bluuebunny/crossref_metadata_2025 huggingface dataset:
Crustal Imaging of Portugal Mainland Using Magnetotelluric Data
Authors: Baltazar‐Soares P. , Martínez‐Moreno F. J. , Alves Ribeiro J. , Monteiro Santos F. A. , Ribeiro P. , Pais M. A. , Mateus A. , Pous J.
Published: July 2023

The comprehensive mapping of resistivities in depth and its interpretation is of great importance to unravel the electrical properties of deep‐seated rocks, providing significant insights into the structure of the crust. The first 3D resistivity model for Portugal mainland is here reported using data from 31 broadband MT soundings spaced 50 × 50 km apart. The model shows large crustal volumes with contrasting resistivity values. The central and northern regions are characterized by a high resistivity crustal domain spreading in‐depth (103–105 Ω.m) that correlates well with voluminous granitoid bodies and high‐grade metamorphic rocks. To the west and the south, roughly corresponding to the Portuguese Western Shore and the South Portuguese Zone (SPZ) respectively, the crustal resistivity tends to decrease unevenly to values between 1 and 103 Ω.m. Interconnected graphite in structural discontinuities, possibly forming a regional mid‐crustal décollement at ≈13–15 km depth, are highlighted by multiple low resistivity crustal domains (1–100 Ω.m). Similarly, the model reveals a very large E‐W low resistivity crustal domain in SPZ possibly representing a deep‐seated major décollement. The present study aims to contribute to a better understanding of the physical properties characterizing the concealed crust in Portugal mainland, providing also indirect information on its composition and structure.
Magnetopause Dynamics at Saturn as Observed by Cassini
Authors: Mo Wenli , Vines Sarah K. , Allen Robert C. , Jackman Caitriona M. , Paranicas Chris
Published: July 2023

The occurrence and impacts of magnetopause processes at outer planets, particularly magnetic reconnection and the Kelvin‐Helmholtz instability (KHI), remains unresolved. From a list of 2,114 magnetopause crossings at Saturn spanning the full duration of the Cassini mission, magnetic field and low‐energy plasma properties are analyzed for each crossing to determine the likelihood of particular dynamical processes at Saturn's magnetopause. Using Cassini magnetic field data, crossings are categorized as (a) those with signatures of possible magnetic reconnection, (b) those near/inside a magnetopause surface wave or vortex arising from KHI, and (c) those during quiescent conditions (i.e., lacking signatures indicative of magnetic reconnection or KH waves). Of magnetopause crossings with valid intervals on both sides of the boundary, nearly half of the crossings met criteria for signatures of reconnection, with little dependence on local time or latitude of the magnetopause crossing location. Crossings identified as associated with KHI are found to more likely occur toward the dawn sector as compared to other local times, but with both flanks likely being quasi‐unstable to the instability. Magnetopause properties for crossings with available low‐energy electron data from Cassini are further explored to provide insight into the local plasma conditions that may be conducive to magnetic reconnection and/or KH waves. This investigation reveals that certain dynamics along the magnetopause of Saturn may be more prevalent than previously considered, and provides a basis for a more comprehensive understanding of magnetopause dynamics and plasma transport at the outer planets.
Comparisons of Raindrop Size Distributions Measured by an Optical Disdrometer and Electrically Charged Raindrops
Authors: Martínez Lucia B. , Pereyra Rodolfo G. , Ávila Eldo E.
Published: July 2023

Raindrop size distributions observed with a particle size velocity disdrometer are contrasted with respect to the size distributions of charged raindrops obtained with a special device designed to determine the size and electric charge of raindrops. The measurements were performed for three thunderstorms occurred in the vicinity of Córdoba, Argentina during RELAMPAGO campaign. In general, the results show that more than 66% of the raindrops measured with the optical disdrometer have diameters <1 mm and more than 90% of the charged raindrops have diameters >1 mm. A systematic difference between both raindrops size distributions was observed, which remains during the whole evolution of the storms. Under the hypothesis that the electrically charged raindrops were melted ice hydrometeors, we analyze if the larger raindrops recorded by the disdrometer during these storms may also have been melted ice particles.
Effects of Bubble Plumes on Lake Dynamics, Near‐Bottom Turbulence, and Transfer of Dissolved Oxygen at the Sediment‐Water Interface
Authors: Wang Binbin , Rezvani Maryam , Bierlein Kevin A. , Bryant Lee D. , Little John C. , Wüest Alfred , Socolofsky Scott A.
Published: July 2023

