bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting Slip Deficit Rates and Its Insights Into Large and Slow Earthquakes at the Nankai Subduction Zone
Authors: Plata‐Martinez Raymundo , Iinuma Takeshi , Tomita Fumiaki , Nakamura Yasuyuki , Nishimura Takuya , Hori Takane 
Published: December 2024

AbstractThe Nankai subduction zone presents significant seismic and tsunami risks, given its historical earthquakes exceeding magnitude 8 and the expectations of similar future events. Slow earthquakes, common at the shallow and deep plate interface, result from different frictional properties linked to interplate slip deficit accumulation. This study estimates slip deficit rates at the Nankai subduction zone using land and ocean‐bottom geodetic data. Previous estimates encountered limitations, often smoothing slip deficits, omitting observational error differences between ocean‐floor and land data, and relying on homogeneous structure models. To address these issues, we employ a novel trans‐dimensional reversible jump Markov Chain Monte Carlo algorithm. This approach dynamically adjusts slip parameters, accommodating data resolution and producing a flexible slip distribution without predetermined spatial constraints. Additionally, it automatically weights data for observational errors and integrates elastic Green functions from a 3D structure of the Nankai region. Our results provide a finer, heterogeneous slip distribution, improving estimates in inland regions. However, limitations remain offshore in areas with sparse data. We revised the spatial distribution of Nankai slow earthquakes and confirmed a good agreement with intermediate slip deficit rates, identifying coupled and uncoupled regions. High slip deficit rates align with rupture areas of historic large earthquakes. Slow earthquakes occur at frictionally weak plate interfaces, and shallow slow earthquakes may result from subducting relief heterogeneities with important pore fluid pressure effects. We introduce an updated distribution of slip deficit rates for the Nankai subduction zone, considering observed slip deficit rates and the fast and slow earthquake occurrence.
National Forest Restoration Projects in China: Cost‐Efficiency, and Trade‐Off Between Carbon Sequestration and Water Consumption
Authors: Zhang Jiehao , Zhang Yulong , Wang Xia , He Tiehu , Xia Huijuan , Zhang Kerong , Zhang Quanfa 
Published: December 2024

AbstractInternational initiatives, such as the Bonn Challenge, Trillion Tree Campaign, New York Declaration on Forests, and United Nations Decade on Ecosystem Restoration, have set ambitious targets for forest restoration. However, the effectiveness and cost‐efficiency of large‐scale forest restoration projects (FRP) in different climatic zones, and the trade‐off between carbon sequestration and water consumption caused by FRP are poorly understood. Here, we conducted a comprehensive examination of 2,778 counties in China, where the world's most ambitious FRP was executed during the past two decades. Results showed that, on average, each square kilometer of FRP yielded an additional 0.6 square kilometers of forests and contributed an extra 1354.9 tC to forest carbon storage, with the aridity index emerging as a key influencer. The actual expenditure incurred per ton of increased forest carbon storage amounted to approximately 118.9 USD in average, with the lowest in Southwest at 50.9 USD. The expansion of forest cover and enhanced biomass storage led to a notable increase in water consumption, and the trade‐off was particularly pronounced in arid regions. Our study provides empirical evidence that FRP is an effective and cost‐efficient climate change mitigation strategy for humid climate zones under current carbon prices. However, FRP is not cost‐efficient in semi‐arid and arid regions. These findings have significant implications for global forest restoration endeavors and formulating sound climate change mitigation policies.
Southern Ocean and Southern African Monsoon Forcing of the Subtropical Indian Ocean Early Pliocene “Biogenic Bloom”
Authors: Tangunan D. N. , Flores J. A. , LeVay L. J. , Jimenez‐Espejo F. J. , Coenen J. J. , Berke M. A. , de Azevedo A. Q. , Fuertes M. A. , Gruetzner J. , Starr A. , Hall I. R. 
Published: December 2024

