bluuebunny/crossref_metadata_2025 huggingface dataset:
Scientific basis, engineering feasibility and system optimization of green sea dykes for temperate mud coasts: a brief overview
Authors: Yu Qian , Jia Jianjun , Gao Shu
Published: August 2024

Green sea dykes, also known as ecosystem-based sea dykes, represent a novel type of coastal defense consisting of both traditional structural engineering and coastal ecosystems, designed to cope with the future trends of sea level rise and intensified storms. Here we focus on the mid-latitude mud coasts (eastern China in particular), which face the most prominent risks of storm surge, storm-induced giant waves, and shoreline erosion, and summarizes the scientific basis of green sea dykes and the current status of engineering practices. We show that the basic mechanisms of nearshore wave energy dissipation include bottom friction, sediment transport, and form drag. These explain the wave damping capacity of oyster reefs and salt marshes on mud coasts. In tidal flat environments, oyster growth increases frictional resistance and even causes wave breaking; the resuspension and transport of fine-grained sediments on salt marsh beds and the movement or resistance to hydrodynamic forcing of salt marsh vegetation stems effectively dissipate wave kinetic energy, and their efficiency increases with the elevation of the bed surface. Based on the wave damping capacity of oyster reefs and salt marshes on mud coasts, ecosystem-based sea dykes are being built in combination with traditional structured sea dykes. By utilizing natural tidal flats outside the dykes or implementing artificial modification projects, a certain scale of salt marshes and/or oyster reefs can be maintained, which serve to protect the sea dykes and enhance their wave resistance functions. From the perspective of system optimization, it is necessary to further improve the efficiency and sustainability of green sea dykes under constraints such as regional environment characteristics, ecosystem health, investment capacity, and ecological resilience. Related scientific issues include the theorization of the wave damping process of salt marshes, the niche and scale control of oyster reef and salt marsh ecosystems, the establishment of engineering standards and the design of the optimal form of sea dykes.
Atomic insight into residual stress and microstructure evolution of amorphous carbon heterostructured films induced by multi-stage phase transformation of high-entropy alloys
Authors: Niu Xinyue , Zhou Yefei , Zhang Tao , Ding Ming , Xing Xiaolei , Yang Qingxiang , Wang Dianlong , Xiao Jianwei , Shi Zhijun
Published: August 2024

The residual stress has significant effects on the microstructure and service performance of films. With good toughness and low stacking fault energy, high-entropy alloy (HEA) can act as dopant to reduce the residual stress of films via self-plastic deformation. Nevertheless, the microscopic mechanism buried deep under the surface is difficult to study by experiments and the dynamic evolution cannot be observed, which the biggest obstacle to investigate the corresponding solutions is. In this paper, diamond-like carbon (DLC) models with different CoCrFeNi HEA doping ratios (1:2, 1:4, 1:6, and 1:8) were designed by molecular dynamics method. The effects of CoCrFeNi doping percentage on the structure and residual stress of this heterostructured films were investigated, and the mechanism of residual stress reduction was revealed. The results show that the phase transformation of HEA causes stress fluctuations in DLC films. The stress fluctuations at different orientations of the heterostructured films is gradually shifted to the right with the increase of HEA percentage, and the difference in stress level between the initial and final strain is significantly decreased. Meanwhile, when the doping ratio is 1:2, the compressive stresses inside the films is lower and the generation of stacking faults is later. With the increase of the HEA doping ratio, the proportion of C atoms with sp3 and sp2 hybridization structures is decreased significantly, and the percentages of the distorted C–C bond length and distorted C–C-C bond angle are also reduced. Therefore, HEA doping affects the number of hybrid atoms and the distribution of bond characteristics in DLC films, which leads to the decrease of the residual stress of the heterostructured films.

Graphical Abstract
MIR99AHG: a novel lncRNA host gene with diverse regulatory roles in cancer
Authors: Si Jiahua , Su Xinming , Xu Hening , Gu Jiayi , Feng Yinuo , Wang Zehua , Xiao Yunxuan , Shentu Jianqiao , Duan Shiwei
Published: August 2024

MIR99AHG, a recently discovered long non-coding RNA (lncRNA), serves as the host gene for the miR-99a/let-7c/miR-125b-2 miRNA cluster. The intricate processing of its three introns yields three distinct micro RNAs (miRNAs). Experimental evidence highlights significant variations in MIR99AHG expression across various cancer types, indicating its potential as a diagnostic marker for cancer. Moreover, FOXA1 acts as an upstream regulator, actively promoting MIR99AHG expression. MIR99AHG, in turn, regulates five downstream proteins (ANXA2, PTBP1, MMP9, PBX3, and PHB2), as well as three competing endogenous RNA (ceRNA) axes and three signaling pathways. This broad spectrum of regulatory effects underscores the pivotal role of MIR99AHG in shaping the behavior of cancer cells. In cancer treatment, MIR99AHG's functions are equally noteworthy. Experimental findings suggest its impact on immune cell activity within the tumor micro-environment and its role in modulating cancer cell resistance to chemotherapeutic drugs. Follow-up studies on patients further confirm the close association between high MIR99AHG expression and poor prognosis across various cancers, exhibiting significant statistical correlations with various pathological behaviors. In summary, MIR99AHG, acting as a multifaceted lncRNA, not only introduces a potential novel marker for cancer diagnosis but also demonstrates significant application value in cancer treatment and prognosis evaluation.
Performance of light weight concrete with different aggregates—a comprehensive review
Authors: Dwarampudi Manasa , Venkateshwari B.
Published: August 2024

