bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Machine Learning Based‐Approach to Predict the Water Content of Mid‐Ocean Ridge Basalts
Authors: Zhou Jingjun , Liu Jia , Xia Qunke , Su Cheng , Kuritani Takeshi , Hanski Eero 
Published: July 2023

AbstractWater is critical in the evolution of the mantle due to its strong influence on the physicochemical properties of mantle rocks. Mid‐ocean ridge basalts (MORBs) are commonly used to study the compositional characteristics of the convecting upper mantle. However, there remains abundant samples in the global MORB data sets without direct measurements of water contents. The commonly observed good correlation between H2O and other incompatible trace components, such as Ce, has been applied to quantify water contents of MORBs. However, this approach assumes constant H2O/Ce in the target samples, which is not always true as the H2O/Ce ratios of MORBs could be rather heterogeneous even in some short ridge segments. Utilizing the present compositional data of global MORB glasses with measured water contents (n = 1,467), we construct a Random Forest Regression model based on machine learning, which can predict water concentrations of samples based on selected major and trace element data, without assuming a ratio between H2O and other trace elements. This model allows us to precisely recover water contents for MORBs with comparable accuracy with traditional analytical methods. The predicted results of MORB glasses from this model (n = 1,931) expand the water content database of global MORBs and indicate a broad existence of high‐H2O MORBs. This new approach allows us to investigate the water content of MORBs from some ridges lacking previous water content measurements (e.g., the Chile Ridge and the Pacific‐Antarctic Ridge) and infer changes in the water content of MORB sources through applying the model to transform fault samples.
Juno's Multi‐Instruments Observations During the Flybys of Auroral Bright Spots in Jupiter's Polar Aurorae
Authors: Haewsantati K. , Bonfond B. , Wannawichian S. , Gladstone G. R. , Hue V. , Greathouse T. K. , Grodent D. , Yao Z. , Gérard J.‐C. , Guo R. , Elliott S. , Mauk B. H. , Clark G. , Gershman D. , Kotsiaros S. , Kurth W. S. , Connerney J. , Szalay J. R. , Phriksee A. 
Published: July 2023

AbstractJuno's arrival at Jupiter in 2016 revealed unprecedented details about Jupiter's ultraviolet aurorae thanks to its unique suite of remote sensing and in situ instruments. Here we present results from in situ observations during Juno flybys above specific bright auroral spots in Jupiter's polar aurora. We compare data observed by Juno‐UVS, JEDI, JADE, Waves, and MAG instruments when Juno was magnetically connected to bright polar auroral spots (or their immediate vicinity) during perijove 3 (PJ3), PJ15, and PJ33. The highly energetic particles observed by JEDI show enhancements dominated by upward electrons, which suggests that the particle acceleration region takes place below the spacecraft. Moreover, brightness and upward particle flux were higher for the northern bright spot in PJ3 than the southern spots found in PJ15 and PJ33. In addition, we notice the intensification of whistler‐mode waves at the time of the particle enhancements, suggesting that wave‐particle interactions contribute to the acceleration of particles that cause the UV aurorae. The MAG data reveal magnetic perturbations during the PJ3 spot detection by Juno, which suggests the presence of significant field‐aligned electric currents. While the stable positions of the bright spots in System III suggest that the phenomenon is fixed to the planet's rotation, the presence of field‐aligned currents leaves the possibility of an origin rooted much farther in the magnetosphere.
Early Formation of a Water Ocean as a Function of Initial CO2 and H2O Contents in a Solidifying Rocky Planet
Authors: Massol H. , Davaille A. , Sarda P. 
Published: July 2023