AbstractThe Pliocene epoch emerges as a pivotal juncture in Earth's climatic evolution, characterized by pronounced warmth and elevated atmospheric carbon dioxide compared to contemporary levels. While the broader climatic context of the Pliocene has garnered attention, there remains an outstanding gap in detailed paleoclimate reconstructions of the early Pliocene, a new potential target for data‐model intercomparison. Addressing this, we investigate the drivers of the early Pliocene “Biogenic Bloom” and implications for nutrient dynamics and climate. By analyzing high‐resolution biotic assemblage and geochemical records from the Agulhas Plateau, southwestern Indian Ocean (International Ocean Discovery Program, IODP Site U1475), we aim to elucidate the forcing and feedback mechanisms driving the early Pliocene marine ecosystems. We identify a distinct shift in coccolithophore assemblages at ∼4.6 million years ago, characterized by a notable change in dominance between the larger and smaller Reticulofenestra and high abundances of Noelaerhabdaceae < 5 µm. Our findings confirm the adaptive strategies of coccolithophore communities to prevailing environmental conditions, underscoring their evolutionary resilience by producing smaller coccoliths while increasing their abundances in a nutrient‐replete ocean. Surface water dynamics, particularly the subtropical front migration and expansion of Southern Ocean waters, in combination with the southern African monsoon variability, emerge as key drivers of phytoplankton productivity during the early Pliocene. We posit that a weakened biological carbon pump, due to increased phytoplankton production driven by intense ocean circulation and mixing during the early Pliocene, served as a potential precursor to the subsequent middle Pliocene abrupt climate extremes.
Limiting serine availability during tumor progression promotes muscle wasting in cancer cachexia
Authors: Pranzini Erica , Muccillo Livio , Nesi Ilaria , Santi Alice , Mancini Caterina , Lori Giulia , Genovese Massimo , Lottini Tiziano , Comito Giuseppina , Caselli Anna , Arcangeli Annarosa , Sabatino Lina , Colantuoni Vittorio , Taddei Maria Letizia , Cirri Paolo , Paoli Paolo 
Published: December 2024

AbstractCancer cachexia is a multifactorial syndrome characterized by a progressive loss of body weight occurring in about 80% of cancer patients, frequently representing the leading cause of death. Dietary intervention is emerging as a promising therapeutic strategy to counteract cancer-induced wasting. Serine is the second most-consumed amino acid (AA) by cancer cells and has emerged to be strictly necessary to preserve skeletal muscle structure and functionality. Here, we demonstrate that decreased serine availability during tumor progression promotes myotubes diameter reduction in vitro and induces muscle wasting in in vivo mice models. By investigating the metabolic crosstalk between colorectal cancer cells and muscle cells, we found that incubating myotubes with conditioned media from tumor cells relying on exogenous serine consumption triggers pronounced myotubes diameter reduction. Accordingly, culturing myotubes in a serine-free medium induces fibers width reduction and suppresses the activation of the AKT-mTORC1 pathway with consequent impairment in protein synthesis, increased protein degradation, and enhanced expression of the muscle atrophy-related genes Atrogin1 and MuRF1. In addition, serine-starved conditions affect myoblast differentiation and mitochondrial oxidative metabolism, finally inducing oxidative stress in myotubes. Consistently, serine dietary deprivation strongly strengthens cancer-associated weight loss and muscle atrophy in mice models. These findings uncover serine consumption by tumor cells as a previously undisclosed driver in cancer cachexia, opening new routes for possible therapeutic approaches.
Predicting electronic screening for fast Koopmans spectral functional calculations
Authors: Schubert Yannick , Luber Sandra , Marzari Nicola , Linscott Edward 
Published: December 2024