Although its usage in civil engineering is due to aspects like cost-effectiveness and design flexibility, which have made light-weight concrete (LWC) increasingly popular in recent decades, its development brought a revolution in civil engineering. Numerous studies have been conducted in this field to examine the structural performance in various scenarios. The goal of the current review is to provide a thorough analysis of lightweight concrete. The main reason for the variance in concrete strength is the use of lightweight aggregates, which include multiple types of lightweight aggregates that can be natural or artificial. Thus, this review paper was put together to give an idea of lightweight concrete by using different aggregates like. There are many light-weight aggregate types, such as expanded clay aggregate, pumice, coconut shell, cenosphere, ceramsite sand, cenomite aggregate, vermiculite, crushed clay bricks, and palm kernel shells, as well as their effects on the properties of LWC. This paper includes the production process of LWC and its characteristics, including, density, compressive strength, split tensile strength, flexural strength, workability and durability.
Poroelastic effects of chemical loading in consolidation of residual soils
Authors: Irheren Dada , Okafor Fidelis Onyebuchi , Onyia Michael Ebie
Published: August 2024

An analytical chemo-hydromechanical model of residual soils was presented in this study. The modeling procedure utilized a unique phenomenological approach, which highlighted some of the macro-mechanical influences responsible for the behavior of residual soils. The macromechanical analysis yielded an extended poroelastic theory. The developed model was applied in solving a typical civil engineering problem of soil consolidation. For a chemical loading treatment, the problem was using requisite boundary conditions. Thereafter, the mathematical software Mathematica was used for solving the ensuing diffusion equations using physico-chemical properties typical of a residual soil sample. Even though the chemical loading was instantaneous, it took some time before its effect could be felt everywhere according to the poroelastic theory. From obtained results the evolution of the generated pore pressure showed increasing segments of the soil returning to their initial state after the passage of the pore pressure front. The vertical displacement showed a slight increase or elevation of the soil surface. The flux of water flow in the soil was initially positive before turning negative, which can be explained by initial successful penetration of the infiltrating liquid until it met increasingly tortuous paths as result of lower permeability. The volume (per unit area) of water leaving the soil after chemical loading demonstrated that a portion of the water flux associated with the infiltrating liquid ends up leaving the soil through the sides. The developed model was later compared with a similar porochemoelastic model found in literature with reasonable agreement.
The need for smart bimetallic nanoparticles in the battle against pathogenic multi-drug resistant bacteria: a brief communication
Authors: El-Sayyad Gharieb S.
Published: August 2024

The expanding threat presented by developing pathogenic multidrug-resistant (MDR) bacteria calls for an urgent need for research, particularly given the growing concern for global public health. Bimetallic nanoparticles (NPs) have the potential to be utilized for a broad variety of pharmacological and biological applications because to their outstanding antibacterial activity at low concentrations and continuous phase stability. This is especially true when it comes to preventing MDR pathogenic bacteria from invading. Several biological synthetic methods for producing bimetallic NPs and the range of analytical methods (used to characterize them) are covered in this brief communication paper. Additionally, I tried to highlight the literature review on the antimicrobial capabilities of several synthesized bimetallic NPs. The final section of this brief communication discussed the structure and mechanism of action of the synthesized bimetallic NPs against pathogenic bacteria. Electrostatic interaction, damage to cell membranes, change of enzymes and proteins, oxidative stress and the production of reactive oxygen species (ROS), binding to proteins that disturbs the electron transport chain and disturbs homeostasis, signal transduction suppression, and genotoxicity are some possible associations with the phenomenon being studied.
Architecture Design and Ground Performance of Netherlands‐China Low‐Frequency Explorer
Authors: Karapakula Sukanth , Brinkerink Christiaan , Vecchio Antonio , Pourshaghaghi Hamid R. , Dolron Peter , Jordans Roel , Bertels Eric , Aalbers Gerard , Ruiter Mark , Boonstra Albert J. , Bentum Mark , Prinsloo David , Arts Michel , Bast Jeanette , Damstra Sieds , van Duin Albert , Ebbendorf Nico , van der Marel Hans , Morawietz Juergen , Witvers Roel , Poiesz Wietse , van Dongen Rico , Cecconi Baptiste , Zarka Philippe , Dekkali Moustapha , Chen Linjie , Wang Mingyuan , Zhang Mo , Huang Maohai , Yan Yihua , Dong Liang , Tan Baolin , Zhang Lihua , Xiong Liang , Sun Ji , Zhang Hongbo , Ping Jinsong , Wolt Marc Klein , Falcke Heino
Published: August 2024