We quantify the lake dynamics, near‐bottom turbulence, flux of dissolved oxygen (DO) across the sediment‐water interface (SWI) and their interactions during oxygenation in two lakes. Field observations show that the lake dynamics were modified by the bubble plumes, showing enhanced mixing in the near‐field of the plumes. The interaction of the bubble‐induced flow with the internal density structure resulted in downwelling of warm water into the hypolimnion in the far‐field of the plumes. Within the bottom boundary layer (BBL), both lakes show weak oscillating flows primarily induced by seiching. The vertical profile of mean velocity within 0.4 m above the bed follows a logarithmic scaling. One lake shows a larger drag coefficient than those in stationary BBLs, where the classic law‐of‐the‐wall is valid. The injection of oxygen elevated the water column DO and hence, altered the DO flux across the SWI. The gas transfer velocity is driven by turbulence and is correlated with the bottom shear velocity. The thickness of the diffusive boundary layer was found to be consistent with the Batchelor length scale. The dynamics of the surface renewal time follow a log‐normal distribution, and the turbulent integral time scale is comparable to the surface renewal time. The analyses suggest that the effect of bubble plumes on the BBL turbulence is limited and that the canonical scales of turbulence emerge for the time‐average statistics, validating the turbulence scaling of gas transfer velocity in low‐energy lakes.
An Object‐Oriented Bayesian Gravity Inversion Scheme for Inferring Density Anomalies in Planetary Interiors
Authors: Izquierdo Kristel , Lekić Vedran , Montési Laurent G. J.
Published: July 2023

Gravity inversions have contributed greatly to our knowledge of the interior of planetary bodies and the processes that shaped them. However, previous global gravity inversion methods neglect the inference of mantle density anomalies when using techniques to decrease the non‐uniqueness of the inversion. In this work, we present a novel global gravity inversion algorithm, named THeBOOGIe, suited to inferring global‐scale density anomalies within the crust and mantle of planetary bodies. The algorithm embraces the nonuniqueness inherent in gravity inversions by not prescribing at the outset a density interface or depth range of interest. Instead, the method combines a Bayesian approach with a flexible incorporation of prior geological or geophysical information to infer density anomalies at any depth. A validation test using synthetic lunar‐like gravity data shows that THeBOOGIe can constrain the lateral location of crustal density anomalies but tends to overestimate their thicknesses. Importantly, THeBOOGIe can detect deep mantle density anomalies and quantify the level of confidence in the inferred density models. Our results show that THeBOOGIe can provide complementary information to one‐dimensional seismic models of the interior of the terrestrial planets and the Moon by constraining density anomalies that are not spherically symmetric. Additionally, THeBOOGIe is specially suited to constraining the interior of partially differentiated bodies where these large‐scale density anomalies are more likely to exist. Finally, thanks to the flexible use of priors, THeBOOGIe is an essential tool to understand the interior of planetary bodies lacking additional constraints.
Characterizing Peridotite Xenoliths From Southern Vietnam: Insight Into the Underlying Lithospheric Mantle
Authors: Hobbs Kirby P. , Elkins Lynne J. , Lassiter John C. , Hoang Nguyen , Burberry Caroline M.
Published: July 2023

We present data for lithospheric mantle xenoliths sampled from two alkali basalts in south‐central Vietnam, Pleiku and Xuan Loc, including fertile spinel peridotites. To better determine the origins of the Indochinese subcontinental lithospheric mantle (SCLM), including impacts of posited tectonic extrusion, we present major and trace elements, and 87Sr/86Sr, 143Nd/144Nd, 176Hf/177Hf, 206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb in xenolith mineral separates. Most peridotites from Pleiku and Xuan Loc have fertile major element compositions, “depleted” and “spoon‐shaped” rare earth element (REE) patterns, interpreted to record prior melt depletion followed by melt metasomatism, and variable but generally depleted isotopic signatures (e.g., 87Sr/86Sr = 0.70238–0.70337 and 143Nd/144Nd = 0.512921–0.514190). A small group of refractory peridotites have “enriched” REE patterns suggesting more extensive metasomatism and enriched isotope ratios (87Sr/86Sr = 0.70405 and 143Nd/144Nd = 0.512755–0.512800). The presence of both fertile and refractory xenoliths records a heterogeneous SCLM beneath Vietnam. Based on geothermobarometry calculations, fertile xenoliths have equilibrium temperatures of 923–1,034°C and pressures of 11.7–15.8 kbar, while refractory xenoliths have comparable temperatures of 923–1,006°C, but lower pressures of 7.1–10.0 kbar, suggesting refractory rocks are dominantly present at shallower depths. We suggest that the lithospheric mantle has experienced variable melt extraction around 1.0–1.3 Ga, producing heterogeneous major element compositions. While we cannot rule out partial removal and replacement of the lithosphere, large‐scale delamination is not necessary to explain observed characteristics. The entire SCLM was more recently metasomatized by melts resembling Cenozoic basalts, suggesting recent asthenospheric melting has modified the SCLM by melt infiltration.
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