AbstractWe present a model for the thermal evolution of Magma Ocean (MO) in interaction with a degassing atmosphere of H2O and CO2. The interior model is based on parameterized convection and is coupled to the atmospheric Model of Marcq et al. (2017, https://doi.org/10.1002/2016JE005224) through heat and volatiles. A new equation for the mass balance of volatiles is implemented, correcting Salvador et al. (2017, https://doi.org/10.1002/2017je005286). We found that the domain for water condensation is extended: for instance, depending on the cloud cover and resulting albedo, 0.13 Earth's ocean mass might be sufficient to form a water ocean on early Venus (instead of 0.3 MEO in Salvador et al. (2017, https://doi.org/10.1002/2017je005286)). Comparing our results with other recent models, we discuss the relative influence of the model hypotheses, such as mantle melting curves (which depend on mantle composition), the treatment of the atmosphere (e.g., gray or convective‐radiative) and the treatment of the last stages of the MO solidification (e.g., episodic resurfacing, stagnant lid…). We also apply our results to exoplanets. They suggest that liquid water might be present at the surface of Trappist‐1e and 1f, provided that those planets' volatile primitive contents were dominated by H2O and CO2.
A platform for integrated spectrometers based on solution-processable semiconductors
Authors: Li Yanhao , Jiang Xiong , Chen Yimu , Wang Yuhan , Wu Yunkai , Yu De , Wang Kaiyang , Bai Sai , Xiao Shumin , Song Qinghai 
Published: July 2023

AbstractAcquiring real-time spectral information in point-of-care diagnosis, internet-of-thing, and other lab-on-chip applications require spectrometers with hetero-integration capability and miniaturized feature. Compared to conventional semiconductors integrated by heteroepitaxy, solution-processable semiconductors provide a much-flexible integration platform due to their solution-processability, and, therefore, more suitable for the multi-material integrated system. However, solution-processable semiconductors are usually incompatible with the micro-fabrication processes. This work proposes a facile and universal platform to fabricate integrated spectrometers with semiconductor substitutability by unprecedently involving the conjugated mode of the bound states in the continuum (conjugated-BIC) photonics. Specifically, exploiting the conjugated-BIC photonics, which remains unexplored in conventional lasing studies, renders the broadband photodiodes with ultra-narrowband detection ability, detection wavelength tunability, and on-chip integration ability while ensuring the device performance. Spectrometers based on these ultra-narrowband photodiode arrays exhibit high spectral resolution and wide/tunable spectral bandwidth. The fabrication processes are compatible with solution-processable semiconductors photodiodes like perovskites and quantum dots, which can be potentially extended to conventional semiconductors. Signals from the spectrometers directly constitute the incident spectra without being computation-intensive, latency-sensitive, and error-intolerant. As an example, the integrated spectrometers based on perovskite photodiodes are capable of realizing narrowband/broadband light reconstruction and in-situ hyperspectral imaging.
Numerical investigation of the dynamics of a rigid spherical particle in a vortical cross-slot flow at moderate inertia
Authors: Kechagidis Konstantinos , Owen Benjamin , Guillou Lionel , Tse Henry , Di Carlo Dino , Krüger Timm 
Published: July 2023

AbstractThe study of flow and particle dynamics in microfluidic cross-slot channels is of high relevance for lab-on-a-chip applications. In this work, we investigate the dynamics of a rigid spherical particle in a cross-slot junction for a channel height-to-width ratio of 0.6 and at a Reynolds number of 120 for which a steady vortex exists in the junction area. Using an in-house immersed-boundary-lattice-Boltzmann code, we analyse the effect of the entry position of the particle in the junction and the particle size on the dynamics and trajectory shape of the particle. We find that the dynamics of the particle depend strongly on its lateral entry position in the junction and weakly on its vertical entry position; particles that enter close to the centre show trajectory oscillations. Larger particles have longer residence times in the junction and tend to oscillate less due to their confinement. Our work contributes to the understanding of particle dynamics in intersecting flows and enables the design of optimised geometries for cytometry and particle manipulation.
Interaction between neutrophil extracellular traps and cardiomyocytes contributes to atrial fibrillation progression
Authors: He Li , Liu Ruiqi , Yue Honghua , Zhang Xiaoxin , Pan Xiaohui , Sun Yutao , Shi Jun , Zhu Guonian , Qin Chaoyi , Guo Yingqiang 
Published: July 2023

