bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase and Amplitude Relationships Between Ozone, Temperature, and Circulation in the Quasi‐Biennial Oscillation
Authors: Ming Alison , Hitchcock Peter , Orbe Clara , Dubé Kimberlee
Published: February 2025

The phase and amplitude relationships between dynamical quantities and ozone within the quasi‐biennial oscillation (QBO) are explored. An initial assessment of this is done by applying a principal oscillation pattern analysis to observations (SWOOSH for Ozone) and reanalysis data (ERA5). This analysis highlights features of the ozone and temperature variability including two peaks in amplitude at different heights in the QBO region as well as more subtle phase differences that cannot be explained by a simple QBO theory. We also quantify the sizes of the ozone and temperature advection terms and show that the contribution of background upwelling on variations in the ozone gradient is not negligible . A radiative‐convective equilibrium and photochemical equilibrium model, with the imposed ERA5 QBO variation in upwelling and OSIRIS variations, is used to further understand ozone and temperature changes. The results show that photochemistry and transport are important at all levels, and it is misleading to divide the QBO into separate regimes. Prominent aspects of the variability can be reproduced if ERA5 upwelling is reduced by between 15 and where ERA5 is likely overpredicting the strength of the secondary meridional circulation. Finally, we demonstrate that nonlocality in the vertical plays a major role in QBO dynamics. This arises from ozone transport, the dependence on column ozone of photochemical production, and radiative transfer between layers.
The Influence of Parameterized Shallow Convection on Trade‐Wind Clouds and Circulations in the HARMONIE‐AROME Mesoscale Model
Authors: Savazzi A. C. M. , Nuijens L. , de Rooy W. , Siebesma A. P.
Published: February 2025

Mesoscale numerical weather prediction models currently operate at kilometer‐scale and even sub‐kilometer‐scale resolutions. Although shallow cumulus convection is partly resolved at these resolutions, it is still common to use a shallow cumulus parameterization (SCP). Within the context of the EUREC4A model intercomparison project, we evaluate how the modeled mesoscale cloud field in the trades responds to parameterized or explicit shallow convection in the mesoscale model HARMONIE‐AROME. We simulate a region of 3,200 × 2,025 east of Barbados using a grid spacing of 2.5 km for a 2 months period (1 January to 29 February 2020). We compare three configurations of HARMONIE‐AROME: (a) one with an active SCP (control), (b) one without parameterized momentum transport by shallow convection, and (c) one with an inactive SCP. The experiments produce different responses in the cloud field that are not incremental. With the SCP inactive, the model produces a warmer lower troposphere with many smaller but deeper clouds that precipitate more. Along with stronger resolved eddy kinetic energy, wider and stronger shallow meridional overturning circulations develop. In the configuration without parameterized momentum transport by shallow convection, the eddy‐diffusivity scheme effectively takes over the missing transport in the sub‐cloud layer up to 800 m. Above that level, horizontal wind variance increases as the total momentum flux decreases, enhancing eddy kinetic energy at scales of 2.5 km and larger. In contrast to the configuration with an inactive SCP, cloud top heights hardly deepen, but stratiform cloudiness below the inversion and mean cloud size increase.
A1AT dysregulation of metabolically stressed hepatocytes by Kupffer cells drives MASH and fibrosis
Authors: Park Jeong-Su , Lee Jin , Wang Feng , Ma Hwan , Zhou Zixiong , Lee Yong-Sun , Oh Kwangyeon , Lee Haram , Sui Guoyan , Lee Sangkyu , Yang Yoon Mee , Lee Jang-Won , Ji Yong-Ha , Park Chun-Woong , Yoo Hwan-Soo , Hwang Bang-Yeon , Han Sang-Bae , Song Nan , Oh Soohwan , Kim Bumseok , Seki Ekihiro , Hong Jin Tae , Roh Yoon Seok
Published: February 2025

Metabolic dysfunction-associated steatohepatitis (MASH) is associated with the activation of Kupffer cells (KCs) and hepatic stellate cells, at which point a metabolically stressed hepatocyte becomes integral to the progression of the disease. We observed a significant reduction in the level of alpha-1-antitrypsin (A1AT), a hepatocyte-derived secreted factor, in both patients with MASH and mice fed a fast-food diet (FFD). KC-mediated hepatic inflammation, most notably IL-1β, led to the transcriptional inhibition of A1AT by HNF4α. In quintuple Serpina1a–e knockout mice, ablation of A1AT worsened MASH through increased activity of proteinase 3 (PR3), a proinflammatory protease produced by F4/80hi/CD11blow/TIM4−/CCR2+ monocyte-derived KCs (MoKCs). Conversely, A1AT restoration or PR3 inhibition mitigated MASH progression. A PR3-bound cytokine array identified IL-32 as a key factor associated with MASH. Combining IL-32 with SERPINA1, the gene encoding A1AT, synergistically predicted patients at risk of MASH through univariate logistic regression analysis. Furthermore, in vivo overexpression of IL-32γ alleviated MASH induced by FFD. However, additional knockout of A1AT increased PR3 activity, consequently abolishing the anti-MASH effects of IL-32γ. Blocking PR3-mediated IL-32γ cleavage via the V104A mutation sustained its protective actions, while the PR3-cleaved C-terminal fragment activated KCs. Additionally, after cleavage, the antifibrogenic effect of IL-32γ is lost, resulting in a failure to prevent the activation of hepatic stellate cells. This study highlights the critical role of hepatocyte-derived A1AT in the PR3/IL-32γ axis during MASH development. Strategies to correct A1AT dysregulation, such as A1AT supplementation or PR3 inhibition with sivelestat, may offer protection against the development and progression of MASH and fibrosis.
Universal conservation laws of the wave-particle-entanglement triad: theory and experiment
Authors: Ding Ziheng , Deng Yaohao , Fei Shao-Ming , Zhou Si-Qi , Chen Xiaojiong , Rui Ziwen , Ma Zhihao , Xiao Yunlong , Wang Jianwei
Published: February 2025