AbstractKoopmans spectral functionals are a powerful extension of Kohn-Sham density-functional theory (DFT) that enables the prediction of spectral properties with state-of-the-art accuracy. The success of these functionals relies on capturing the effects of electronic screening through scalar, orbital-dependent parameters. These parameters have to be computed for every calculation, making Koopmans spectral functionals more expensive than their DFT counterparts. In this work, we present a machine-learning model that—with minimal training—can predict these screening parameters directly from orbital densities calculated at the DFT level. We show in two prototypical use cases that using the screening parameters predicted by this model, instead of those calculated from linear response, leads to orbital energies that differ by less than 20 meV on average. Since this approach dramatically reduces run times with minimal loss of accuracy, it will enable the application of Koopmans spectral functionals to classes of problems that previously would have been prohibitively expensive, such as the prediction of temperature-dependent spectral properties. More broadly, this work demonstrates that measuring violations of piecewise linearity (i.e., curvature in total energies with respect to occupancies) can be done efficiently by combining frozen-orbital approximations and machine learning.
Predicting the replicability of social and behavioural science claims in COVID-19 preprints
Authors: Marcoci Alexandru , Wilkinson David P. , Vercammen Ans , Wintle Bonnie C. , Abatayo Anna Lou , Baskin Ernest , Berkman Henk , Buchanan Erin M. , Capitán Sara , Capitán Tabaré , Chan Ginny , Cheng Kent Jason G. , Coupé Tom , Dryhurst Sarah , Duan Jianhua , Edlund John E. , Errington Timothy M. , Fedor Anna , Fidler Fiona , Field James G. , Fox Nicholas , Fraser Hannah , Freeman Alexandra L. J. , Hanea Anca , Holzmeister Felix , Hong Sanghyun , Huggins Raquel , Huntington-Klein Nick , Johannesson Magnus , Jones Angela M. , Kapoor Hansika , Kerr John , Kline Struhl Melissa , Kołczyńska Marta , Liu Yang , Loomas Zachary , Luis Brianna , Méndez Esteban , Miske Olivia , Mody Fallon , Nast Carolin , Nosek Brian A. , Simon Parsons E. , Pfeiffer Thomas , Reed W. Robert , Roozenbeek Jon , Schlyfestone Alexa R. , Schneider Claudia R. , Soh Andrew , Song Zhongchen , Tagat Anirudh , Tutor Melba , Tyner Andrew H. , Urbanska Karolina , van der Linden Sander 
Published: December 2024

Abstract
Replications are important for assessing the reliability of published findings. However, they are costly, and it is infeasible to replicate everything. Accurate, fast, lower-cost alternatives such as eliciting predictions could accelerate assessment for rapid policy implementation in a crisis and help guide a more efficient allocation of scarce replication resources. We elicited judgements from participants on 100 claims from preprints about an emerging area of research (COVID-19 pandemic) using an interactive structured elicitation protocol, and we conducted 29 new high-powered replications. After interacting with their peers, participant groups with lower task expertise (‘beginners’) updated their estimates and confidence in their judgements significantly more than groups with greater task expertise (‘experienced’). For experienced individuals, the average accuracy was 0.57 (95% CI: [0.53, 0.61]) after interaction, and they correctly classified 61% of claims; beginners’ average accuracy was 0.58 (95% CI: [0.54, 0.62]), correctly classifying 69% of claims. The difference in accuracy between groups was not statistically significant and their judgements on the full set of claims were correlated (r(98) = 0.48, P < 0.001). These results suggest that both beginners and more-experienced participants using a structured process have some ability to make better-than-chance predictions about the reliability of ‘fast science’ under conditions of high uncertainty. However, given the importance of such assessments for making evidence-based critical decisions in a crisis, more research is required to understand who the right experts in forecasting replicability are and how their judgements ought to be elicited.
Automated orthogonal tRNA generation
Authors: Spinck Martin , Guppy Amir , Chin Jason W. 
Published: December 2024

AbstractThe ability to generate orthogonal, active tRNAs—central to genetic code expansion and reprogramming—is still fundamentally limited. In this study, we developed Chi-T, a method for the de novo generation of orthogonal tRNAs. Chi-T segments millions of isoacceptor tRNA sequences into parts and then assembles chimeric tRNAs from these parts. Chi-T fixes the parts, containing identity elements, and combinatorially varies all other parts to generate chimeric sequences. Chi-T also filters the variable parts and chimeric sequences to minimize host identity elements. We show here that experimentally characterized orthogonal tRNAs are more likely to have predicted minimum free energy cloverleaf structures, and Chi-T filters for sequences with a predicted cloverleaf structure. We report RS-ID for the identification of synthetases that may acylate the tRNAs generated by Chi-T. We computationally identified new orthogonal tRNAs and engineered an orthogonal pair generated by Chi-T/RS-ID to direct non-canonical amino acid incorporation, in response to both amber codons and sense codons, with an efficiency similar to benchmark genetic code expansion systems.
Semi-local Time sensitive Anonymization of Clinical Data
Authors: Hammer Freimut Gebhard Herbert , Buglowski Mateusz , Stollenwerk André 
Published: December 2024