Water 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

Juno'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

We 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

Acquiring 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

The 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

Atrial 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

Despite 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

Cutaneous 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

Being 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

Prebiotics 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

Interest 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

The 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

Determining 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

Experiments 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%.
Giant Dzyaloshinskii-Moriya interaction, strong XXZ-type biquadratic coupling, and bimeronic excitations in the two-dimensional CrMnI6 magnet
Authors: Zhang Shunhong , Li Xiaoyin , Zhang Huisheng , Cui Ping , Xu Xiaohong , Zhang Zhenyu
Published: July 2023

Two-dimensional magnets have been discovered recently as a new class of quantum matter exhibiting a broad wealth of exotic phenomena, including notably various topological excitations rooted in emergent exchange couplings between the localized magnetic moments. By analyzing the anisotropies in the single-ion magnetization and two-body exchange couplings obtained from first-principles calculations, we reveal coexistence of both giant Dzyaloshinskii–Moriya interaction and strong anisotropic XXZ-type biquadratic coupling in a recently predicted monolayer CrMnI6 magnet. The former is induced by the spontaneous in-plane inversion symmetry breaking in the bipartite system, the latter is inherently tied to the distinct high-spin state of the Mn sublattice, while the large magnitudes of both stem from the significant spin-orbit coupling. Next, we use atomistic magnetics simulations to demonstrate the vital role of Dzyaloshinskii–Moriya interaction in harboring topological bimeronic excitations, and show that the biquadratic coupling favors a Berezinskii–Kosterlitz–Thouless-like transition as the system reduces its temperature from the paramagnetic phase. These findings substantially enrich our understanding of the microscopic couplings in 2D magnets, with appealing application potentials.
Global nitrogen deposition inputs to cropland at national scale from 1961 to 2020
Authors: Vishwakarma Srishti , Zhang Xin , Dobermann Achim , Heffer Patrick , Zhou Feng
Published: July 2023

Nitrogen (N) deposition is a significant nutrient input to cropland and consequently important for the evaluation of N budgets and N use efficiency (NUE) at different scales and over time. However, the spatiotemporal coverage of N deposition measurements is limited globally, whereas modeled N deposition values carry uncertainties. Here, we reviewed existing methods and related data sources for quantifying N deposition inputs to crop production on a national scale. We utilized different data sources to estimate N deposition input to crop production at national scale and compared our estimates with 14 N budget datasets, as well as measured N deposition data from observation networks in 9 countries. We created four datasets of N deposition inputs on cropland during 1961–2020 for 236 countries. These products showed good agreement for the majority of countries and can be used in the modeling and assessment of NUE at national and global scales. One of the datasets is recommended for general use in regional to global N budget and NUE estimates.
AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures
Authors: Kleven Heidi , Gillespie Thomas H. , Zehl Lyuba , Dickscheid Timo , Bjaalie Jan G. , Martone Maryann E. , Leergaard Trygve B.
Published: July 2023

Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.
Air-quality prediction based on the ARIMA-CNN-LSTM combination model optimized by dung beetle optimizer
Authors: Duan Jiahui , Gong Yaping , Luo Jun , Zhao Zhiyao
Published: July 2023

Air pollution is a serious problem that affects economic development and people’s health, so an efficient and accurate air quality prediction model would help to manage the air pollution problem. In this paper, we build a combined model to accurately predict the AQI based on real AQI data from four cities. First, we use an ARIMA model to fit the linear part of the data and a CNN-LSTM model to fit the non-linear part of the data to avoid the problem of blinding in the CNN-LSTM hyperparameter setting. Then, to avoid the blinding dilemma in the CNN-LSTM hyperparameter setting, we use the Dung Beetle Optimizer algorithm to find the hyperparameters of the CNN-LSTM model, determine the optimal hyperparameters, and check the accuracy of the model. Finally, we compare the proposed model with nine other widely used models. The experimental results show that the model proposed in this paper outperforms the comparison models in terms of root mean square error (RMSE), mean absolute error (MAE) and coefficient of determination (R2). The RMSE values for the four cities were 7.594, 14.94, 7.841 and 5.496; the MAE values were 5.285, 10.839, 5.12 and 3.77; and the R2 values were 0.989, 0.962, 0.953 and 0.953 respectively.
Histone deacetylase inhibitors inhibit lung adenocarcinoma metastasis via HDAC2/YY1 mediated downregulation of Cdh1
Authors: Wang Dongmei , Yang Yixiao , Cao Yuxiang , Meng Meiyao , Wang Xiaobo , Zhang Zhengxun , Fu Wei , Duan Shichao , Tang Liming
Published: July 2023