When observed, a quantum system exhibits either wave-like or particle-like properties, depending on how it is measured. However, this duality is affected by the entanglement of the system with its quantum memory, raising a fundamental question: how are wave–particle duality and entanglement related? Here, we broaden the scope of wave–particle duality to include entanglement, introduce universal conservation laws for the wave–particle–entanglement triad, and perform demonstrations on silicon–integrated nanophotonic quantum chips. Our experiments not only mark the first confirmation of universal conservation laws but also highlight the potential of integrated photonics for exploring complex quantum phenomena in high-dimensional systems.
Exome sequencing identifies HELB as a novel susceptibility gene for non-mucinous, non-high-grade-serous epithelial ovarian cancer
Authors: Dicks Ed M. , Tyrer Jonthan P. , Ezquina Suzana , Jones Michelle , Baierl John , Peng Pei-Chen , Diaz Michael , Goode Ellen , Winham Stacey J. , Dörk Thilo , Gorp Toon Van , Fazio Anna De , Bowtell David D. L. , Garsed Dale W. , Odunsi Kunle , Moysich Kirsten , Pavanello Marina , Fostira Florentia , Webb Penelope M. , Soukupová Jana , Cohen Paul A. , Sieh Weiva , Fortner Renée Turzanski , Ricker Charite , Karlan Beth , Campbell Ian , Brenton James D. , Ramus Susan J. , Gayther Simon A. , Pharoah Paul D. P.
Published: February 2025

Rare, germline loss-of-function variants in a handful of DNA repair genes are associated with epithelial ovarian cancer. The aim of this study was to evaluate the role of rare, coding, loss-of-function variants across the genome in epithelial ovarian cancer. We carried out a gene-by-gene burden test with various histotypes using data from 2573 non-mucinous cases and 13,923 controls. Twelve genes were associated at a False Discovery Rate of less than 0.1 of which seven were the known ovarian cancer susceptibility genes BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, MSH6 and PALB2. The other five genes were OR2T35, HELB, MYO1A and GABRP which were associated with non-high-grade serous ovarian cancer and MIGA1 which was associated with high-grade serous ovarian cancer. Further support for the association of HELB association comes from the observation that loss-of-function variants in HELB are associated with age at natural menopause and Mendelian randomisation analysis shows an association between genetically predicted age at natural menopause and endometrioid ovarian cancer, but not high-grade serous ovarian cancer.
Long term analysis of microbiological isolates and antibiotic susceptibilities in acute-onset postoperative endophthalmitis: a UK multicentre study
Authors: Teh Boon Lin , Ong Ariel Yuhan , Mehta Ankur , Hoang Vy , Settle Chris , Lotery Andrew J. , Charbel Issa Peter , Smith Jonathan , Steel David H.
Published: February 2025

Objectives

To review the trend of microbial isolates for postoperative endophthalmitis (POE) in the United Kingdom (UK) and determine the sensitivity to current empirical intravitreal antibiotic treatment.

Methods

We conducted a long term multicentre consecutive case review of POE across 3 geographically distant tertiary eye centres in the UK: Sunderland Eye Infirmary (2000–2022), Oxford Eye Hospital (2016–2022), and Southampton General Hospital (2016–2022). Data on the microbial samples taken and results including sensitivities to antibiotics agents given were collected. Poisson regression was used to analyse microbial trends and outcomes were considered statistically significant at a level of p < 0.05.

Results

179 consecutive eyes of 177 patients with POE met our inclusion criteria. The most common primary procedure was phacoemulsification and IOL insertion followed by intravitreal injections. 104 (58.1%) were culture positive and most were Gram-positive bacteria (85, 81.7%). The microbial trend consistently showed Staphylococcus epidermidis and unspecified coagulase-negative Staphylococci to be the most prevalent pathogens. Poisson regression showed no statistically significant change in any of the bacterial isolates over our study period. Antibiotic sensitivity data was available for 74% of the culture positive samples (77/104). All Gram-positive bacteria (68/68, 100%) and most (8/9, 88.9%) Gram-negative bacteria were sensitive to the empirical antibiotics (Vancomycin and Ceftazidime/Amikacin) given at presentation.

Conclusions

Most of the bacterial isolates causing POE in the UK are Gram-positive bacteria, and the trend has remained stable over more than two decades. Current empirical treatment with intravitreal Vancomycin and Ceftazidime/Amikacin provides effective broad coverage for the vast majority of cases.
Fast capillary waves on an underwater superhydrophobic surface
Authors: Fauconnier Maxime , Karunakaran Bhuvaneshwari , Drago-González Alex , Wong William S. Y. , Ras Robin H. A. , Nieminen Heikki J.
Published: February 2025

