bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fully addressable designer superstructures assembled from one single modular DNA origami
Authors: Weck Johann M. , Heuer-Jungemann Amelie 
Published: February 2025

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.