bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling of Tectonics, Climate, and Lithology in Orogenic Systems: Insights From Cosmogenic 10Be Erosion Rates and River Profile Inversion Modeling in the Talesh Mountains, NW Iranian Plateau
Authors: Moumeni Mohammad , Delchiaro Michele , Ballato Paolo , Della Seta Marta , Nozaem Reza , Clementucci Romano , Tikhomirov Dmitry , Christl Marcus , Egli Markus 
Published: February 2025

AbstractThe landscape of the Talesh Mountains, located in the NW sector of the Iranian Plateau (within the Arabia‐Eurasia collision zone), results from the interplay of multiple forces. To explore the interaction between tectonics, climate, and lithology we present 11 new erosion rates derived from meteoric 10Be on the eastern (wetter) and western (drier) flanks of the range. The erosion rates range from approximately 100 to 400 m/Myr, with lower values in the more arid plateau interior and higher values in the more humid plateau exterior (western and eastern Talesh flanks, respectively). These rates exhibit a positive correlation with topographic metrics and a moderate correlation with mean annual precipitation, suggesting a tectonic control possibly enhanced by the across‐strike precipitation gradient. Conversely, erosion rates do not correlate with rock strength. However, along‐ and across‐strike changes in rock erodibility suggest that lithology may have influenced the landscape response time to evolving boundary conditions. Furthermore, relative rock‐uplift histories from river profile inversion analysis indicate that mountain‐building processes accelerated around 12–10 Ma, possibly due to a combination of short‐wavelength (i.e., shallower) processes, such as thrusting, and long‐wavelength (i.e., deeper) processes, such as lower mantle inflow. This led to a progressive precipitation concentration along the windward side of the orogen, leading to efficient mass removal via erosion and further enhancing tectonic activity. Additionally, an increase in erosion rates occurred during the 0.6–1.5 km lowering of the Caspian Sea base‐level between ∼6 and 3.2 Ma. Overall, the efficient erosion on the wetter side likely concentrated tectonic deformation, ultimately contributing to the development of a stationary wedge.
Evaluation of magnesium-based scaffolds fabricated using a modified sintering technique and two types of space holding agents (in vitro study)
Authors: Ghabour Omnia , Taha Nahla , Aboul Gheit Salma , Mohy El Din Mona 
Published: February 2025

Abstract

Objective
The aim of this work was to study the mechanical, degradation behavior and bioactivity of porous magnesium-based scaffolds alloyed with zinc and hydroxyapatite, fabricated using two different types of space holding agents and a modified powder metallurgy route.

Methods
Powder particles of magnesium, zinc, hydroxyapatite (HA) and spacers were mixed, then mixtures were divided into 6 groups: IA (urea/0%HA), IB (urea/5%HA), IC (urea/7.5%HA), IIA (ammonium bicarbonate/0%HA), IIB (ammonium bicarbonate/5%HA) and IIC (ammonium bicarbonate/7.5%HA). A modified powder metallurgy route was used to fabricate the composites. Porosity analysis and microstructural characterization using Scanning Electron Microscope (SEM), Energy Dispersive X-ray Analysis (EDX), and X-ray Diffraction Analysis (XRD) were done. Evaluation of mechanical properties, in-vitro degradation rate in simulated body fluid (SBF) and in-vitro bioactivity using SEM and XRD were done. Data were statistically analyzed using two-way and three-way repeated ANOVA tests.

Results
All scaffolds were found to be highly porous. Significant differences were observed regarding mechanical properties, degradation rate and concentration of magnesium released during degradation (P  < 0.0001). The results showed that group IIB had the lowest strength and fastest corrosion rate, while IB had the highest strength and elastic modulus and the slowest corrosion rate among all groups. Bioactivity evaluation revealed extensive formation of calcium phosphate crystals and precipitations covering the scaffolds’ surfaces.