The propagation of interfacial waves in free and constrained conditions, such as deep and shallow water, has been broadly studied over centuries. It is a common event that anyone can witness, while contemplating the ocean waves washing ashore. As a complementary configuration, this work introduces waves propagating on an interface restricted by its pinning to the solid microstructures of an underwater superhydrophobic surface. The latter has the ability to stabilize a well-defined microscale gas layer, called a plastron, trapped between the water and the solid phase. The acoustic radiation force produced with focused MHz ultrasound successfully triggers kHz “plastronic waves”, i.e., capillary waves travelling on a plastron’s gas-water interface. The exposed waves possess interesting features, i.e., (i) a high propagation speed up to 45 times faster than conventional deep water capillary waves of comparable wavelength and (ii) a relation of the propagation speed with the geometry of the microstructures. Based on this and on the observed variation of wave speed over time in conditions of gas-undersaturated or -supersaturated water, the usefulness of the plastronic waves for the non-destructive monitoring of the plastron’s stability and the spontaneous air diffusion is eventually demonstrated.
Negative refraction of light in an atomic medium
Authors: Ruks L. , Ballantine K. E. , Ruostekoski J.
Published: February 2025

The quest to manipulate light propagation in ways not possible with natural media has driven the development of artificially structured metamaterials. One of the most striking effects is negative refraction, where the light beam deflects away from the boundary normal. However, due to material characteristics, the applications of this phenomenon, such as lensing that surpasses the diffraction limit, have been constrained. Here, we demonstrate negative refraction of light in an atomic medium without the use of artificial metamaterials, employing essentially exact simulations of light propagation. High transmission negative refraction is achieved in atomic arrays for different level structures and lattice constants, within the scope of currently realised experimental systems. We introduce an intuitive description of negative refraction based on collective excitation bands, whose transverse group velocities are antiparallel to the excitation quasi-momenta. We also illustrate how this phenomenon is robust to lattice imperfections and can be significantly enhanced through subradiance.
Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues
Authors: Shin Tay Won , Wang Hao , Zhang Chi , An Bobae , Lu Yangning , Zhang Elizabeth , Lu Xiaotang , Karagiannis Emmanouil D. , Kang Jeong Seuk , Emenari Amauche , Symvoulidis Panagiotis , Asano Shoh , Lin Leanne , Costa Emma K. ,   IMAXT Grand Challenge Consortium, Marblestone Adam H. , Kasthuri Narayanan , Tsai Li-Huei , Boyden Edward S.
Published: February 2025

Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validate the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supports the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrate the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yields ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.
EXPERT expands prime editing efficiency and range of large fragment edits
Authors: Xiong Youcai , Su Yinyu , He Ruigao , Han Xiaosong , Li Sheng , Liu Minghuan , Xi Xiaoning , Liu Zijia , Wang Heng , Xie Shengsong , Xu Xuewen , Li Kui , Zhang Jifeng , Xu Jie , Li Xinyun , Zhao Shuhong , Ruan Jinxue
Published: February 2025

Prime editing systems (PEs) hold great promise in modern biotechnology. However, their editing range is limited as PEs can only modify the downstream sequences of the pegRNA nick. Here, we report the development of the extended prime editor system (EXPERT) to overcome this limitation by using an extended pegRNA (ext-pegRNA) with modified 3’ extension, and an additional sgRNA (ups-sgRNA) targeting the upstream region of the ext-pegRNA. We demonstrate that EXPERT can efficiently perform editing on both sides of the ext-pegRNA nick, a task that is unattainable by canonical PEs. EXPERT exhibits prominent capacity in replacing sequences up to 88 base pairs and inserting sequences up to 100 base pairs within the upstream region of the ext-pegRNA nick. Compared to canonical PEs such as PE2, the utilization of the EXPERT strategy significantly enhances the editing efficiency for large fragment edits with an average improvement of 3.12-fold, up to 122.1 times higher. Safety wise, the use of ups-sgRNA does not increase the rates of undesirable insertions and deletions (indels), as the two nicks are on the same strand. Moreover, we do not observe increased off-target editing rates genome-wide. Our work introduces EXPERT as a PE tool with significant potential in life sciences.
Fully addressable designer superstructures assembled from one single modular DNA origami
Authors: Weck Johann M. , Heuer-Jungemann Amelie
Published: February 2025

DNA nanotechnology and especially the DNA origami method are primal tools to create precise nanoscale objects. For DNA origami, a long ssDNA scaffold strand is folded by a multitude of smaller staple strands into base-pair accurate shapes, allowing for precise modification and incorporation of guest molecules. However, DNA origami are limited in size, and thus is the area that can be controlled with nanoscale precision. Prior methods of creating larger assemblies were either costly or lacked structural control. Here, we incorporate two methods of modularity into one exemplary modular DNA origami (moDON). The modularity allows for the creation of over 50,000 diverse monomers and subsequently the assembly of a plethora of fully addressable designer superstructures while keeping the construction cost very low. The here-introduced methods for modularity in DNA origami design offer an efficient, cost-effective solution for constructing precisely organized, and fully addressable structures on a variety of scales.
Intercellular adhesion boots collective cell migration through elevated membrane tension
Authors: Bijonowski Brent M. , Park Jongkwon , Bergert Martin , Teubert Christina , Diz-Muñoz Alba , Galic Milos , Wegner Seraphine V.
Published: February 2025