AbstractA method for the anonymization of time-continuous data, which preserves the relation between the time- and value dimension is proposed in this work. The approach protects against linking- and distribution attacks by providing k-anonymity and t-closeness. Distributions can be generated from given sets using Distribution Clustering, according to the similarity of the curves, which serve as a replacement for the population distribution. Before the data is anonymized, it is split along the time-axis using Windowed Fréchet Splitting, to reduce the duration and information loss. The proposed approach employs bucketization using the Fréchet distance with an implicit maximum cost and implied t for closeness and multiple redistribution phases. The information loss, median relative error and achieved t for the closeness is low, and the runtime was reduced with the introduction of semi-local decisions.
Unravelling 2-oxoglutarate turnover and substrate oxidation dynamics in 5-methylcytosine-oxidising TET enzymes
Authors: Šimelis Klemensas , Belle Roman , Kawamura Akane 
Published: December 2024

AbstractFe(II)- and 2-oxoglutarate (2OG)-dependent dioxygenases use 2OG and O2 cofactors to catalyse substrate oxidation and yield oxidised product, succinate, and CO2. Simultaneous detection of substrate and cofactors is difficult, contributing to a poor understanding of the dynamics between substrate oxidation and 2OG decarboxylation activities. Here, we profile 5-methylcytosine (5mC)-oxidising Ten-Eleven Translocation (TET) enzymes using MS and 1H NMR spectroscopy methods and reveal a high degree of substrate oxidation-independent 2OG turnover under a range of conditions. 2OG decarboxylase activity is substantial (>20% 2OG turned over after 1 h) in the absence of substrate, while, under substrate-saturating conditions, half of total 2OG consumption is uncoupled from substrate oxidation. 2OG kinetics are affected by substrate and non-substrate DNA oligomers, and the sequence-agnostic effects are observed in amoeboflagellate Naegleria gruberi NgTet1 and human TET2. TET inhibitors also alter uncoupled 2OG kinetics, highlighting the potential effect of 2OG dioxygenase inhibitors on the intracellular balance of 2OG/succinate.
A one-step route for the conversion of Cd waste into CdS quantum dots by Acidithiobacillus sp. via unique biosynthesis pathways
Authors: Li Xiao-Ju , Wang Tian-Qi , Qi Lu , Li Feng-Wei , Xia Yong-Zhen , Bin-Jin  , Zhang Cheng-Jia , Chen Lin-Xu , Lin Jian-Qun 
Published: December 2024

Acidithiobacillus sp. serves as biological factories for the synthesis of CdS quantum dots by directly using its bioleaching Cd ion from cadmium waste as source.
Revenue stream tokenization with tranching of claim seniority in electricity markets
Authors: de Villiers Almero , Byrne Julie , Cuffe Paul 
Published: December 2024

AbstractThis paper proposes tokenising generators' revenue streams as a novel financial instrument for electricity market risk management. The core idea is that tokenised revenue streams (RevToks) holders can directly claim a portion of a generator's energy market revenues. The novelty lies in exploring a tranched structure, creating a tiered hierarchy of RevTok claims. This approach addresses the financial challenges of non‐dispatchable renewable energy generation and volatile electricity spot markets, which expose generation firms to volumetric and price risks, potentially deterring project financiers. The manuscript introduces tranching, a scheme for fractionalising energy market revenues based on RevTok seniority. Project financiers might hold senior RevToks, ensuring first claim on generator revenues, while bulk offtakers could purchase junior RevToks as a hedge against high wholesale prices. Case study market simulations indicate that these tranched revenue sharing arrangements can, in principle, help generators, financiers, and offtakers to better manage their risk exposure. The proposed system would allow RevTok holders to directly claim shares of specific generators' revenue streams, offering a new risk management tool for various electricity market participants.
Sun-related variability in the light curves of compact radio sources
Authors: Marchili N. , Witzel G. , Aller M. F. 
Published: December 2024