AbstractAtrial fibrillation (AF) is a frequent arrhythmia associated with cardiovascular morbidity and mortality. Neutrophil extracellular traps (NETs) are DNA fragments with cytoplasm proteins released from neutrophils, which are involved in various cardiovascular diseases. To elucidate the role of NETs in AF, we investigated the effect of NETs on AF progression and the secretion of NETs in AF. Results showed that: NETs induced the autophagic apoptosis of cardiomyocytes, and NETs also led to mitochondrial injury by promoting mitochondrial depolarization and ROS production. Ongoing tachy-pacing led to the structural loss of cardiomyocytes and provided potent stimuli to induce NETs secretion from neutrophils. In the meanwhile, increased Ang II in AF facilitated NETs formation through the upregulation of AKT phosphorylation, while it could not directly initiate NETosis as the autophagy was not induced. In vivo, DNase I was administrated to abrogate NETs formation, and AF-related fibrosis was ameliorated as expected. Correspondingly, the duration of the induced AF was reduced. Our study addresses the formation mechanism of NETs in AF and demonstrates the lethal effects of NETs on cardiomyocytes through the induction of mitochondrial injury and autophagic cell death, which comprehensively describes the positive feedback comprised of NETs and stimuli secreted by cardiomyocytes that sustains the progression of AF and AF related fibrosis.
Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma
Authors: Bintener Tamara , Pacheco Maria Pires , Philippidou Demetra , Margue Christiane , Kishk Ali , Del Mistro Greta , Di Leo Luca , Moscardó Garcia Maria , Halder Rashi , Sinkkonen Lasse , De Zio Daniela , Kreis Stephanie , Kulms Dagmar , Sauter Thomas 
Published: July 2023

AbstractDespite high initial response rates to targeted kinase inhibitors, the majority of patients suffering from metastatic melanoma present with high relapse rates, demanding for alternative therapeutic options. We have previously developed a drug repurposing workflow to identify metabolic drug targets that, if depleted, inhibit the growth of cancer cells without harming healthy tissues. In the current study, we have applied a refined version of the workflow to specifically predict both, common essential genes across various cancer types, and melanoma-specific essential genes that could potentially be used as drug targets for melanoma treatment. The in silico single gene deletion step was adapted to simulate the knock-out of all targets of a drug on an objective function such as growth or energy balance. Based on publicly available, and in-house, large-scale transcriptomic data metabolic models for melanoma were reconstructed enabling the prediction of 28 candidate drugs and estimating their respective efficacy. Twelve highly efficacious drugs with low half-maximal inhibitory concentration values for the treatment of other cancers, which are not yet approved for melanoma treatment, were used for in vitro validation using melanoma cell lines. Combination of the top 4 out of 6 promising candidate drugs with BRAF or MEK inhibitors, partially showed synergistic growth inhibition compared to individual BRAF/MEK inhibition. Hence, the repurposing of drugs may enable an increase in therapeutic options e.g., for non-responders or upon acquired resistance to conventional melanoma treatments.
Cutaneous squamous cell carcinoma-derived extracellular vesicles exert an oncogenic role by activating cancer-associated fibroblasts
Authors: Li Chen , Sun Chengxi , Lohcharoenkal Warangkana , Ali Mohamad Moustafa , Xing Pengwei , Zheng Wenyi , Görgens André , Gustafsson Manuela O. , EL Andaloussi Samir , Sonkoly Enikö , Pivarcsi Andor 
Published: July 2023