Conclusion
This study showed that using up to 5% HA as a reinforcing element with moderate compaction pressure and urea as a space holding agent can result in the fabrication of magnesium scaffolds suitable for orthopedic applications.
HNF4A mitigates sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and promoting macrophage polarization towards M2 phenotype
Authors: Yang Yu-Hang , Wen Ri , Huang Xin-Mei , Zhang Tao , Yang Ni , Liu Chun-Feng , Zhang Tie-Ning 
Published: February 2025

Abstract
Sepsis can trigger systemic inflammation and lead to detrimental effects on several organs, with particular emphasis on the lungs. In sepsis-associated lung injury, macrophages assume a pivotal role, as their overactivation could facilitate the secretion of inflammatory factors and the imbalance of polarization. Hepatocyte nuclear factor 4 alpha (HNF4A) has been reported its potential involvement in the regulation of inflammatory response and macrophage polarization. This study discusses the role and mechanism of HNF4A in sepsis-induced lung damage. HNF4A exhibits a decrease in expression by analyzing the differentially expressed genes in the lungs of septic mice from the Gene Expression Omnibus dataset GSE15379. Then, we established a mouse sepsis model through a cecal ligation and puncture method and observed that the expression of HNF4A was reduced in both lung tissues and alveolar macrophages. To evaluate the function of HNF4A, we overexpressed HNF4A mediated by adenovirus vectors, which were injected into mice. We found that HNF4A overexpression resulted in a higher survival rate in septic mice and an amelioration of pulmonary damage. Meanwhile, HNF4A overexpression mitigated the infiltration of inflammatory cells and impeded the M1 polarization but facilitated the M2 polarization of macrophages in the lung tissues or the alveolar lavage fluid. In vitro, we treated bone marrow-derived macrophages with interleukin-4. Consistent results were obtained that HNF4A overexpression promoted the M2 polarization of macrophages. Mechanistically, we found that HNF4A transcriptionally regulate the expression of nuclear receptor coactivator 2 (NCOA2) through binding to its promoter region. NCOA2 interacted with glucocorticoid receptor (GR). Stabilin 1 (STAB1) was selected as a possible target by transcriptome sequencing analysis. Functional experiments confirmed STAB1 as a downstream target of the HNF4A/NCOA2/GR axis. Overall, this research investigated the potential impact of HNF4A on pulmonary injury in sepsis. It is suggested that one of the regulatory mechanisms involved in this association may be the NCOR2/GR/STAB1 axis.
Structural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9
Authors: Lee Yeongmok , Demes-Causse Elsa , Yoo Jaemin , Jang Seo Young , Jung Seoyeon , Jaślan Justyna , Hwang Geum-Sook , Yoo Jejoong , De Angeli Alexis , Lee Sangho 
Published: February 2025

Abstract
In plant cells, ALMTs are key plasma and vacuolar membrane-localized anion channels regulating plant responses to the environment. Vacuolar ALMTs control anion accumulation in plant cells and, in guard cells, they regulate stomata aperture. The activation of vacuolar ALMTs depends on voltage and cytosolic malate, but the underlying molecular mechanisms remain elusive. Here we report the cryo-EM structures of ALMT9 from Arabidopsis thaliana (AtALMT9), a malate-activated vacuolar anion channel, in plugged and unplugged lipid-bound states. In all these states, membrane lipids interact with the ion conduction pathway of AtALMT9. We identify two unplugged states presenting two distinct pore width profiles. Combining structural and functional analysis we identified conserved residues involved in ion conduction and in the pore lipid interaction. Molecular dynamics simulations revealed a peculiar anion conduction mechanism in AtALMT9. We propose a voltage-dependent activation mechanism based on the competition between pore lipids and malate at the cytosolic entrance of the channel.
Entanglement growth from squeezing on the MPS manifold
Authors: Leontica Sebastian , Green Andrew G. 
Published: February 2025