Metastasis is a leading cause of mortality in patients with lung adenocarcinoma. Histone deacetylases have emerged as promising targets for anti-tumor drugs, with histone deacetylase inhibitors (HDACi) being an active area of research. However, the precise mechanisms by which HDACi inhibits lung cancer metastasis remain incompletely understood. In this study, we employed a range of techniques, including qPCR, immunoblotting, co-immunoprecipitation, chromatin-immunoprecipitation, and cell migration assays, in conjunction with online database analysis, to investigate the role of HDACi and HDAC2/YY1 in the process of lung adenocarcinoma migration. The present study has demonstrated that both trichostatin A (TSA) and sodium butyrate (NaBu) significantly inhibit the invasion and migration of lung cancer cells via Histone deacetylase 2 (HDAC2). Overexpression of HDAC2 promotes lung cancer cell migration, whereas shHDAC2 effectively inhibits it. Further investigation revealed that HDAC2 interacts with YY1 and deacetylates Lysine 27 and Lysine9 of Histone 3, thereby inhibiting Cdh1 transcriptional activity and promoting cell migration. These findings have shed light on a novel functional mechanism of HDAC2/YY1 in lung adenocarcinoma cell migration.
Dosage of the pseudoautosomal gene SLC25A6 is implicated in QTc interval duration
Authors: Skakkebæk Anne , Kjær-Sørensen Kasper , Matchkov Vladimir V. , Christensen Lise-Lotte , Just Jesper , Cömert Cagla , Andersen Niels Holmark , Oxvig Claus , Gravholt Claus Højbjerg
Published: July 2023

The genetic architecture of the QT interval, defined as the period from onset of depolarisation to completion of repolarisation of the ventricular myocardium, is incompletely understood. Only a minor part of the QT interval variation in the general population has been linked to autosomal variant loci. Altered X chromosome dosage in humans, as seen in sex chromosome aneuploidies such as Turner syndrome (TS) and Klinefelter syndrome (KS), is associated with altered QTc interval (heart rate corrected QT), indicating that genes, located in the pseudoautosomal region 1 of the X and Y chromosomes may contribute to QT interval variation. We investigate the dosage effect of the pseudoautosomal gene SLC25A6, encoding the membrane ADP/ATP translocase 3 in the inner mitochondrial membrane, on QTc interval duration. To this end we used human participants and in vivo zebrafish models. Analyses in humans, based on 44 patients with KS, 44 patients with TS, 59 male and 22 females, revealed a significant negative correlation between SLC25A6 expression level and QTc interval duration. Similarly, downregulation of slc25a6 in zebrafish increased QTc interval duration with pharmacological inhibition of KATP channels restoring the systolic duration, whereas overexpression of SLC25A6 shortened QTc, which was normalized by pharmacological activation of KATP channels. Our study demonstrate an inverse relationship between SLC25A6 dosage and QTc interval indicating that SLC25A6 contributes to QT interval variation.
Effects of N and P addition on nutrient and stoichiometry of rhizosphere and non-rhizosphere soils of alfalfa in alkaline soil
Authors: Gu Xudong , Zhang Fengju , Xie Xiaowei , Cheng Yunlong , Xu Xing
Published: July 2023

Nitrogen (N) and phosphorus (P) are important nutrients for plant growth and development. Soil alkalization is one of the main obstacles limiting the sustainable development of agriculture. Northern Ningxia is located in the arid and semi-arid region, with serious soil alkalinization. Alfalfa has the advantages of strong saline-alkali tolerance, high yield, high quality, and wide adaptability. It is an important forage for the comprehensive improvement and rational utilization of saline-alkali land and has great significance for solving land resource shortages, improving the ecological environment, and ensuring food security. It is important to study soil organic carbon (SOC), total N (TN), total P (TP), and stoichiometry of the rhizosphere and non-rhizosphere of alfalfa in alkaline soils. Therefore, N and P were added to the alkaline alfalfa field in the Yinchuan Plain of Hetao Basin in our experiment. Six treatments were set up, i.e., N-free (WN), medium N (MN) for 90 kg/hm2, high N (HN) for 180 kg/hm2, P-free (WP), medium P (MP) for 135 kg/hm2, and high P (HP) for 270 kg/hm2. The results are as follows: The N addition promotes SOC and TN but inhibits TP, and P addition promotes SOC and TP but inhibits TN of three soil layers. The N addition decreases C/N but increases C/P and N/P, while the P addition increases C/N but decreases C/P and N/P of three soil layers. The SOC, TN, TP, C/N, C/P, and N/P under HN and HP treatment reach the significance level (P < 0.05). Appropriate additions of N and P can improve rhizosphere and non-rhizosphere nutrients and stoichiometric structure, facilitating absorption and utilization by alfalfa and improve the production potential of alfalfa in alkaline soil.
Standardized assessment of vascular reconstruction kernels in photon-counting CT angiographies of the leg using a continuous extracorporeal perfusion model
Authors: Gruschwitz Philipp , Hartung Viktor , Kleefeldt Florian , Ergün Süleyman , Lichthardt Sven , Huflage Henner , Hendel Robin , Kunz Andreas Steven , Pannenbecker Pauline , Kuhl Philipp Josef , Augustin Anne Marie , Bley Thorsten Alexander , Petritsch Bernhard , Grunz Jan-Peter
Published: July 2023