AbstractCutaneous squamous cell carcinoma (cSCC) is a fast-increasing cancer with metastatic potential. Extracellular vesicles (EVs) are small membrane-bound vesicles that play important roles in intercellular communication, particularly in the tumor microenvironment (TME). Here we report that cSCC cells secrete an increased number of EVs relative to normal human epidermal keratinocytes (NHEKs) and that interfering with the capacity of cSCC to secrete EVs inhibits tumor growth in vivo in a xenograft model of human cSCC. Transcriptome analysis of tumor xenografts by RNA-sequencing enabling the simultaneous quantification of both the human and the mouse transcripts revealed that impaired EV-production of cSCC cells prominently altered the phenotype of stromal cells, in particular genes related to extracellular matrix (ECM)-formation and epithelial-mesenchymal transition (EMT). In line with these results, co-culturing of human dermal fibroblasts (HDFs) with cSCC cells, but not with normal keratinocytes in vitro resulted in acquisition of cancer-associated fibroblast (CAF) phenotype. Interestingly, EVs derived from metastatic cSCC cells, but not primary cSCCs or NHEKs, were efficient in converting HDFs to CAFs. Multiplex bead-based flow cytometry assay and mass-spectrometry (MS)-based proteomic analyses revealed the heterogenous cargo of cSCC-derived EVs and that especially EVs derived from metastatic cSCCs carry proteins associated with EV-biogenesis, EMT, and cell migration. Mechanistically, EVs from metastatic cSCC cells result in the activation of TGFβ signaling in HDFs. Altogether, our study suggests that cSCC-derived EVs mediate cancer-stroma communication, in particular the conversion of fibroblasts to CAFs, which eventually contribute to cSCC progression.
Nrf2: a dark horse in doxorubicin-induced cardiotoxicity
Authors: Zhao Xiaopeng , Tian Zheng , Sun Mingli , Dong Dan 
Published: July 2023

AbstractBeing a broad-spectrum anticancer drug, doxorubicin is indispensable for clinical treatment. Unexpectedly, its cardiotoxic side effects have proven to be a formidable obstacle. Numerous studies are currently devoted to elucidating the pathological mechanisms underlying doxorubicin-induced cardiotoxicity. Nrf2 has always played a crucial role in oxidative stress, but numerous studies have demonstrated that it also plays a vital part in pathological mechanisms like cell death and inflammation. Numerous studies on the pathological mechanisms associated with doxorubicin-induced cardiotoxicity demonstrate this. Several clinical drugs, natural and synthetic compounds, as well as small molecule RNAs have been demonstrated to prevent doxorubicin-induced cardiotoxicity by activating Nrf2. Consequently, this study emphasizes the introduction of Nrf2, discusses the role of Nrf2 in doxorubicin-induced cardiotoxicity, and concludes with a summary of the therapeutic modalities targeting Nrf2 to ameliorate doxorubicin-induced cardiotoxicity, highlighting the potential value of Nrf2 in doxorubicin-induced cardiotoxicity.
Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease
Authors: Wen Tao , Xie Penghao , Liu Hongwei , Liu Ting , Zhao Mengli , Yang Shengdie , Niu Guoqing , Hale Lauren , Singh Brajesh K. , Kowalchuk George A. , Shen Qirong , Yuan Jun 
Published: July 2023

AbstractPrebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato (Solanum lycopersicum) suffering from wilt disease (caused by Ralstonia solanacearum) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R. solanacearum) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g−1 soil effectively protects tomato and other Solanaceae crops, pepper (Capsicum annuum) and eggplant (Solanum melongena), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.
Virtual alignment of pathology image series for multi-gigapixel whole slide images
Authors: Gatenbee Chandler D. , Baker Ann-Marie , Prabhakaran Sandhya , Swinyard Ottilie , Slebos Robbert J. C. , Mandal Gunjan , Mulholland Eoghan , Andor Noemi , Marusyk Andriy , Leedham Simon , Conejo-Garcia Jose R. , Chung Christine H. , Robertson-Tessi Mark , Graham Trevor A. , Anderson Alexander R. A. 
Published: July 2023