Abstract
Finding suitable characterizations of quantum chaos is a major challenge in many-body physics, with a central difficulty posed by the linearity of the Schrödinger equation. A possible solution for recovering non-linearity is to project the dynamics onto some variational manifold. The classical chaos induced via this procedure may be used as a signature of quantum chaos in the full Hilbert space. Here, we demonstrate analytically a previously heuristic connection between the Lyapunov spectrum from projection onto the matrix product state (MPS) manifold and the growth of entanglement. This growth occurs by squeezing a localized distribution on the variational manifold. The process qualitatively resembles the Cardy-Calabrese picture, where local perturbations to a moving MPS reference are interpreted as bosonic quasi-particles. Taking careful account of the number of distinct channels for these processes recovers the connection to the Lyapunov spectrum. Our results rigorously establish the physical significance of the projected Lyapunov spectrum, suggesting it as an alternative method of characterizing chaos in quantum many-body systems, one that is manifestly linked to classical chaos.
Bacteria invade the brain following intracortical microelectrode implantation, inducing gut-brain axis disruption and contributing to reduced microelectrode performance
Authors: Hoeferlin George F. , Grabinski Sarah E. , Druschel Lindsey N. , Duncan Jonathan L. , Burkhart Grace , Weagraff Gwendolyn R. , Lee Alice H. , Hong Christopher , Bambroo Meera , Olivares Hannah , Bajwa Tejas , Coleman Jennifer , Li Longshun , Memberg William , Sweet Jennifer , Hamedani Hoda Amani , Acharya Abhinav P. , Hernandez-Reynoso Ana G. , Donskey Curtis , Jaskiw George , Ricky Chan E. , Shoffstall Andrew J. , Bolu Ajiboye A. , von Recum Horst A. , Zhang Liangliang , Capadona Jeffrey R. 
Published: February 2025

Abstract
Brain-machine interface performance can be affected by neuroinflammatory responses due to blood-brain barrier (BBB) damage following intracortical microelectrode implantation. Recent findings suggest that certain gut bacterial constituents might enter the brain through damaged BBB. Therefore, we hypothesized that damage to the BBB caused by microelectrode implantation could facilitate microbiome entry into the brain. In our study, we found bacterial sequences, including gut-related ones, in the brains of mice with implanted microelectrodes. These sequences changed over time. Mice treated with antibiotics showed a reduced presence of these bacteria and had a different inflammatory response, which temporarily improved microelectrode recording performance. However, long-term antibiotic use worsened performance and disrupted neurodegenerative pathways. Many bacterial sequences found were not present in the gut or in unimplanted brains. Together, the current study established a paradigm-shifting mechanism that may contribute to chronic intracortical microelectrode recording performance and affect overall brain health following intracortical microelectrode implantation.
Topologically cloaked magnetic colloidal transport
Authors: Rossi Anna M. E. B. , Märker Thomas , Stuhlmüller Nico C. X. , Kuświk Piotr , Stobiecki Feliks , Urbaniak Maciej , Akhundzada Sapida , Vereijken Arne J. , Ehresmann Arno , de las Heras Daniel , Fischer Thomas M. 
Published: February 2025

Abstract
Cloaking is a method of making obstacles undetectable. Here we cloak unit cells of a magnetic pattern squeezed into an otherwise periodic pattern from a magnetically driven colloidal flow. We apply a time-periodic external magnetic field loop to an ensemble of paramagnetic colloidal particles on the deformed periodic magnetic pattern. There exist topological loops where the particles avoid to trespass the cloaked regions by robustly traveling around the cloak. Afterwards the ensemble of particles continues with a motion identical to the motion as if the distorted region were nonexistent and the ensemble would have trespassed the undeformed region. We construct the cloak by continuously squeezing new conformally mapped unit cells between those of the originally undeformed and periodic pattern. We find a cloaking/decloaking transition as a function of the size and shape of the newly squeezed-in region. A cloak is scalable to arbitrary size if the biholomorphic map from the undistorted periodic lattice to the region outside the cloak locally rotates by less than an angle of forty five degrees. The work generalizes cloaking from waves toward particles.
Peroxisomal core structures segregate diverse metabolic pathways
Authors: Bäcker Nils , Ast Julia , Martorana Domenica , Renicke Christian , Berger Jil , Mais Cristopher-Nils , Christ Marvin , Stehlik Thorsten , Heimerl Thomas , Wernet Valentin , Taxis Christof , Pané-Farré Jan , Bölker Michael , Klatt Judith M. , Sandrock Björn , Schink Kay Oliver , Bange Gert , Freitag Johannes 
Published: February 2025