Context. Compact radio sources can show remarkable flux density variations at gigahertz frequencies on a wide range of timescales. The origin of the variability is a mix of source-intrinsic mechanisms and propagation effects, the latter being generally identified with scattering from the interstellar medium. Some of the most extreme episodes of variability, however, show characteristics that are not consistent with any of the explanations commonly proposed.
Aims. We carried out an in-depth analysis of variability at radio frequencies on light curves from the impressive database of the US Navy’s extragalactic source monitoring program at the Green Bank Interferometer (GBI) – a long-term project mainly aimed at the investigation of extreme scattering events. The GBI data have been complemented for selected sources by light curves from the University of Michigan Radio Astronomy Observatory (UMRAO). The purpose of the present work is to identify events of flux density variations that appear to correlate with the position of the Sun.
Methods. We inspected the 2 GHz and 8 GHz light curves observed in the framework of the GBI monitoring program in order to search for one-year periodic patterns in the data. Variations on timescales below one year were isolated through a de-trending algorithm and analysed, with the aim of looking for possible correlations with the Sun’s position relative to the sources.
Results. Objects at an ecliptic latitude below ∼20° show one-year periodic drops in flux densities, centred close to the time of minimum solar elongation. Both interplanetary scintillation and instrumental effects may contribute to these events. However, in some cases, the drops extend to much larger angular distances, affecting sources at high ecliptic latitudes and causing variability on timescales of months. Three different kinds of such events have been identified in the data, and their exact nature is not yet known.
Conclusions. In the present study we show that the variability of compact radio sources is heavily influenced by effects that correlate with solar angular distance. This unexpected contribution significantly alters the sources’ variability characteristics estimated at gigahertz frequencies. In particular, we found that many extreme scattering events previously identified in the GBI monitoring program are actually the consequence of Sun-related effects; others occur simultaneously in several objects, which excludes interstellar scattering as their possible cause. These discoveries have a severe impact on our understanding of extreme scattering events. Furthermore, Sun-related variability, given its amplitude and timescale, can significantly alter results of variability studies, which are very powerful tools for the investigation of active galactic nuclei. Without a thorough comprehension of the mechanisms that cause these variations, the estimation of some essential information about the emitting regions, such as their size and all the derived quantities, might be seriously compromised.
Relativistic reconnection with effective resistivity
Authors: Bugli M. , Lopresti E. F. , Figueiredo E. , Mignone A. , Cerutti B. , Mattia G. , Del Zanna L. , Bodo G. , Berta V. 
Published: December 2024

Context. Relativistic magnetic reconnection is one of the most fundamental mechanisms that is considered responsible for the acceleration of relativistic particles in astrophysical jets and magnetospheres of compact objects. Understanding the properties of the dissipation of magnetic fields and the formation of non-ideal electric fields is of paramount importance to quantify the efficiency of reconnection at energizing charged particles.
Aims. Recent results from particle-in-cell (PIC) simulations suggest that the fundamental properties of how magnetic fields dissipate in a current sheet might be captured by an “effective resistivity” formulation, which would locally enhance the amount of magnetic energy dissipated and favor the onset of fast reconnection. Our goal is to assess this ansatz quantitatively by comparing fluid models of magnetic reconnection with a non-constant magnetic diffusivity and fully kinetic models.
Methods. We performed 2D resistive relativistic magnetohydrodynamic (ResRMHD) simulations of magnetic reconnection combined to PIC simulations using the same initial conditions (i.e., a Harris current sheet). We explored the impact of crucial parameters such as the plasma magnetization, its mass density, the grid resolution, and the characteristic plasma skin depth.
Results. Our ResRMHD models with effective resistivity are able to quantitatively reproduce the dynamics of fully kinetic models of relativistic magnetic reconnection. In particular, they lead to reconnection rates consistent with PIC simulations, whereas for constant-resistivity fluid models, the reconnection dynamics is generally ten times slower. Even at modest resolutions, adopting an effective resistivity can qualitatively capture the properties of kinetic reconnection models and produce reconnection rates compatible with collisionless models (i.e., on the order of ∼10−1).