In multicellular systems, the migration pattern of individual cells critically relies on the interactions with neighboring cells. Depending on the strength of these interactions, cells either move as a collective, as observed during morphogenesis and wound healing, or migrate individually, as it is the case for immune cells and fibroblasts. Mediators of cell-cell adhesions, such as cadherins coordinate collective dynamics by linking the cytoskeleton of neighboring cells. However, whether intercellular binding alone triggers signals that originate from within the plasma membrane itself, remains unclear. Here, we address this question through artificial photoswitchable cell-cell adhesions that selectively connect adjacent plasma membranes without linking directly to cytoskeletal elements. We find that these intercellular adhesions are sufficient to achieve collective cell migration. Linking adjacent cells increases membrane tension, which activates the enzyme phospholipase D2. The resulting increase in phosphatidic acid, in turn, stimulates the mammalian target of rapamycin, a known actuator of collective cell migration. Collectively, these findings introduce a membrane-based signaling axis as promotor of collective cell dynamics, which is independent of the direct coupling of cell-cell adhesions to the cytoskeleton.
Structural insights into tecovirimat antiviral activity and poxvirus resistance
Authors: Vernuccio Riccardo , Martínez León Alejandro , Poojari Chetan S. , Buchrieser Julian , Selverian Christopher N. , Jaleta Yakin , Meola Annalisa , Guivel-Benhassine Florence , Porrot Françoise , Haouz Ahmed , Chevreuil Maelenn , Raynal Bertrand , Mercer Jason , Simon-Loriere Etienne , Chandran Kartik , Schwartz Olivier , Hub Jochen S. , Guardado-Calvo Pablo
Published: February 2025

Mpox is a zoonotic disease endemic to Central and West Africa. Since 2022, two human-adapted monkeypox virus (MPXV) strains have caused large outbreaks outside these regions. Tecovirimat is the most widely used drug to treat mpox. It blocks viral egress by targeting the viral phospholipase F13; however, the structural details are unknown, and mutations in the F13 gene can result in resistance against tecovirimat, raising public health concerns. Here we report the structure of an F13 homodimer using X-ray crystallography, both alone (2.1 Å) and in complex with tecovirimat (2.6 Å). Combined with molecular dynamics simulations and dimerization assays, we show that tecovirimat acts as a molecular glue that promotes dimerization of the phospholipase. Tecovirimat resistance mutations identified in clinical MPXV isolates map to the F13 dimer interface and prevent drug-induced dimerization in solution and in cells. These findings explain how tecovirimat works, allow for better monitoring of resistant MPXV strains and pave the way for developing more potent and resilient therapeutics.
Intrinsic electrical activity drives small-cell lung cancer progression
Authors: Peinado Paola , Stazi Marco , Ballabio Claudio , Margineanu Michael-Bogdan , Li Zhaoqi , Colón Caterina I. , Hsieh Min-Shu , Pal Choudhuri Shreoshi , Stastny Victor , Hamilton Seth , Le Marois Alix , Collingridge Jodie , Conrad Linus , Chen Yinxing , Ng Sheng Rong , Magendantz Margaret , Bhutkar Arjun , Chen Jin-Shing , Sahai Erik , Drapkin Benjamin J. , Jacks Tyler , Vander Heiden Matthew G. , Kopanitsa Maksym V. , Robinson Hugh P. C. , Li Leanne
Published: February 2025

Elevated or ectopic expression of neuronal receptors promotes tumour progression in many cancer types1,2; neuroendocrine (NE) transformation of adenocarcinomas has also been associated with increased aggressiveness3. Whether the defining neuronal feature, namely electrical excitability, exists in cancer cells and impacts cancer progression remains mostly unexplored. Small-cell lung cancer (SCLC) is an archetypal example of a highly aggressive NE cancer and comprises two major distinct subpopulations: NE cells and non-NE cells4,5. Here we show that NE cells, but not non-NE cells, are excitable, and their action potential firing directly promotes SCLC malignancy. However, the resultant high ATP demand leads to an unusual dependency on oxidative phosphorylation in NE cells. This finding contrasts with the properties of most cancer cells reported in the literature, which are non-excitable and rely heavily on aerobic glycolysis. Additionally, we found that non-NE cells metabolically support NE cells, a process akin to the astrocyte–neuron metabolite shuttle6. Finally, we observed drastic changes in the innervation landscape during SCLC progression, which coincided with increased intratumoural heterogeneity and elevated neuronal features in SCLC cells, suggesting an induction of a tumour-autonomous vicious cycle, driven by cancer cell-intrinsic electrical activity, which confers long-term tumorigenic capability and metastatic potential.
Cliopatria - A geospatial database of world-wide political entities from 3400BCE to 2024CE
Authors: Bennett James S. , Mutch Erin , Tollefson Andrew , Chalstrey Ed , Benam Majid , Cioni Enrico , Reddish Jenny , Zsambok Jakob , Levine Jill , Cook C. Justin , Francois Pieter , Hoyer Daniel , Turchin Peter
Published: February 2025

The scientific understanding of the complex dynamics of global history – from the rise and spread of states to their declines and falls, from their peaceful interactions with economic or diplomatic exchanges to violent confrontations – requires, at its core, a consistent and explicit encoding of historical political entities, their locations, extents and durations. Numerous attempts have been made to produce digital geographical compendia of polities with different time depths and resolutions. Most have been limited in scope and many of the more comprehensive geospatial datasets must either be licensed or are stored in proprietary formats, making access for scholarly analysis difficult. To address these issues we have developed Cliopatria, a comprehensive open-source geospatial dataset of worldwide states from 3400BCE to 2024CE. Presently it comprises over 1600 political entities sampled at varying timesteps and spatial scales. Here, we discuss its construction, its scope, and its current limitations.
The 30 m land cover dataset for capturing land cover changes induced by ecological restoration from 1990 to 2022 on the Chinese Loess Plateau
Authors: Wang Zhihui , Shi Xiaogang , Dou Shentang , Cheng Miaomiao , Miao Lulu
Published: February 2025