The Netherlands‐China Low‐Frequency Explorer (NCLE) (Boonstra et al., 2017, https://www.ursi.org/proceedings/procGA17/papers/Paper_J19‐2(1603).pdf; Chen et al., 2020, https://ui.adsabs.harvard.edu/abs/2020AAS…23610203C/abstract) is a radio instrument for astrophysical studies in the low‐frequency range (80 kHz–80 MHz). As a technology demonstrator, NCLE shall inform the design of future radio receivers that aim at low‐frequency radio astronomy. NCLE can make observations at very high spectral resolution (<1 kHz) and generate radio sky maps at an angular resolution of ≈1.5 radians. NCLE uses three monopole antennas, each 5 m long, and three identical analog signal chains to process the signal from each antenna. A single digital receiver samples the signal and calculates the auto‐correlated and cross‐correlated spectra. The instrument's analog and digital signal chains are extensively configurable. They can be fine‐tuned to produce broadband spectra covering the instrument's complete operating frequency range or sub‐bands. NCLE was developed within a veryshort timescale of 2 years, and currently, it is on board Queqiao, the relay spacecraft of the Chang'e‐ 4 mission, in a halo orbit around the Earth‐Moon L2 point. This paper outlines the science cases, instrument architecture with focus on the signal chain, and discusses the laboratory measurements during the pre‐launch phase.
Spatial Variations of Jovian Tropospheric Ammonia via Ground‐Based Imaging
Authors: Hill S. M. , Irwin P. G. J. , Alexander C. , Rogers J. H.
Published: August 2024

Current understanding of the ammonia distribution in Jupiter's atmosphere is provided by observations from major ground‐based facilities and spacecraft, and analyzed with sophisticated retrieval models that recover high fidelity information, but are limited in spatial and temporal coverage. Here we show that the ammonia abundance in Jupiter's upper troposphere, which tracks the overturning atmospheric circulation, can be simply, but reliably determined from continuum‐divided ammonia and methane absorption‐band images made with a moderate‐sized Schmidt‐Cassegrain telescope (SCT). In 2020–2021, Jupiter was imaged in the 647‐nm ammonia absorption band and adjacent continuum bands with a 0.28‐m SCT, demonstrating that the spatially resolved ammonia optical depth could be determined with such a telescope. In 2022–2023, a 619 nm methane‐band filter was added to provide a constant reference against which to correct the ammonia abundances (column‐averaged mole fraction) for cloud opacity variations. These 0.28‐m SCT results are compared with observations from: (a) the MUSE instrument on ESO's Very Large Telescope (b) the TEXES mid‐infrared spectrometer used on NASA's InfraRed Telescope Facility; and (c) the Gemini telescopes, and are shown to provide reliable maps of ammonia abundance. Meridional and longitudinal features are examined, including the Equatorial Zone (EZ) ammonia enhancement, the North Equatorial Belt depletion, depletion above the Great Red Spot, and longitudinal enhancements in the northern EZ. This work demonstrates meaningful ammonia monitoring can be achieved with small telescopes that can complement spacecraft and major ground‐based facility observations.
Extremely Long‐Range Observations of Ionospheric Irregularities in a Large Longitude Zone From Pacific to Africa Using a Low Latitude Over‐The‐Horizon Radar in China
Authors: Hu Lianhuan , Li Guozhu , Ning Baiqi , Dai Guofeng , Sun Wenjie , Zhao Xiukuan , Xie Haiyong , Li Yi , Xiong Bo , Li Yu , Nishioka Michi , Perwitasari Septi
Published: August 2024

Monitoring the generation and movement of equatorial plasma bubbles (EPBs) in a large longitude region is crucial important for better understanding their day‐to‐day variability. Using the newly developed Low lAtitude long Range Ionospheric raDar (LARID) at Dongfang (19.2°N, 108.8°E, dip lat. 13.8°N), China, an extremely long‐range experiment for observing EPB irregularities in a range of ±9,600 km to the radar site was first carried out. The results show that EPB irregularities with ranges up to 7,000 and 9,500 km were observed by the east and west beams of LARID, respectively. By incorporating simultaneous observations from GNSS receiver and ionosonde networks, it is demonstrated that the EPBs generated from post‐sunset to sunrise over a very wide longitude of ∼140°, from Pacific to Africa could be observed by LARID. The results, for the first time, demonstrate the possibility for tracing global EPBs in real time using a few low latitude over‐the‐horizon radars.
Modeling the Probability of Dry Lightning‐Induced Wildfires in Tasmania: A Machine Learning Approach
Authors: Wickramasinghe Amila M. K. , Boer Matthias M. , Cunningham Calum X. , Nolan Rachael H. , Bowman David M. J. S. , Williamson Grant J.
Published: August 2024

Dry lightning is a prevalent episodic natural ignition source for wildfires, particularly in remote regions where such fires can escalate into uncontrollable events, burning extensive areas. In this study, we aimed to understand the interplay of environmental, fuel, and geographical factors in evaluating the probability of fire initiation following dry lightning strikes in Tasmania, Australia. We integrated dry lightning, active fire records, and gridded data on fire weather, fuel, and topography into a binary classification framework for both fire‐initiating and non‐fire‐causing lightning strikes. Employing statistical and machine learning techniques, we quantified the likelihood of fire initiation due to dry lightning, with the resampled Random Forest model exhibiting notable performance with an ROC‐AUC value of 0.98. Our findings highlight how fuel characteristics and moisture content associated with particular vegetation types influence fire initiation and provide an objective approach for identifying susceptible regions of dry lightning ignitions, informing associated fire management responses.
Tectonic Implications of Seismic Anisotropy Layering Beneath the Southern Tibetan Plateau Revealed by Integrated Shear Wave Splitting and Receiver Function Analyses
Authors: Shen Cong , Gao Stephen S. , Kong Fansheng , Liu Kelly H.
Published: August 2024

