine , Clauss Adam , Alterman Julia F. , Khvorova Anastasia , Harris John E. 
Published: November 2023

AbstractInhibition of Janus kinase (JAK) family enzymes is a popular strategy for treating inflammatory and autoimmune skin diseases. In the clinic, small molecule JAK inhibitors show distinct efficacy and safety profiles, likely reflecting variable selectivity for JAK subtypes. Absolute JAK subtype selectivity has not yet been achieved. Here, we rationally design small interfering RNAs (siRNAs) that offer sequence-specific gene silencing of JAK1, narrowing the spectrum of action on JAK-dependent cytokine signaling to maintain efficacy and improve safety. Our fully chemically modified siRNA supports efficient silencing of JAK1 expression in human skin explant and modulation of JAK1-dependent inflammatory signaling. A single injection into mouse skin enables five weeks of duration of effect. In a mouse model of vitiligo, local administration of the JAK1 siRNA significantly reduces skin infiltration of autoreactive CD8+ T cells and prevents epidermal depigmentation. This work establishes a path toward siRNA treatments as a new class of therapeutic modality for inflammatory and autoimmune skin diseases.
Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination in male mice
Authors: Rowland Megan E. , Jiang Yan , Shafiq Sarfraz , Ghahramani Alireza , Pena-Ortiz Miguel A. , Dumeaux Vanessa , Bérubé Nathalie G. 
Published: November 2023

AbstractMyelin, an extension of the oligodendrocyte plasma membrane, wraps around axons to facilitate nerve conduction. Myelination is compromised in ATR-X intellectual disability syndrome patients, but the causes are unknown. We show that loss ofATRXleads to myelination deficits in male mice that are partially rectified upon systemic thyroxine administration. Targeted ATRX inactivation in either neurons or oligodendrocyte progenitor cells (OPCs) reveals OPC-intrinsic effects on myelination. OPCs lacking ATRX fail to differentiate along the oligodendrocyte lineage and acquire a more plastic state that favors astrocytic differentiation in vitro and in vivo. ATRX chromatin occupancy in OPCs greatly overlaps with that of the chromatin remodelers CHD7 and CHD8 as well as H3K27Ac, a mark of active enhancers. Overall, our data indicate that ATRX regulates the onset of myelination systemically via thyroxine, and by promoting OPC differentiation and suppressing astrogliogenesis. These functions of ATRX identified in mice could explain white matter pathogenesis observed in ATR-X syndrome patients.
Heat current-driven topological spin texture transformations and helical q-vector switching
Authors: Yasin Fehmi Sami , Masell Jan , Karube Kosuke , Shindo Daisuke , Taguchi Yasujiro , Tokura Yoshinori , Yu Xiuzhen 
Published: November 2023

AbstractThe use of magnetic states in memory devices has a history dating back decades, and the experimental discovery of magnetic skyrmions and subsequent demonstrations of their control via magnetic fields, heat, and electric/thermal currents have ushered in a new era for spintronics research and development. Recent studies have experimentally discovered the antiskyrmion, the skyrmion’s antiparticle, and while several host materials have been identified, control via thermal current remains elusive. In this work, we use thermal current to drive the transformation between skyrmions, antiskyrmions and non-topological bubbles, as well as the switching of helical states in the antiskyrmion-hosting ferromagnet (Fe0.63Ni0.3Pd0.07)3P at room temperature. We discover that a temperature gradient $${{{{{\boldsymbol{\nabla }}}}}}T$$
∇
T
drives a transformation from antiskyrmions to non-topological bubbles to skyrmions while under a magnetic field and observe the opposite, unidirectional transformation from skyrmions to antiskyrmions at zero-field, suggesting that the antiskyrmion, more so than the skyrmion, is robustly metastable at zero field.
Nucleophilic aromatization of monoterpenes from isoprene under nickel/iodine cascade catalysis
Authors: Zhang Wei-Song , Ji Ding-Wei , Yang Yang , Song Ting-Ting , Zhang Gong , Wang Xiao-Yu , Chen Qing-An 
Published: November 2023