This study evaluated the influence of different vascular reconstruction kernels on the image quality of CT angiographies of the lower extremity runoff using a 1st-generation photon-counting-detector CT (PCD-CT) compared with dose-matched examinations on a 3rd-generation energy-integrating-detector CT (EID-CT). Inducing continuous extracorporeal perfusion in a human cadaveric model, we performed CT angiographies of eight upper leg arterial runoffs with radiation dose-equivalent 120 kVp acquisition protocols (CTDIvol 5 mGy). Reconstructions were executed with different vascular kernels, matching the individual modulation transfer functions between scanners. Signal-to-noise-ratios (SNR) and contrast-to-noise-ratios (CNR) were computed to assess objective image quality. Six radiologists evaluated image quality subjectively using a forced-choice pairwise comparison tool. Interrater agreement was determined by calculating Kendall’s concordance coefficient (W). The intraluminal attenuation of PCD-CT images was significantly higher than of EID-CT (414.7 ± 27.3 HU vs. 329.3 ± 24.5 HU; p < 0.001). Using comparable kernels, image noise with PCD-CT was significantly lower than with EID-CT (p ≤ 0.044). Correspondingly, SNR and CNR were approximately twofold higher for PCD-CT (p < 0.001). Increasing the spatial frequency for PCD-CT reconstructions by one level resulted in similar metrics compared to EID-CT (CNRfat; EID-CT Bv49: 21.7 ± 3.7 versus PCD-CT Bv60: 21.4 ± 3.5). Overall image quality of PCD-CTA achieved ratings superior to EID-CTA irrespective of the used reconstruction kernels (best: PCD-CT Bv60; worst: EID-CT Bv40; p < 0.001). Interrater agreement was good (W = 0.78). Concluding, PCD-CT offers superior intraluminal attenuation, SNR, and CNR compared to EID-CT in angiographies of the upper leg arterial runoff. Combined with improved subjective image quality, PCD-CT facilitates the use of sharper convolution kernels and ultimately bears the potential of improved vascular structure assessability.
Investigation of the rate-mediated form-function relationship in biological puncture
Authors: Zhang Bingyang , Anderson Philip S. L.
Published: July 2023

Puncture is a vital mechanism for survival in a wide range of organisms across phyla, serving biological functions such as prey capture, defense, and reproduction. Understanding how the shape of the puncture tool affects its functional performance is crucial to uncovering the mechanics underlying the diversity and evolution of puncture-based systems. However, such form-function relationships are often complicated by the dynamic nature of living systems. Puncture systems in particular operate over a wide range of speeds to penetrate biological tissues. Current studies on puncture biomechanics lack systematic characterization of the complex, rate-mediated, interaction between tool and material across this dynamic range. To fill this knowledge gap, we establish a highly controlled experimental framework for dynamic puncture to investigate the relationship between the puncture performance (characterized by the depth of puncture) and the tool sharpness (characterized by the cusp angle) across a wide range of bio-relevant puncture speeds (from quasi-static to $$\sim$$
∼
50 m/s). Our results show that the sensitivity of puncture performance to variations in tool sharpness reduces at higher puncture speeds. This trend is likely due to rate-based viscoelastic and inertial effects arising from how materials respond to dynamic loads. The rate-dependent form-function relationship has important biological implications: While passive/low-speed puncture organisms likely rely heavily on sharp puncture tools to successfully penetrate and maintain functionalities, higher-speed puncture systems may allow for greater variability in puncture tool shape due to the relatively geometric-insensitive puncture performance, allowing for higher adaptability during the evolutionary process to other mechanical factors.