To investigate continental dynamics underneath the south‐central Tibetan plateau, which composes the Himalayan, Lhasa, and Qiangtang blocks, we have conducted comprehensive examinations of seismic azimuthal anisotropy in the crust using receiver functions (RFs) and crustal and mantle anisotropy using teleseismic shear wave splitting (SWS) analysis. In the Qiangtang block, the observed predominantly E‐W fast orientations from RF and SWS analyses with similar magnitude are interpreted as resulting from eastward crustal flow with minor contributions from the mantle. In the Lhasa block, the crustal anisotropy is approximately N‐S oriented, which is parallel to the strike of rift basins and southward crustal flow. Anisotropy revealed by SWS demonstrates a rotation from E‐W in the north to NE‐SW in the south, which can be interpreted as reflecting mantle flow field induced by the northward movement of the subducting Indian plate. The addition of PKS and SKKS measurements and extension of epicentral distance range to 171.8° for SWS analysis revealed dominantly strong E‐W oriented anisotropy in most parts of the Himalayan block, where most previous studies reported pervasively null measurements. The absence of azimuthal anisotropy is observed in two regions in the Himalayan block which is attributable to mantle upwelling through a previously identified slab window. A two‐layered anisotropy structure with different fast orientations for the upper and lower layers can be constrained in the southern Qiangtang and the vicinity of the Main Boundary Thrust.
Volatile and Trace Element Storage in a Crystallizing Martian Magma Ocean
Authors: Sim Shi J. , Hirschmann Marc M. , Hier‐Majumder Saswata
Published: August 2024

Immediately following core formation on Mars, the planet underwent a magma ocean phase. Volatiles released from the magma ocean fostered a primitive atmosphere which modulated heat loss from the cooling planet through the greenhouse effect. The solidification and degassing of the magma ocean are therefore coupled. In this work, we investigate two important aspects of this evolution: (a) the dynamics of melt trapping at the freezing front of the residual mantle and (b) the oxidation state during crystallization. For crystallization rates applicable to the martian magma, compaction is inefficient, leading to large fractions of melt trapped together with the crystals accumulating in the residual mantle. The H2O content of the martian residual mantle is strongly influenced by dynamic melt trapping. Following magma ocean crystallization, up to 55.4% of the initial H2O in the magma ocean is sequestered in the residual mantle, with the rest outgassed to the surface. Dynamic melt trapping also limits variations in trace element concentrations and fractionations. Resulting variations in important isotopic parent/daughter ratios (Sm/Nd, Lu/Hf) cannot account for all of the isotopic diversity inferred for martian basalt source regions, hence requiring alternative mechanisms. The redox state of the magma ocean exerts a strong control on the total CO2 content of the residual mantle and the time of crystallization. Under oxidizing conditions, the residual mantle stores 0.01% of the delivered CO2 but under the most reducing conditions we examined, the residual mantle can sequester 80.4% in the form of trapped carbonated melt and graphite/diamond.
Highly efficient AlGaN-based deep-ultraviolet light-emitting diodes: from bandgap engineering to device craft
Authors: Liu Xu , Lv Zhenxing , Liao Zhefu , Sun Yuechang , Zhang Ziqi , Sun Ke , Zhou Qianxi , Tang Bin , Geng Hansong , Qi Shengli , Zhou Shengjun
Published: August 2024

AlGaN-based light-emitting diodes (LEDs) operating in the deep-ultraviolet (DUV) spectral range (210–280 nm) have demonstrated potential applications in physical sterilization. However, the poor external quantum efficiency (EQE) hinders further advances in the emission performance of AlGaN-based DUV LEDs. Here, we demonstrate the performance of 270-nm AlGaN-based DUV LEDs beyond the state-of-the-art by exploiting the innovative combination of bandgap engineering and device craft. By adopting tailored multiple quantum wells (MQWs), a reflective Al reflector, a low-optical-loss tunneling junction (TJ) and a dielectric SiO2 insertion structure (IS-SiO2), outstanding light output powers (LOPs) of 140.1 mW are achieved in our DUV LEDs at 850 mA. The EQEs of our DUV LEDs are 4.5 times greater than those of their conventional counterparts. This comprehensive approach overcomes the major difficulties commonly faced in the pursuit of high-performance AlGaN-based DUV LEDs, such as strong quantum-confined Stark effect (QCSE), severe optical absorption in the p-electrode/ohmic contact layer and poor transverse magnetic (TM)-polarized light extraction. Furthermore, the on-wafer electroluminescence characterization validated the scalability of our DUV LEDs to larger production scales. Our work is promising for the development of highly efficient AlGaN-based DUV LEDs.
MDH2 regulates the sensitivity of clear cell renal cell carcinoma to ferroptosis through its interaction with FSP1
Authors: Feng Baijie , Su Wei , Guo Xianzhi , Ding Tingting , Duan Yingchun , Hu Lina , Yu Minghua
Published: August 2024