AbstractAs a large number of organic compounds possessing two isoprene units, monoterpenes and monoterpenoids play important roles in pharmaceutical, cosmetic, agricultural, and food industries. In nature, monoterpenes are constructed from geranyl pyrophosphate (C10) via various transformations. Herein, the bulk C5 chemical—isoprene, is used for the creation of various monoterpenoids via a nucleophilic aromatization of monoterpenes under cascade catalysis of nickel and iodine. Drugs and oil mixtures from conifer and lemon can be convergently transformed to the desired monoterpenoid. Preliminary mechanistic studies are conducted to get insights about reaction pathway. Two types of cyclic monoterpenes can be respectively introduced onto two similar heterocycles via orthogonal C–H functionalization. And various hybrid terpenyl indoles are programmatically assembled from abundant C5 or C10 blocks. This work not only contributes a high chemo-, regio-, and redox-selective transformation of isoprene, but also provides a complementary approach for the creation of unnatural monoterpenoids.
Bioinspired soft robots for deep-sea exploration
Authors: Li Guorui , Wong Tuck-Whye , Shih Benjamin , Guo Chunyu , Wang Luwen , Liu Jiaqi , Wang Tao , Liu Xiaobo , Yan Jiayao , Wu Baosheng , Yu Fajun , Chen Yunsai , Liang Yiming , Xue Yaoting , Wang Chengjun , He Shunping , Wen Li , Tolley Michael T. , Zhang A-Man , Laschi Cecilia , Li Tiefeng 
Published: November 2023

AbstractThe deep ocean, Earth’s untouched expanse, presents immense challenges for exploration due to its extreme pressure, temperature, and darkness. Unlike traditional marine robots that require specialized metallic vessels for protection, deep-sea species thrive without such cumbersome pressure-resistant designs. Their pressure-adaptive forms, unique propulsion methods, and advanced senses have inspired innovation in designing lightweight, compact soft machines. This perspective addresses challenges, recent strides, and design strategies for bioinspired deep-sea soft robots. Drawing from abyssal life, it explores the actuation, sensing, power, and pressure resilience of multifunctional deep-sea soft robots, offering game-changing solutions for profound exploration and operation in harsh conditions.
Tailoring grain boundary stability of zinc-titanium alloy for long-lasting aqueous zinc batteries
Authors: Zhao Yunxiang , Guo Shan , Chen Manjing , Lu Bingan , Zhang Xiaotan , Liang Shuquan , Zhou Jiang 
Published: November 2023

AbstractThe detrimental parasitic reactions and uncontrolled deposition behavior derived from inherently unstable interface have largely impeded the practical application of aqueous zinc batteries. So far, tremendous efforts have been devoted to tailoring interfaces, while stabilization of grain boundaries has received less attention. Here, we demonstrate that preferential distribution of intermetallic compounds at grain boundaries via an alloying strategy can substantially suppress intergranular corrosion. In-depth morphology analysis reveals their thermodynamic stability, ensuring sustainable potency. Furthermore, the hybrid nucleation and growth mode resulting from reduced Gibbs free energy contributes to the spatially uniform distribution of Zn nuclei, promoting the dense Zn deposition. These integrated merits enable a high Zn reversibility of 99.85% for over 4000 cycles, steady charge-discharge at 10 mA cm−2, and impressive cyclability for roughly 3500 cycles in Zn-Ti//NH4V4O10 full cell. Notably, the multi-layer pouch cell of 34 mAh maintains stable cycling for 500 cycles. This work highlights a fundamental understanding of microstructure and motivates the precise tuning of grain boundary characteristics to achieve highly reversible Zn anodes.
IL-21R-STAT3 signalling initiates a differentiation program in uterine tissue-resident NK cells to support pregnancy
Authors: Han Mengwei , Hu Luni , Wu Di , Zhang Yime , Li Peng , Zhao Xingyu , Zeng Yanyu , Ren Guanqun , Hou Zhiyuan , Pang Yanli , Zhao Tongbiao , Zhong Chao 
Published: November 2023

AbstractTissue-resident Natural Killer (trNK) cells are crucial components of local immunity that activate rapidly upon infection. However, under steady state conditions, their responses are tightly controlled to prevent unwanted tissue damage. The mechanisms governing their differentiation and activation are not fully understood. Here, we characterise uterine trNK cells longitudinally during pregnancy by single cell RNA sequencing and find that the combined expression pattern of 4-1BB and CD55 defines their three distinct stages of differentiation in mice. Mechanistically, an IL-21R-STAT3 axis is essential for initiating the trNK cell differentiation. The fully differentiated trNK cells demonstrate enhanced functionality, which is necessary for remodelling spiral arteries in the decidua. We identify an apoptotic program that is specific to the terminal differentiation stage, which may preclude tissue damage by these highly activated trNK cells. In summary, uterine trNK cells become intensely active and effective during pregnancy, but tightly controlled via a differentiation program that also limits potential harm, suggesting an intricate mechanism for harnessing trNK cells in maintaining pregnancy.
Neurodevelopmental disorders and cancer networks share pathways, but differ in mechanisms, signaling strength, and outcome
Authors: Yavuz Bengi Ruken , Arici M. Kaan , Demirel Habibe Cansu , Tsai Chung-Jung , Jang Hyunbum , Nussinov Ruth , Tuncbag Nurcan 
Published: November 2023