Continuous time-series of land cover is critical for attributing runoff, sediment and carbon changes on the Chinese Loess Plateau (CLP). However, current land cover products with annal temporal resolution lack spatial identification accuracy, particularly in capturing authentic changes of cropland, forest and grassland. To address these issues, a 30 m annual land cover dataset was proposed by the Yellow River Conservancy Commission (YRCC_LPLC) for the CLP from 1990 to 2022. Different levels of land cover were classified using different combinations of spectral, monthly and annual temporal and topographic features and Random Forest classifier. Compared to other land cover products (45.64%–73.38%), the accuracy of YRCC_LPLC has a better performance with an overall accuracy of 85.16%. The YRCC_LPLC is capable of capturing not only the explicit spatial variation but also the change direction and change time of land cover, especially for the most critical conversion of cropland into forest and grassland induced by implementation of Grain to Green Program on the CLP.
Experimental and theoretical assessment to investigate the impact of Gast Reg drug on the copper corrosion control in an acidic environment
Authors: Syam S. M. , Nady H. , Eid Salah , El-Katori Emad E.
Published: February 2025

Herein, a corrosion inhibitor called the Gast Reg drug (GRD) was used to prevent the copper from corroding. The aggressive solution used in this investigation was HCl acid solution. A mix of electrochemical and quantum investigations are used to assess GRD’s anti-corrosion properties. It has been discovered that the GRD is essential for stopping copper from corroding in a 2 M HCl solution. The study’s results indicated that GRD shown considerable corrosion prevention capabilities for copper in 2 M HCl solution. The inhibitory effectiveness of GRD was seen to rise with higher concentrations of GRD. It is noteworthy that the maximum levels of inhibitory effectiveness (82.1%) for HCl solution were obtained at 123.87 × 10− 5 M. The primary cause of GRD’s anti-corrosion properties is its propensity to adsorb on the surface of copper via its heteroatoms. The inhibitor’s adsorption behavior was described using the Langmuir model. Surface assessments with Energy Dispersive X-ray (EDX), Scanning Electron Microscope (SEM), and Atomic Force Microscope (AFM) demonstrated the development of a prominent adsorbed film on the copper surface. The correlation between molecule structure and its inhibitory effect has been investigated and analyzed using DFT and Monte Carlo simulation. The actual adsorption occurs through a variety of active centers and physical and chemical processes that are coordinated with the calculated quantum parameters. The outcomes gathered from electrochemical, surface, and theoretical studies are well correlated.
ANFIS algorithm for mapping computational data of water reservoir homogenization with air bubble flows
Authors: Kolsi Lioua , Behroyan Iman , Darweesh Moustafa S. , Alshammari Badr M. , Armaghani T. , Babanezhad Meisam
Published: February 2025

Air as an inert gas is usually applied for homogenization and mixing liquids. In the current research, we study a 3-D bubble column reactor (BCR) filled with water by using an Artificial intelligence algorithm (AI) and CFD. We used one of the adaptive networks and fuzzy inference systems (ANFIS) to study fluid flow and see its effect on the accuracy of the AI. Therefore, the Gaussian membership function was used to have a prediction in the 3-D BCR. Also, the grid partition system was used to cluster the data. The number of membership functions increases in the training process of the AI system, from 2 to 5. The influence of input numbers on AI data prediction is analyzed. The four inputs in the training process included air velocity and pressure, as well as the x-direction and z-direction. Finally, air vorticity was considered as the output parameter of the study in the predictions. Correlations were developed to predict the air vorticity in each node using x and z direction, air velocity, and pressure. The results showed the AI accuracy increased by the rise of membership and input numbers. The AI intelligence level was found by five memberships and four inputs. The AI and CFD were in suitable agreement (regression number around 1). The developed correlations could simplify the calculation of air vorticity instead of using the complicated and time-consuming CFD simulation. As far as the authors know, there are no studies that have developed correlations to find the air vorticity in bubble column reactors.
Instrumental variable estimation for compositional treatments
Authors: Ailer Elisabeth , Müller Christian L. , Kilbertus Niki
Published: February 2025

Many scientific datasets are compositional in nature. Important biological examples include species abundances in ecology, cell-type compositions derived from single-cell sequencing data, and amplicon abundance data in microbiome research. Here, we provide a causal view on compositional data in an instrumental variable setting where the composition acts as the cause. First, we crisply articulate potential pitfalls for practitioners regarding the interpretation of compositional causes from the viewpoint of interventions and warn against attributing causal meaning to common summary statistics such as diversity indices in microbiome data analysis. We then advocate for and develop multivariate methods using statistical data transformations and regression techniques that take the special structure of the compositional sample space into account while still yielding scientifically interpretable results. In a comparative analysis on synthetic and real microbiome data we show the advantages and limitations of our proposal. We posit that our analysis provides a useful framework and guidance for valid and informative cause-effect estimation in the context of compositional data.
Multi spectroscopic investigation of maisine-based microemulsions as convenient carriers for co-delivery of anticancer and anti-inflammatory drugs
Authors: Nistor Mirela , Nicolescu Alina , Amarandi Roxana-Maria , Pui Aurel , Stiufiuc Rares-Ionut , Dragoi Brindusa
Published: February 2025