Malate dehydrogenase 2 is a pivotal enzyme in the tricarboxylic acid cycle. Recent studies have highlighted the significant involvement of MDH2 in the pathogenesis and progression of diverse types of tumors, yet its precise mechanistic underpinnings remain elusive. This study revealed a significant decrease in MDH2 expression in renal cancer tissues. And knocking out MDH2 was observed to hinder the proliferation of normal renal tubular epithelial cells but notably enhance the proliferation of ccRCC. Furthermore, mechanistically, we found that MDH2 inhibits the proliferation of ccRCC by promoting ferroptosis, while enhancing the sensitivity of ccRCC to ferroptosis inducers, promoting lipid peroxidation. We also demonstrated that MDH2 regulates the ubiquitination of FSP1 through protein-protein interactions, leading to a decrease in FSP1 protein levels and maintaining high sensitivity of ccRCC to ferroptosis. In conclusion, our study demonstrates that the reduced MDH2 expression in ccRCC results in increased expression of FSP1, thereby reducing its sensitivity to ferroptosis. It unveils a non-metabolic role for the downregulation of MDH2 in ccRCC progression.
Combined association of aerobic and muscle strengthening activity with mortality in individuals with hypertension
Authors: Choi Younghwan , Lee Duck-chul , Han Yunmin , Sung Hoyong , Yoon Jiyeon , Kim Yeon Soo
Published: August 2024

Evidence on the association between meeting both aerobic physical activity (PA) and muscle-strengthening activity (MSA) guidelines with mortality in individuals with hypertension is scarce. We included 34,990 adults from the 2007 to 2013 Korea National Health and Nutrition Examination Survey, linking mortality follow-up data until 2019. Adherence to PA guidelines was assessed based on the current PA guidelines using a self-reported questionnaire and categorized as follows: meeting MSA only, aerobic PA only, both MSA and aerobic PA, or neither. Associations of hypertension and adherence to PA guidelines with all-cause and cardiovascular disease (CVD) mortality were examined using Cox proportional hazard models. Over 9.2 years, 1948 participants died from any cause and 419 from CVD. Meeting both PA guidelines was associated with the lowest risk of all-cause and CVD mortalities in the total sample regardless of hypertension status. In individuals with hypertension, meeting aerobic PA guidelines only had a 24% lower risk of both all-cause and CVD mortality, and meeting both PA guidelines further reduced risks by 40% and 43%, respectively; however, meeting MSA guidelines only was not associated with either all-cause or CVD mortality. In individuals without hypertension, only meeting both MSA and aerobic PA guidelines, but not meeting either MSA or aerobic PA guidelines, showed reduced risk of CVD mortality. In Korean population, non-hypertensive individuals who met both guidelines had a lower risk of CVD mortality. However, hypertensive individuals showed a reduced risk of both all-cause and CVD mortality when meeting aerobic PA or both guidelines, but not MSA alone.
network-based constraint to evaluate climate sensitivity
Authors: Ricard Lucile , Falasca Fabrizio , Runge Jakob , Nenes Athanasios
Published: August 2024

The 2015 Paris agreement was established to limit Greenhouse gas (GHG) global warming below 1.5°C above preindustrial era values. Knowledge of climate sensitivity to GHG levels is central for formulating effective climate policies, yet its exact value is shroud in uncertainty. Climate sensitivity is quantitatively expressed in terms of Equilibrium Climate Sensitivity (ECS) and Transient Climate Response (TCR), estimating global temperature responses after an abrupt or transient doubling of CO2. Here, we represent the complex and highly-dimensional behavior of modelled climate via low-dimensional emergent networks to evaluate Climate Sensitivity (netCS), by first reconstructing meaningful components describing regional subprocesses, and secondly inferring the causal links between these to construct causal networks. We apply this methodology to Sea Surface Temperature (SST) simulations and investigate two different metrics in order to derive weighted estimates that yield likely ranges of ECS (2.35–4.81°C) and TCR (1.53-2.60°C). These ranges are narrower than the unconstrained distributions and consistent with the ranges of the IPCC AR6 estimates. More importantly, netCS demonstrates that SST patterns (at “fast” timescales) are linked to climate sensitivity; SST patterns over the historical period exclude median sensitivity but not low-sensitivity (ECS < 3.0°C) or very high sensitivity (ECS ≥ 4.5°C) models.
SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia
Authors: Luo Yu-Wei , Zhou Jiang-Peng , Ji Hongyu , Xu Doudou , Zheng Anqi , Wang Xin , Dai Zhizheng , Luo Zhicheng , Cao Fang , Wang Xing-Yue , Bai Yunfang , Chen Di , Chen Yueming , Wang Qi , Yang Yaying , Zhang Xinghai , Chiu Sandra , Peng Xiaozhong , Huang Ai-Long , Tang Kai-Fu
Published: August 2024

Though RNAi and RNA-splicing machineries are involved in regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, their precise roles in coronavirus disease 2019 (COVID-19) pathogenesis remain unclear. Herein, we show that decreased RNAi component (Dicer and XPO5) and splicing factor (SRSF3 and hnRNPA3) expression correlate with increased COVID-19 severity. SARS-CoV-2 N protein induces the autophagic degradation of Dicer, XPO5, SRSF3, and hnRNPA3, inhibiting miRNA biogenesis and RNA splicing and triggering DNA damage, proteotoxic stress, and pneumonia. Dicer, XPO5, SRSF3, and hnRNPA3 knockdown increases, while their overexpression decreases, N protein-induced pneumonia’s severity. Older mice show lower expression of Dicer, XPO5, SRSF3, and hnRNPA3 in their lung tissues and exhibit more severe N protein-induced pneumonia than younger mice. PJ34, a poly(ADP-ribose) polymerase inhibitor, or anastrozole, an aromatase inhibitor, ameliorates N protein- or SARS-CoV-2-induced pneumonia by restoring Dicer, XPO5, SRSF3, and hnRNPA3 expression. These findings will aid in developing improved treatments for SARS-CoV-2-associated pneumonia.
End-to-end reproducible AI pipelines in radiology using the cloud
Authors: Bontempi Dennis , Nuernberg Leonard , Pai Suraj , Krishnaswamy Deepa , Thiriveedhi Vamsi , Hosny Ahmed , Mak Raymond H. , Farahani Keyvan , Kikinis Ron , Fedorov Andrey , Aerts Hugo J. W. L.
Published: August 2024