AbstractEpidemiological studies suggest that individuals with neurodevelopmental disorders (NDDs) are more prone to develop certain types of cancer. Notably, however, the case statistics can be impacted by late discovery of cancer in individuals afflicted with NDDs, such as intellectual disorders, autism, and schizophrenia, which may bias the numbers. As to NDD-associated mutations, in most cases, they are germline while cancer mutations are sporadic, emerging during life. However, somatic mosaicism can spur NDDs, and cancer-related mutations can be germline. NDDs and cancer share proteins, pathways, and mutations. Here we ask (i) exactly which features they share, and (ii) how, despite their commonalities, they differ in clinical outcomes. To tackle these questions, we employed a statistical framework followed by network analysis. Our thorough exploration of the mutations, reconstructed disease-specific networks, pathways, and transcriptome levels and profiles of autism spectrum disorder (ASD) and cancers, point to signaling strength as the key factor: strong signaling promotes cell proliferation in cancer, and weaker (moderate) signaling impacts differentiation in ASD. Thus, we suggest that signaling strength, not activating mutations, can decide clinical outcome.
Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis
Authors: Wang Yanlin , Wang Yixin , Yang Yujia , Ni Gang , Li Yulong , Chen Muyan 
Published: November 2023

AbstractAsterias amurensis has attracted widespread concern because of its population outbreaks, which has impacted fisheries and aquaculture, as well as disrupting local ecosystems. A high-quality reference genome is necessary to better investigate mechanisms of outbreak and adaptive changes. Combining PacBio HiFi and Hi-C sequencing data, we generated a chromosome-level A. amurensis genome with a size of 491.53 Mb. The contig N50 and scaffold N50 were 8.05 and 23.75 Mb, respectively. The result of BUSCO analysis revealed a completeness score of 98.85%. A total of 16,531 protein-coding genes were predicted in the genome, of which 94.63% were functionally annotated. The high-quality genome assembly resulting from this study will provide a valuable genetic resource for future research on the mechanism of population outbreaks and invasion ecology.
Towards fully automated inner ear analysis with deep-learning-based joint segmentation and landmark detection framework
Authors: Stebani Jannik , Blaimer Martin , Zabler Simon , Neun Tilmann , Pelt Daniël M. , Rak Kristen 
Published: November 2023

AbstractAutomated analysis of the inner ear anatomy in radiological data instead of time-consuming manual assessment is a worthwhile goal that could facilitate preoperative planning and clinical research. We propose a framework encompassing joint semantic segmentation of the inner ear and anatomical landmark detection of helicotrema, oval and round window. A fully automated pipeline with a single, dual-headed volumetric 3D U-Net was implemented, trained and evaluated using manually labeled in-house datasets from cadaveric specimen ($$N=43$$

N
=
43

) and clinical practice ($$N=9$$

N
=
9

). The model robustness was further evaluated on three independent open-source datasets ($$N = 23{} + 7{} + 17$$

N
=
23

+
7

+
17

scans) consisting of cadaveric specimen scans. For the in-house datasets, Dice scores of $$\text{0.97 and 0.94}$$

0.97 and 0.94

, intersection-over-union scores of $$\text{0.94 and 0.89}$$

0.94 and 0.89

and average Hausdorff distances of $$0.065{}$$

0.065

and $$0.14{}$$

0.14

voxel units were achieved. The landmark localization task was performed automatically with an average localization error of $$\text{3.3 and 5.2}$$

3.3 and 5.2

voxel units. A robust, albeit reduced performance could be attained for the catalogue of three open-source datasets. Results of the ablation studies with 43 mono-parametric variations of the basal architecture and training protocol provided task-optimal parameters for both categories. Ablation studies against single-task variants of the basal architecture showed a clear performance benefit of coupling landmark localization with segmentation and a dataset-dependent performance impact on segmentation ability.