Abstract
Peroxisomes are single membrane-bounded oxidative organelles with various metabolic functions including β-oxidation of fatty acids. Peroxisomes of many species confine certain metabolic enzymes into sub-compartments sometimes visible as electron dense cores. Why these structures form is largely unknown. Here, we report that in the smut fungus Ustilago maydis detergent resistant core structures are enriched for different enzymes excluding several key enzymes of the β-oxidation pathway. This confinement contributes to generation of peroxisome subpopulations that differ in their enzyme content. We identify short amino acid motifs necessary and sufficient for protein self-assembly into aggregates in vitro. The motifs trigger enrichment in cores in vivo and are active in mammalian cells. Perturbation of core assembly via variation of such motifs affects peroxisome function in U. maydis strains challenged with fatty acids. Thus, protein core structures serve to compartmentalize the lumen of peroxisomes thereby preventing interference of biochemical reactions. Metabolic compartmentalization of peroxisomes via assembly of specific proteins may occur in other organisms as well.
Accelerating crystal structure search through active learning with neural networks for rapid relaxations
Authors: Hessmann Stefaan S. P. , Schütt Kristof T. , Gebauer Niklas W. A. , Gastegger Michael , Oguchi Tamio , Yamashita Tomoki 
Published: February 2025

Abstract
Global optimization of crystal compositions is a significant yet computationally intensive method to identify stable structures within chemical space. The specific physical properties linked to a three-dimensional atomic arrangement make this an essential task in the development of new materials. We present a method that efficiently uses active learning of neural network force fields for structure relaxation, minimizing the required number of steps in the process. This is achieved by neural network force fields equipped with uncertainty estimation, which iteratively guide a pool of randomly generated candidates toward their respective local minima. Using this approach, we are able to effectively identify the most promising candidates for further evaluation using density functional theory (DFT). Our method not only reliably reduces computational costs by up to two orders of magnitude across the benchmark systems Si16, Na8Cl8, Ga8As8 and Al4O6 but also excels in finding the most stable minimum for the unseen, more complex systems Si46 and Al16O24. Moreover, we demonstrate at the example of Si16 that our method can find multiple relevant local minima while only adding minor computational effort.
Site-specific activation of the proton pump inhibitor rabeprazole by tetrathiolate zinc centres
Authors: Marker Teresa , Steimbach Raphael R. , Perez-Borrajero Cecilia , Luzarowski Marcin , Hartmann Eric , Schleich Sibylle , Pastor-Flores Daniel , Espinet Elisa , Trumpp Andreas , Teleman Aurelio A. , Gräter Frauke , Simon Bernd , Miller Aubry K. , Dick Tobias P. 
Published: February 2025

Abstract
Proton pump inhibitors have become top-selling drugs worldwide. Serendipitously discovered as prodrugs that are activated by protonation in acidic environments, proton pump inhibitors inhibit stomach acid secretion by covalently modifying the gastric proton pump. Despite their widespread use, alternative activation mechanisms and potential target proteins in non-acidic environments remain poorly understood. Employing a chemoproteomic approach, we found that the proton pump inhibitor rabeprazole selectively forms covalent conjugates with zinc-binding proteins. Focusing on DENR, a protein with a C4 zinc cluster (that is, zinc coordinated by four cysteines), we show that rabeprazole is activated by the zinc ion and subsequently conjugated to zinc-coordinating cysteines. Our results suggest that drug binding, activation and conjugation take place rapidly within the zinc coordination sphere. Finally, we provide evidence that other proton pump inhibitors can be activated in the same way. We conclude that zinc acts as a Lewis acid, obviating the need for low pH, to promote the activation and conjugation of proton pump inhibitors in non-acidic environments.
Response coupling with an auxiliary neural signal for enhancing brain signal detection
Authors: Gupta Ekansh , Sivakumar Raghupathy 
Published: February 2025

Abstract
Brain-computer interfaces (BCIs) offer an implicit, non-linguistic communication channel between users and machines. Despite their potential, BCIs are far from becoming a mainstream communication modality like text and speech. While non-invasive BCIs, such as Electroencephalography, are favored for their ease of use, their broader adoption is limited by challenges related to signal noise, artifacts, and variability across users. In this paper, we propose a novel method called response coupling, aimed at enhancing brain signal detection and reliability by pairing a brain signal with an artificially induced auxiliary signal and leveraging their interaction. Specifically, we use error-related potentials (ErrPs) as the primary signal and steady-state visual evoked potentials (SSVEPs) as the auxiliary signal. SSVEPs, known for their phase-locked responses to rhythmic stimuli, are selected because rhythmic neural activity plays a critical role in sensory and cognitive processes, with evidence suggesting that reinforcing these oscillations can improve neural performance. By exploring the interaction between these two signals, we demonstrate that response coupling significantly improves the detection accuracy of ErrPs, especially in the parietal and occipital regions. This method introduces a new paradigm for enhancing BCI performance, where the interaction between a primary and an auxiliary signal is harnessed to enhance the detection performance. Additionally, the phase-locking properties of SSVEPs allow for unsupervised rejection of suboptimal data, further increasing BCI reliability.
Epidemiologic trends and increasing inequalities in orthognathic surgery in Germany: a nationwide analysis 2005–2022
Authors: Meisgeier Axel , Pienkohs Simon , Salomia Constantin , Moosdorf Laura , Neff Andreas 
Published: February 2025