Artificial intelligence (AI) algorithms hold the potential to revolutionize radiology. However, a significant portion of the published literature lacks transparency and reproducibility, which hampers sustained progress toward clinical translation. Although several reporting guidelines have been proposed, identifying practical means to address these issues remains challenging. Here, we show the potential of cloud-based infrastructure for implementing and sharing transparent and reproducible AI-based radiology pipelines. We demonstrate end-to-end reproducibility from retrieving cloud-hosted data, through data pre-processing, deep learning inference, and post-processing, to the analysis and reporting of the final results. We successfully implement two distinct use cases, starting from recent literature on AI-based biomarkers for cancer imaging. Using cloud-hosted data and computing, we confirm the findings of these studies and extend the validation to previously unseen data for one of the use cases. Furthermore, we provide the community with transparent and easy-to-extend examples of pipelines impactful for the broader oncology field. Our approach demonstrates the potential of cloud resources for implementing, sharing, and using reproducible and transparent AI pipelines, which can accelerate the translation into clinical solutions.
The solvation shell probed by resonant intermolecular Coulombic decay
Authors: Dupuy Rémi , Buttersack Tillmann , Trinter Florian , Richter Clemens , Gholami Shirin , Björneholm Olle , Hergenhahn Uwe , Winter Bernd , Bluhm Hendrik
Published: August 2024

Molecules involved in solvation shells have properties differing from those of the bulk solvent, which can in turn affect reactivity. Among key properties of these molecules are their nature and electronic structure. Widely used tools to characterize this type of property are X-ray-based spectroscopies, which, however, usually lack the capability to selectively probe the solvation-shell molecules. A class of X-ray triggered “non-local” processes has the recognized potential to provide this selectivity. Intermolecular Coulombic decay (ICD) and related processes involve neighbouring molecules in the decay of the X-ray-excited target, and are thus naturally sensitive to its immediate environment. Applying electron spectroscopy to aqueous solutions, we explore the resonant flavours of ICD and demonstrate how it can inform on the first solvation shell of excited solvated cations. One particular ICD process turns out to be a potent marker of the formation of ion pairs. Another gives a direct access to the electron binding energies of the water molecules in the first solvation shell, a quantity previously elusive to direct measurements. The resonant nature of the processes makes them readily measurable, providing powerful new spectroscopic tools.
A momentum-resolved view of polaron formation in materials
Authors: Britt Tristan L. , Caruso Fabio , Siwick Bradley J.
Published: August 2024

An ab-initio computational methodology for interrogating the phonon contribution to polaron formation in real materials is developed that can be directly compared to experiment. Using LiF as an example, we show that the recent ab-initio theory of Sio et al.1 makes predictions of the momentum- and branch dependent phonon amplitudes in polaron quasiparticles that are testable using ultrafast electron diffuse scattering (UEDS) and related techniques. The large electron polaron in LiF has UEDS signatures that are qualitatively similar to those expected from a simple isotropic strain field model, but the small hole polaron exhibits a profoundly anisotropic UEDS pattern that is in poor agreement with an isotropic strain field. We also show that these polaron diffuse scattering signatures are directly emblematic of the underlying polaron wavefunction. The combination of new time and momentum resolved experimental probes of nonequilibrium phonons with novel computational methods promises to complement the qualitative results obtained via model Hamiltonians with a first principles, material-specific quantitative understanding of polarons and their properties.
Reducing climate change impacts from the global food system through diet shifts
Authors: Li Yanxian , He Pan , Shan Yuli , Li Yu , Hang Ye , Shao Shuai , Ruzzenenti Franco , Hubacek Klaus
Published: August 2024

How much and what we eat and where it is produced can create huge differences in GHG emissions. On the basis of detailed household-expenditure data, we evaluate the unequal distribution of dietary emissions from 140 food products in 139 countries or areas and further model changes in emissions of global diet shifts. Within countries, consumer groups with higher expenditures generally cause more dietary emissions due to higher red meat and dairy intake. Such inequality is more pronounced in low-income countries. The present global annual dietary emissions would fall by 17% with the worldwide adoption of the EAT-Lancet planetary health diet, primarily attributed to shifts from red meat to legumes and nuts as principal protein sources. More than half (56.9%) of the global population, which is presently overconsuming, would save 32.4% of global emissions through diet shifts, offsetting the 15.4% increase in global emissions from presently underconsuming populations moving towards healthier diets.
A quantitative assessment of continuous versus structured methods for the detection of marine mammals and seabirds via opportunistic shipboard surveys
Authors: Viola Benjamin , Puskic Peter , Corney Stuart , Barrett Neville , Davies Bronwyn , Clausius Ella , Jutzeler Martin , Lea Mary-Anne
Published: August 2024