Lipid-based drug delivery systems are very promising in addressing critical medical needs associated with cancer because they are able to enhance the efficacy of the therapeutic agents loaded in. Yet, their transferability from bench to bedside is still a challenge as it hits many barriers. Among them, the absence of a clear design made on the deeper understanding of the intermolecular forces underlying the formation of the drug-carrier system and the controlled release of the drug is relevant. In this contribution, we rationally designed and prepared lipid-based formulations of an anticancer drug, fluorouracil (FU - hydrophilic) and an anti-inflammatory drug, ibuprofen (IBU - hydrophobic) to thoroughly characterize the specific intermolecular interactions between drugs and components of the carrier matrix. Microemulsions (ME) were selected as the main carriers for this study, but a comparison with liposomes was performed to observe if different organization of the lipophilic and hydrophilic compartments influences the loading capacity and controlled release of these two drugs. Using Maisine CC, a biocompatible oil, and Tween 20 as the surfactant, normal oil-in-water ME loaded with FU and IBU (1:1, 1:3, 1:6, wt:wt) were prepared by the water titration method. MEs were characterized by DLS, Zeta potential, and DOSY spectroscopies to assess their droplet size, surface charge, structure and type of emulsion. Intermolecular interactions between drugs and components of the ME’s matrix were investigated by FT-IR, RAMAN and 1H-NMR spectroscopies. The experimental results of DOSY revealed that all components of MEs are gathered in normal oil-in-water ME. Due to their different affinities for the main components of the ME, FU, and IBU were mainly distributed in the aqueous and oily phases, respectively, as supported by the droplet size measured by DLS. It was observed that co-loading the two drugs impacted the release behavior, assessed by the dialysis bag method, as compared with the mono-drug formulations. Based on the findings of this work, a release mechanism for FU and IBU was proposed, as well. Overall, the ME proved to be more suitable nanocarriers since the drugs, which were loaded in higher amounts as compared to liposomes, followed a controlled and sustained release of at least 96 h.
ZCCHC4 regulates esophageal cancer progression and cisplatin resistance through ROS/c-myc axis
Authors: Yao Lihua , Wu Piao , Yao Fangyi , Huang Bo , Zhong Fangmin , Wang Xiaozhong
Published: February 2025

Zinc finger CCHC-type containing 4 (ZCCHC4) is a newly discovered N
6-methyladenosine (m6A) RNA methyltransferase (MTase), which possesses an m6A MTase domain and an RNA-binding protein (RBP) Znf domain. Aberrantly expressed ZCCHC4 has been found to be correlated with poor prognosis and chemoresistance in various tumors, such as hepatocellular carcinoma, lung cancer and colorectal cancer. However, the expression and functional analysis of the role of ZCCHC4 in esophageal cancer (ESCA) is still elusive. The expression of ZCCHC4 in esophageal cancer tissues was evaluated by qPT-PCR and western blot. Serum esophageal tumor markers are detected by electrochemiluminescence immunoassay. Relationship between ZCCHC4 expression and pathway enrichment analysis were analyzed by R. The reactive oxygen species (ROS), cell proliferation, cell cycle and apoptosis of ZCCHC4 in esophageal squamous cell carcinoma (ESCC) cells tested by CCK8 assay and flow cytometry assay. Aberrant expression of ZCCHC4 is associated with cancer stages, lymph node metastasis (LNM), and tumor histology, and poorer Overall Survival (OS) in esophageal cancer. The mRNA level of ZCCHC4 in esophageal cancer patients correlates with serum carcinoembryonic antigen (CEA) levels, Squamous Cell Carcinoma (SCC) markers, and tissue polypeptide antigen (TPA) levels. Knockdown of ZCCHC4 induces DNA damage, leading to an elevation of reactive oxygen species (ROS), which in turn triggers S-phase arrest, enhances apoptosis, augments sensitivity to cisplatin treatment, and inhibits proliferation in esophageal cancer cells. Conversely, overexpression of ZCCHC4 promotes proliferation, inhibits apoptosis, and increases resistance to cisplatin in esophageal cancer cells. Furthermore, scavenging ROS reverses the effects of ZCCHC4 downregulation on both proliferation and apoptosis in esophageal cancer cells. Additionally, downregulation of ZCCHC4 inhibits the progression of esophageal cancer and reduces cisplatin resistance in vivo. In summary, downregulation of ZCCHC4 leads to increased sensitivity of ESCC cells to cisplatin, inhibits proliferation, and promotes apoptosis in esophageal cancer cells, potentially via the ROS/c-myc axis. The study suggests a potential adjunctive role for ZCCHC4 in the diagnosis and treatment of esophageal cancer and aids in further understanding the underlying mechanisms in ESCA progression.
Invasive tree species affect terricolous bryophytes biomass and biodiversity in nutrient-poor but not nutrient-rich temperate forests
Authors: Bury Sebastian , Dyderski Marcin K.
Published: February 2025

Although invasive tree species pose a significant threat to biodiversity, their impact on terricolous bryophytes has been insufficiently recognized. In addition, almost all previous studies focused on differences between invaded and uninvaded stands, not accounting for the effect of invader abundance. Here we aimed to assess the impact of Prunus serotina and Robinia pseudoacacia on terricolous bryophytes on nutrient-poor (Pinus sylvestris stands) and nutrient-rich (Quercus spp. stands) sites, along a gradient of invader biomass. We assessed the cover and species richness of bryophytes by vegetation surveys in 160 study plots (100 m2) and biomass in eight 0.264 m2 circular subplots. Both tree species affected the cover and biomass of bryophytes, while R. pseudoacacia also reduced species richness. Although we did not confirm their impact on species composition except R. pseudoacacia in nutrient-poor sites, we revealed the negative individual responses of three species to invader biomass: Pleurozium schreberi, Dicranum polysetum, and D. scoparium. However, these impacts occurred only on nutrient-poor sites, but not on nutrient-rich sites. We provided the first quantitative assessment of P. serotina and R. pseudoacacia impacts on terricolous bryophytes along its biomass gradient. We showed low vulnerability of terricolous bryophytes in nutrient-rich broadlevaed sites while high in nutrient-poor coniferous sites, showing that there is no safe level of invader biomass.
Assessment of water quality and health hazards using water quality index and human health risk evaluation in district Talagang Pakistan
Authors: Rehman Nazir ur , Khan Mumtaz Ali , Ullah Shuja , Siab Afra , Islam Fakhrul , Elbeltagi Ahmed , Salem Ali
Published: February 2025