AbstractInterest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and access to technology. An alternative approach is to register collections of whole slide images (WSI), generating spatially aligned datasets. WSI registration is a two-part problem, the first being the alignment itself and the second the application of transformations to huge multi-gigapixel images. To address both challenges, we developed Virtual Alignment of pathoLogy Image Series (VALIS), software which enables generation of highly multiplexed images by aligning any number of brightfield and/or immunofluorescent WSI, the results of which can be saved in the ome.tiff format. Benchmarking using publicly available datasets indicates VALIS provides state-of-the-art accuracy in WSI registration and 3D reconstruction. Leveraging existing open-source software tools, VALIS is written in Python, providing a free, fast, scalable, robust, and easy-to-use pipeline for registering multi-gigapixel WSI, facilitating downstream spatial analyses.
AlphaMat: a material informatics hub connecting data, features, models and applications
Authors: Wang Zhilong , Chen An , Tao Kehao , Cai Junfei , Han Yanqiang , Gao Jing , Ye Simin , Wang Shiwei , Ali Imran , Li Jinjin 
Published: July 2023

AbstractThe development of modern civil industry, energy and information technology is inseparable from the rapid explorations of new materials. However, only a small fraction of materials being experimentally/computationally studied in a vast chemical space. Artificial intelligence (AI) is promising to address this gap, but faces many challenges, such as data scarcity and inaccurate material descriptors. Here, we develop an AI platform, AlphaMat, that can complete data preprocessing and downstream AI models. With high efficiency and accuracy, AlphaMat exhibits strong powers to model typical 12 material attributes (formation energy, band gap, ionic conductivity, magnetism, bulk modulus, etc.). AlphaMat’s capabilities are further demonstrated to discover thousands of new materials for use in specific domains. AlphaMat does not require users to have strong programming experience, and its effective use will facilitate the development of materials informatics, which is of great significance for the implementation of AI for Science (AI4S).
An advanced analytical approach to assess the long-term degradation of microplastics in the marine environment
Authors: Maddison Carbery , Sathish C. I. , Lakshmi Daggubati , Wayne O’Connor , Palanisami Thava 
Published: July 2023

AbstractDetermining the hazards posed by microplastics (MPs, <5 mm) requires an understanding of plastic degradation processes when exposed to environmental weathering forces. However, despite their perceived risks, limited information exists on the natural weathering progression of microplastics in marine environments. Our findings from environmentally realistic conditions reveal that long-term marine weathering resulted in significant degradation of plastic surfaces and bulk-phases, which varied by time and plastic polymer type. Plastics displayed biofouling, and an altered surface morphology, thermal stability and chemical signature. Secondary micronanoplastics (MNPs, <1 µm) were formed from weathered plastic surfaces, supported by a significant reduction in the size of PCL and PVC pellets. Using real world data, we reveal that plastic surfaces can degrade at a rate of up to 469.73 µm per year, 12 times greater than previous estimates. Our time-series data contributes valuable information towards developing plastic specific risk assessment frameworks and future plastics policy.
High-fidelity trapped-ion qubit operations with scalable photonic modulators
Authors: Hogle C. W. , Dominguez D. , Dong M. , Leenheer A. , McGuinness H. J. , Ruzic B. P. , Eichenfield M. , Stick D. 
Published: July 2023

AbstractExperiments with trapped ions and neutral atoms typically employ optical modulators in order to control the phase, frequency, and amplitude of light directed to individual atoms. These elements are expensive, bulky, consume substantial power, and often rely on free-space I/O channels, all of which pose scaling challenges. To support many-ion systems like trapped-ion quantum computers or miniaturized deployable devices like clocks and sensors, these elements must ultimately be microfabricated, ideally monolithically with the trap to avoid losses associated with optical coupling between physically separate components. In this work we design, fabricate, and test an optical modulator capable of monolithic integration with a surface-electrode ion trap. These devices consist of piezo-optomechanical photonic integrated circuits configured as multi-stage Mach-Zehnder modulators that are used to control the intensity of light delivered to a single trapped ion on a separate chip. We use quantum tomography employing hundreds of multi-gate sequences to enhance the sensitivity of the fidelity to the types and magnitudes of gate errors relevant to quantum computing and better characterize the performance of the modulators, ultimately measuring single qubit gate fidelities that exceed 99.7%.