Marine monitoring efforts are increasingly supported by opportunistic shipboard surveys. However, opportunistic survey methods often require adaptation to suit the vessel and the operations being conducted onboard. Whilst best-practice techniques for surveying marine wildlife on vessels of opportunity are yet to be established, testing and development of alternative methods can provide means for capturing ecological information in otherwise under-surveyed areas. Explicitly, survey methods can be improved while baseline ecological data for new regions are gathered simultaneously. Herein, we tested different survey approaches on a vessel of opportunity in a remote offshore area where little is known about the community composition of top-order marine vertebrate predators: western and south-western Tasmania, Australia. We found that continuous surveys provide greater species counts than structured “snapshot” surveys over the course of a voyage, but that structured surveys can be more practical when managing factors such as observer fatigue. Moreover, we provide a baseline dataset on the marine vertebrate community encountered in western and south-western Tasmania. This information will be critically important for industry and conservation management objectives, and is key to our understanding of the offshore ecosystem around Tasmania.
Cross-modality sub-image retrieval using contrastive multimodal image representations
Authors: Breznik Eva , Wetzer Elisabeth , Lindblad Joakim , Sladoje Nataša
Published: August 2024

In tissue characterization and cancer diagnostics, multimodal imaging has emerged as a powerful technique. Thanks to computational advances, large datasets can be exploited to discover patterns in pathologies and improve diagnosis. However, this requires efficient and scalable image retrieval methods. Cross-modality image retrieval is particularly challenging, since images of similar (or even the same) content captured by different modalities might share few common structures. We propose a new application-independent content-based image retrieval (CBIR) system for reverse (sub-)image search across modalities, which combines deep learning to generate representations (embedding the different modalities in a common space) with robust feature extraction and bag-of-words models for efficient and reliable retrieval. We illustrate its advantages through a replacement study, exploring a number of feature extractors and learned representations, as well as through comparison to recent (cross-modality) CBIR methods. For the task of (sub-)image retrieval on a (publicly available) dataset of brightfield and second harmonic generation microscopy images, the results show that our approach is superior to all tested alternatives. We discuss the shortcomings of the compared methods and observe the importance of equivariance and invariance properties of the learned representations and feature extractors in the CBIR pipeline. Code is available at: https://github.com/MIDA-group/CrossModal_ImgRetrieval.
Attentional dynamics of evidence accumulation explain why more numerate people make better decisions under risk
Authors: Zilker Veronika
Published: August 2024

In decisions under risk, more numerate people are typically more likely to choose the option with the highest expected value (EV) than less numerate ones. Prior research indicates that this finding cannot be explained by differences in the reliance on explicit EV calculation. The current work uses the attentional Drift Diffusion Model as a unified computational framework to formalize three candidate mechanisms of pre-decisional information search and processing—namely, attention allocation, amount of deliberation, and distorted processing of value—which may differ between more and less numerate people and explain differences in decision quality. Computational modeling of an eye-tracking experiment on risky choice demonstrates that numeracy is linked to how people allocate their attention across the options, how much evidence they require before committing to a choice, and also how strongly they distort currently non-attended information during preference formation. Together, especially the latter two mechanisms largely mediate the effect of numeracy on decision quality. Overall, the current work disentangles and quantifies latent aspects of the dynamics of preference formation, explicates how their interplay may give rise to manifest differences in decision quality, and thereby provides a fully formalized, mechanistic explanation for the link between numeracy and decision quality in risky choice.
Correlating physico-chemical properties of analytes with Hansen solubility parameters of solvents using machine learning algorithm for predicting suitable extraction solvent
Authors: Mostafa Eman A. , Azim Mohammad Abdul , ElZaher Asmaa A. , ElKady Ehab F. , Fouad Marwa A. , Ghazy Fatma H. , Radi Esraa A. , El Makarim Saleh Mahmoud Abo , El Kerdawy Ahmed M.
Published: August 2024

Artificial neural networks (ANNs) are biologically inspired algorithms designed to simulate the way in which the human brain processes information. In sample preparation for bioanalysis, liquid–liquid extraction (LLE) represents an important step with the extraction solvent selection is the key laborious step. In the current work, a robust and reliable ANNs model for LLE solvent prediction was generated which could predict the suitable solvent for analyte extraction. The developed ANNs model takes a set of chosen descriptors for the cited analyte as an input and predicts the corresponding Hansen solubility parameters of the suitable extraction solvent as a model output. Then, from the solvent combination’s appendix, the analyst can identify the proposed extraction solvents' combination for the cited analyte easily and efficiently. For the experimental validation of the model prediction capabilities, twenty structurally diverse drugs belonging to different pharmacological classes were extracted from human plasma. The extraction process was performed using the predicted extraction solvent combination for each drug and quantitively estimated by HPLC/UV methods to assess their extraction recovery. The developed LLE solvent prediction model is in- line with the global trend towards green chemistry since it limits the consumption of organic solvents.
Contextualizing wild cereal harvesting at Middle Palaeolithic Ghar-e Boof in the southern Zagros
Authors: Riehl Simone , Karakaya Doğa , Zeidi Mohsen , Conard Nicholas J.
Published: August 2024