Abstract
Orthognathic surgery (OS) has become a widely used treatment option for moderate to severe dento-skeletal malocclusions. The aim of this study was to analyze the incidence and time trends of OS and potential influencing factors in the German healthcare system. Nationwide data regarding the national diagnosis-related-group (DRG) inpatient billing system was received from the German Federal Statistical Office. We estimated age-gender standardized incidence of OS-associated procedures between 2005 and 2022 and evaluated age- and gender-adjusted time trends using Poisson regression analysis. The total standardized incidence rate of OS-associated procedures in the observational period 2005–2022 was 11.1 (♀13.0; ♂ 9.2) per 100,000 person years. A significant increase of 61.8% (♀+48.7%; ♂+82.9%) in OS-associated procedures was observed within the observational period, mainly due to the increase of the procedures in the age groups 15–34 years (+ 53.6%), 35–59 years (+ 66.7%) and 60–79 years (+ 20.0%). Mandibular procedures increased by 45.0%, while maxillary procedures increased by 88.2%. There were significant differences of the incidence of OS-associated procedures between the various federal states in Germany, indicating a higher incidence and stronger increase in more affluent regions. The age- and gender-standardized incidence of OS-associated procedures increased among all genders and the most relevant age groups in Germany in the last two decades. There is an ongoing trend to implement maxillary and combined procedures. These effects are limited to more affluent regions only, reflecting the impact of socioeconomic and regional factors on healthcare accessibility.
The histone demethylase dLsd1 regulates organ size by silencing transposable elements
Authors: Selmi Ines , Texier Manuela , Aguirrenbegoa Marion , Merce Clémentine , Fraisse-lepourry Laurence , Mugat Bruno , Mohamed Mourdas , Chambeyron Séverine , Cribbs David , Di Stefano Luisa 
Published: February 2025

Abstract
The specific role of chromatin modifying factors in the timely execution of transcriptional changes in gene expression to regulate organ size remains largely unknown. Here, we report that in Drosophila melanogaster depletion of the histone demethylase dLsd1 results in the reduction of wing size. dLsd1 depletion affects cell proliferation and causes an increase in DNA damage and cell death. Mechanistically, we have identified Transposable Elements (TEs) as critical dLsd1 targets for organ size determination. We found that upon dLsd1 loss many TE families are upregulated, and new TE insertions appear. By blocking this new TE activity, we could rescue the wing size phenotype. Collectively, our results reveal that the histone demethylase dLsd1 and maintenance of TE homeostasis are required to ensure proper wing size.
BLADE: Energy‐efficient attention accelerator with fused kernel and bit‐level redundancy elimination
Authors: Lin Zhiwei , Qin Yubin , Wang Jiachen , Wang Yang , Wang Huanyu , Zheng Zhe , Cui Wenpeng , Wei Shaojun , Hu Yang , Yin Shouyi 
Published: February 2025

AbstractAttention‐based transformer model has achieved remarkable performance in various artificial intelligence fields, while the attention computation, being a combination of matrix multiplication and softmax function, is still sub‐optimized in terms of hardware implementation. Normally, it needs 3 pass of input memory access to compute attention, and the on‐chip storage requirement is coupled with the input length, both of which pose significant memory issues. Further, the computation burden is heavy for long inputs. This paper proposes an algorithm‐hardware co‐design for attention. On algorithm side, it uses a linear‐softmax fused kernel to fuse the matrix multiplication and non‐linear functions, which enables high on‐chip memory source utilization. On hardware side, it shows an accelerator named BLADE with identical partial product removing, which eliminates unnecessary computation by exploiting math feature of softmax. Experiment on ViT, Swin transformer, GPT‐2, and LLaMA2 show that the proposed design achieves – of energy efficiency improvement compared to state‐of‐the‐art FlashAttention implementations.