This work was carried out for the determination of the water quality in the Talagang District of Pakistan, as water is essential for agriculture and drinking uses. This study aims to assess the water quality for irrigation, drinking, and health risks using the Water Quality Index (WQI) and Human Health Risk Assessment (HHRA) tools to identify regions with contaminated water, and to evaluate the associated risks. A total of 98 water samples were taken at various points from diverse sources such as hand pumps, streams, springs, dug wells, and tube wells for physio-chemical assessment. In the current study, the effectiveness of the irrigation water quality index (IWQI), human health risk assessment (HHRA), and water quality index (WQI) tools have been assessed. The characteristics of subterranean water are influenced by evaporation, ion exchange, rock-water interaction, and parent-rock weathering, as shown by the Piper and Gibbs diagram. According to the WQI results, the water quality is 20. 89% and 27.46% of the sample sites are moderate and poor, making them unfit for human intake. Based on HHRA, compared to adult males and females in the study area, children are deemed to be at a higher risk. A larger number of the sample localities are appropriate for irrigation purposes. The study assists in identifying contaminated regions and in monitoring newly implemented remediation actions to manage the source of contaminants in the study area.
Benchmarking the diagnostic performance of open source LLMs in 1933 Eurorad case reports
Authors: Kim Su Hwan , Schramm Severin , Adams Lisa C. , Braren Rickmer , Bressem Keno K. , Keicher Matthias , Platzek Paul-Sören , Paprottka Karolin Johanna , Zimmer Claus , Hedderich Dennis M. , Wiestler Benedikt
Published: February 2025

Recent advancements in large language models (LLMs) have created new ways to support radiological diagnostics. While both open-source and proprietary LLMs can address privacy concerns through local or cloud deployment, open-source models provide advantages in continuity of access, and potentially lower costs. This study evaluated the diagnostic performance of fifteen open-source LLMs and one closed-source LLM (GPT-4o) in 1,933 cases from the Eurorad library. LLMs provided differential diagnoses based on clinical history and imaging findings. Responses were considered correct if the true diagnosis appeared in the top three suggestions. Models were further tested on 60 non-public brain MRI cases from a tertiary hospital to assess generalizability. In both datasets, GPT-4o demonstrated superior performance, closely followed by Llama-3-70B, revealing how open-source LLMs are rapidly closing the gap to proprietary models. Our findings highlight the potential of open-source LLMs as decision support tools for radiological differential diagnosis in challenging, real-world cases.
A neural network-based synthetic diagnostic of laser-accelerated proton energy spectra
Authors: McQueen Christopher J. G. , Wilson Robbie , Frazer Timothy P. , King Martin , Alderton Matthew , Bacon Ewan F. J. , Dolier Ewan J. , Dzelzainis Thomas , Patel Jesel K. , P. Peat Maia , Torrance Ben C. , Gray Ross J. , McKenna Paul
Published: February 2025

Machine learning can revolutionize the development of laser-plasma accelerators by enabling real-time optimization, predictive modeling and experimental automation. Given the broad range of laser and plasma parameters and shot-to-shot variability in laser-driven ion acceleration at present, continuous monitoring with real-time, non-disruptive ion diagnostics is crucial for consistent operation. Machine learning provides effective solutions for this challenge. We present a synthetic diagnostic method using deep neural networks to predict the energy spectrum of laser-accelerated protons. This model combines variational autoencoders for dimensionality reduction with feed-forward networks for predictions based on secondary diagnostics of the laser-plasma interactions. Trained on data from fewer than 700 laser-plasma interactions, the model achieves an error level of 13.5%, and improves with more data. This non-destructive diagnostic enables high-repetition laser operations with the approach extendable to a fully surrogate model for predicting realistic ion beam properties, unlocking potential for diverse applications of these promising sources.
Calcite is an efficient and low-cost material to enhance benthic weathering in shelf sediments of the Baltic Sea
Authors: Fuhr Michael , Dale Andrew W. , Wallmann Klaus , Bährle Rebecca , Kalapurakkal Habeeb Thanveer , Sommer Stefan , Spiegel Timo , Dobashi Ryo , Buchholz Björn , Schmidt Mark , Perner Mirjam , Geilert Sonja
Published: February 2025

Recent studies have proposed calcite and dunite as possible alkaline materials for enhanced benthic weathering in shallow depocenters of the Baltic Sea as a marine carbon dioxide removal strategy. In this study, insights on calcite and dunite weathering from laboratory incubations and long-term benthocosm experiments are combined with a numerical box-model to assess the carbon dioxide uptake potential of mineral addition to organic-rich sediments in the southwest Baltic Sea. The results reveal that calcite has an up to 10-fold higher carbon dioxide uptake efficiency and is therefore the preferable material for enhanced benthic weathering as a marine carbon dioxide removal method, with costs per tonne of sequestered carbon dioxide ranging between 82 and 462 euro for calcite while reaching 558–1920 euro for dunite. These findings could be applicable to other areas in the Baltic Sea and also globally to sediments in the wider coastal shelf with similar geochemical properties.
Early signs of long-term pain: prospective network profiles from late adolescence and lifelong follow-up
Authors: Thompson William Hedley , Thern Emelie , Gedin Filip , Andreasson Anna , Jensen Karin B. , Lalouni Maria
Published: February 2025