A stratigraphic sequence from Ghar-e Boof, a cave site in Iran, covering a period of c. 80,000–30,000 BP and containing more than 20,000 seed and chaff remains, allows a detailed study of the use of annual seed species of Palaeolithic hunter-gatherer groups and its evolution under the influence of changing environmental conditions. Taxonomic changes in the archaeobotanical assemblage and the stable carbon isotope data of pistachio support a considerable change in environmental conditions over the sequence from MIS 5a to MIS 3. The exceptional dominance of wild ancestors of modern crop species, including glume wheat and large-seeded legumes from Middle Palaeolithic layers AH VI (OSL ranges 72–81 ka BP), coincides broadly with the transition from MIS 5a to MIS 4. With the beginning of MIS 4 these taxa are strongly reduced, corresponding with a strong decrease in global CO2 concentrations and in the Δ13C values of Pistacia khinjuk/atlantica from the site. Wild glume wheat completely disappears after Middle Palaeolithic AH Vb and never reappears at the site. We hypothesize that the Middle Palaeolithic niche that allowed the harvesting and consumption of wild cereals and legumes ended with a destabilization of the vegetation in early MIS 4.
Insights into hydro thermal gasification process of microplastic polyethylene via reactive molecular dynamics simulations
Authors: Ha Do Tuong , Tong Hien Duy , Trinh Thuat T.
Published: August 2024

Microplastics have become a pressing environmental issue due to their widespread presence in our ecosystems. Among various plastic components, polyethylene (PE) is a prevalent and persistent contaminant. Hydrothermal gasification (HTG), a promising technology for converting PE into syngas, holds great promise for mitigating the microplastic problem. In this study, we employ ReaxFF molecular dynamics simulations to investigate the HTG process of PE, shedding light on the intricate relationships between temperature, water content, carbon conversion efficiency, and product distributions. The results reveal that hydrothermal gasification of PE is a complex process involving multiple reaction pathways. Consistently with experimental findings, the calculations indicate that the gas phase exhibits a substantial hydrogen fraction, reaching up to 70%. Interestingly, our simulations reveal a dual role of water content in the HTG process. On one hand, water enhances hydrogen production by promoting the gas formation. On the other hand, it elevates the activation energy required for PE decomposition. Depending on the water content, the calculated activation energies range from 176 to 268 kJ/mol, which are significantly lower than those reported for thermal gasification (TG). This suggests that HTG may be a more efficient route for PE conversion. Furthermore, this study highlights the importance of optimizing both temperature and water content in HTG systems to achieve high yields of hydrogen-rich syngas. The results obtained from our ReaxFF MD simulations demonstrate the robustness of this computational methodology in elucidating complex chemical reactions under extreme conditions. Our findings offer critical insights into the design of advanced waste management strategies for microplastics and contribute to the development of sustainable practices for resource recovery. This work underscores the potential of HTG as a key technology for addressing the global challenge of plastic pollution.
Integrated transcriptomics- and structure-based drug repositioning identifies drugs with proteasome inhibitor properties
Authors: Larsson Peter , De Rosa Maria Cristina , Righino Benedetta , Olsson Maxim , Florea Bogdan Iulius , Forssell-Aronsson Eva , Kovács Anikó , Karlsson Per , Helou Khalil , Parris Toshima Z.
Published: August 2024

Computational pharmacogenomics can potentially identify new indications for already approved drugs and pinpoint compounds with similar mechanism-of-action. Here, we used an integrated drug repositioning approach based on transcriptomics data and structure-based virtual screening to identify compounds with gene signatures similar to three known proteasome inhibitors (PIs; bortezomib, MG-132, and MLN-2238). In vitro validation of candidate compounds was then performed to assess proteasomal proteolytic activity, accumulation of ubiquitinated proteins, cell viability, and drug-induced expression in A375 melanoma and MCF7 breast cancer cells. Using this approach, we identified six compounds with PI properties ((-)-kinetin-riboside, manumycin-A, puromycin dihydrochloride, resistomycin, tegaserod maleate, and thapsigargin). Although the docking scores pinpointed their ability to bind to the β5 subunit, our in vitro study revealed that these compounds inhibited the β1, β2, and β5 catalytic sites to some extent. As shown with bortezomib, only manumycin-A, puromycin dihydrochloride, and tegaserod maleate resulted in excessive accumulation of ubiquitinated proteins and elevated HMOX1 expression. Taken together, our integrated drug repositioning approach and subsequent in vitro validation studies identified six compounds demonstrating properties similar to proteasome inhibitors.
Label free tracking to quantify nanoparticle diffusion through biological media
Authors: Schleyer Genevieve , Patterson Eann A. , Curran Judith M.
Published: August 2024

Nanotechnology is a rapidly evolving field and has been extensively studied in biological applications. An understanding of the factors that influence nanoparticle diffusion in biofluids can aid in the development of diverse technologies. The development of real-time, label-free tracking technologies would allow the expansion of current knowledge of the diffusion and activity of nanoparticles. Fluorescence-based microscopy is one of the most widespread tools to monitor and track nanoparticle dynamics; however, the influence of fluorescent tags on diffusion and biological activity is still unclear. In this study, we experimentally determined the diffusion coefficient of gold nanoparticles using a label-free, optical tracking technique and evaluated the influence of protein concentration, charge and diameter on nanoparticle diffusion through biological media. We dispersed positively- and negatively-charged nanoparticles with diameters varying from 10 to 100 nm in a common cell culture media with different concentrations of serum proteins. Our results show that dynamic protein interactions influence nanoparticle diffusion in the range of serum concentrations tested. Experimental regimes to obtain quantitative information on the factors that influence the dynamics of nanoparticles in biological media have been developed.