This study applies network theory to registry data to identify prospective differences between individuals who develop long-term pain later in life and those who do not. The research is based on assessments of biological, psychological, and social variables in late adolescence during military conscription in Sweden. The analysis reveals significant differences in the network profiles of adolescent men who later developed long-term pain. These differences are reflected in several network-based outputs, including global, nodal, and edge levels, revealing a consistent picture of the pain-associated network profile. This profile demonstrates how those vulnerable to long-term pain have a specific configuration of variables that skew away from the rest of the population, mainly relating to psychosocial aspects.
Shifted-excitation Raman difference spectroscopy and charge-shifting detection coupled with spatially offset Raman spectroscopy for heritage science
Authors: Lux Alberto , Conti Claudia , Botteon Alessandra , Mosca Sara , Matousek Pavel
Published: February 2025

SERDS and charge-shifting technologies can be combined with SORS for the non-invasive in situ investigations of the subsurface of cultural heritage materials while simultaneously rejecting ambient light and fluorescence interfering contributions.
Enhanced combination therapy through tumor microenvironment-activated cellular uptake and ROS-sensitive drug release using a dual-sensitive nanogel
Authors: Yuan Jianming , Chen Qinfeng , Zuo Mingxiang , Li Xiaoxia , Ou ChiYi , Chen Qinghua , Yu Dongsheng , Li Haowen , Hao Chenhui , Yang Jing , Liu Shuang , Cheng Du
Published: February 2025

A facile approach for enhanced combination therapy using a low pH and NIR irradiation-dual sensitive nanogel.
Selective binding of rare-earth ions in polymerizable cages
Authors: Ou Jou-Tsen , Taylor Mercedes K.
Published: February 2025

An alkene-terminated ligand self-assembles with rare-earth ions, yielding polymerizable cages and subsequently rare-earth-binding polymer networks.
An anion exchange membrane of layered silicalite nanosheets with surface quaternary ammonium cations
Authors: Sharma Yukta , Singh Devraj , Cao Zishu , Gabski Jan , Dong Junhang
Published: February 2025

An anion exchange membrane made of quaternary ammonium action templated silicalite nanosheets is demonstrated for high-performance in an alkaline water electrolyzer.
First principles assessment of solvent induced cage effects on intramolecular hydrogen transfer in the free radical polymerization of acrylates
Authors: Serse Francesco , Salvalaglio Matteo , Pelucchi Matteo
Published: February 2025

Theoretical assessment of solvent effects on the intramolecular hydrogen transfer of poly-butyl acrylate. The calculated rate parameters are validated against experimental rate constants and polymerization rates from the literature.
Engineering topological phases in transition-metal-doped penta-hexa-graphene: towards spintronics applications
Authors: Chen Rongrong , Yang Lei , Gao Jin , Xue Desheng , Jia Chenglong , Tao Kun
Published: February 2025

The roles of Pd and Pt doping in penta-hexa-graphene (PH-G) were studied using first principles DFT calculations, which may lead to a better understanding of the dopant effects and further help to expand the application potential of PH-G.
Steric effects in the adsorption of O2 on a Cu(111) surface
Authors: Wu Lok Yiu , Roman Maksymilian J. , Heazlewood Brianna R. , Kurahashi Mitsunori
Published: February 2025

Probing the stereodynamics of a gas–surface interaction is a useful tool to investigate the mechanisms responsible for adsorption.
Size-dependent catalytic reactivity of NO reduction by CO mediated by RhnV2O3− clusters (n = 2–5)
Authors: Chen Jin-You , Zhu Hai , Ma Tong-Mei , Li Xiao-Na
Published: February 2025

We theoretically demonstrated that RhnV2O3–5– (n = 2–5) clusters can catalytically reduce NO into N2 selectively by CO, and a size-dependent behavior of NO reduction was discovered and rationalized.
Redox mediator-modified self-assembled monolayer stabilizes a buried interface in efficient inverted perovskite solar cells
Authors: Qu Shujie , Yang Fu , Huang Hao , Li Yiyi , Sun Changxu , Zhang Qiang , Du Shuxian , Yan Luyao , Lan Zhineng , Wang Zhiwei , Jiang Tongtong , Cui Peng , Ai Xicheng , Li Meicheng
Published: February 2025

The redox material methylene blue was utilized to construct a selective redox cycle at the NiOx/perovskite interface and optimize the dispersion of SAMs through π–π interactions, resulting in high-efficiency PSCs with excellent operational stability.
Anti-solvent engineering for efficient and stable perovskite solar cells with preferentially orientated 2-dimensional/3-dimensional heterojunctions
Authors: Zhang Zhinan , Xu Yinghao , Wang Shaofu , Peng Chuan , Liu Peiran , Du Shengjie , Pu Dexin , Zhao Xingzhong , Shang Minghui , Fang Guojia , Yu Zhenhua
Published: February 2025

A (001) facet out-of-plane-oriented 2D/3D perovskite was achieved by introducing 4-MeO-PEAI and n-HeXAI into hybrid anti-solvents, exhibiting a PCE of 26.02% and VOC of 1.218 V.