bluuebunny/crossref_metadata_2025_split huggingface dataset:
ONTOLOGICAL PURITY FOR FORMAL PROOFS
Authors: MARTINOT ROBIN 
Published: November 2023

AbstractPurity is known as an ideal of proof that restricts a proof to notions belonging to the ‘content’ of the theorem. In this paper, our main interest is to develop a conception of purity for formal (natural deduction) proofs. We develop two new notions of purity: one based on an ontological notion of the content of a theorem, and one based on the notions of surrogate ontological content and structural content. From there, we characterize which (classical) first-order natural deduction proofs of a mathematical theorem are pure. Formal proofs that refer to the ontological content of a theorem will be called ‘fully ontologically pure’. Formal proofs that refer to a surrogate ontological content of a theorem will be called ‘secondarily ontologically pure’, because they preserve the structural content of a theorem. We will use interpretations between theories to develop a proof-theoretic criterion that guarantees secondary ontological purity for formal proofs.
Spatiotemporal Evolution of Riparian Redox Zonation in Response to River Stage Fluctuation and Dynamic Biofilm Growth
Authors: Zhu Yonghui , Dai Heng , Wen Zhang , Liu Hui , Yuan Songhu 
Published: November 2023

AbstractRiparian zones are one of the most complex redox‐dynamic systems, where sequential redox zones of dissolved oxygen, nitrate, manganese dioxide, ferric hydroxide and sulfate reduction commonly form. River stage dynamics and microbes are two key controls on nutrient transformation in the riparian zone. Microbial growth, on one hand, increases the biogeochemical reaction rate by altering the microbial population. On the other hand, decreases the permeability of the media due to clogging effects, thereby increasing the residence time of solutes. However, previous studies have often concentrated on steady‐state flow systems and overlooked the impacts of river stage fluctuations and dynamic microbial growth on redox zonation. In this study, we investigated the interactions among river fluctuations, nutrient supplies, microbial metabolisms, and sediment physical properties in a dynamic riparian system. A column experiment was conducted, and a one‐dimensional modeling framework that coupled flow, reactive solute transport, dynamic microbial growth and bioclogging processes was developed to study the spatiotemporal evolution of redox zonation in response to river stage fluctuations and microbial growth. Our results showed that two redox zonation patterns, including a typical sequence and an interlaced sequence, could form in the dynamic riparian zone. Increasing exogenous dissolved organic carbon concentration facilitates the occurrence of anomalous sequence redox zonation. Modeling results also indicated that ignoring microbial growth leads to a significant difference in the spatiotemporal characterization of the redox zonation, especially for a more permeable sediment. Our results implicate the occurrence of more complicated redox zonation in a dynamic riparian system than previously reported.
Differentiating EDRs From the Background Magnetopause Current Sheet: A Statistical Study
Authors: Beedle J. M. H. , Gershman D. J. , Uritsky V. M. , Phan T. D. , Giles B. L. 
Published: November 2023

AbstractThe solar wind is a continuous outflow of charged particles from the Sun's atmosphere into the solar system. At Earth, the solar wind's outward pressure is balanced by the Earth's magnetic field in a boundary layer known as the magnetopause. Plasma density and temperature differences across the boundary layer generate the Chapman‐Ferraro current which supports the magnetopause. Along the dayside magnetopause, magnetic reconnection can occur in electron diffusion regions (EDRs) embedded into the larger ion diffusion regions (IDRs). These diffusion regions form when opposing magnetic field lines in the solar wind and Earth's magnetic field merge, releasing magnetic energy into the surrounding plasma. While previous studies have given us a general understanding of the structure of the diffusion regions, we still do not have a good grasp of how they are statistically differentiated from the non‐diffusion region magnetopause. By investigating 251 magnetopause crossings from NASA's Magnetospheric Multiscale (MMS) Mission, we demonstrate that EDR magnetopause crossings show current densities an order of magnitude higher than regular magnetopause crossings—crossings that either passed through the reconnection exhausts or through the non‐reconnecting magnetopause, providing a baseline for the magnetopause current sheet under a wide range of driving conditions. Significant current signatures parallel to the local magnetic field in EDR crossings are also identified, which is in contrast to the dominantly perpendicular current found in the regular magnetopause. Additionally, we show that the ion velocity along the magnetopause is highly correlated with a crossing's location, indicating the presence of magnetosheath flows inside the magnetopause.
Increased DIN Storage and ΔDIC/ΔDIN Ratio in the Subsurface Water of the Canada Basin, 1990‒2015
Authors: Zhang Tianzhen , Hao Qiang , Jin Haiyan , Bai Youcheng , Zhuang Yanpei , Qi Di , Chen Jianfang 
Published: November 2023

AbstractThe subsurface layer of the Canada Basin contains large reservoirs of dissolved inorganic nitrogen and carbon (DIN and DIC, respectively). Under rapid change of Arctic climate system, these reservoirs may not only serve as potential material bases for primary production, but also for carbon source and sink. However, the long‐term trends in reservoirs and the interaction between reservoirs and the upper ocean are not fully understood. This study used two data sets to evaluate the long‐term trends in the DIN and DIC reservoirs in the subsurface layer of the Canada Basin during 1990–2015. The results indicate an increase of ∼35% in the subsurface DIN reservoir over 25 years, whereas the DIN concentration remained fairly constant. The discrepancy between the DIN reservoir and DIN concentration was primarily owing to the expansion of the subsurface layer, which increased the DIN stock but maintained a relatively stable DIN concentration. Additionally, the ΔDIC/ΔDIN ratio in the subsurface layer increased by ∼33% over 25 years, primarily due to denitrification on the pathway of Pacific inflow, such as Chukchi shelf. In the Canada Basin, the enhanced mixing between the subsurface and surface layers may promote primary production and render the subsurface layer a carbon source. Consequently, when studying the biogeochemical cycles in the changing Arctic Ocean, the long‐term interactions between the subsurface and surface layers in the Canada Basin should be further considered.
Enhanced Phosphate Consumption Stimulated by Nitrogen Fixation Within a Cyclonic Eddy in the Northwest Pacific
Authors: Yuan Zhongwei , Browning Thomas J. , Du Chuanjun , Shen Hui , Wang Lei , Ma Yifan , Jiang Zong‐Pei , Liu Zhiyu , Zhou Kuanbo , Kao Shuh‐Ji , Dai Minhan 
Published: November 2023

AbstractMesoscale eddies are common in the subtropical Northwest Pacific, however, relatively little is known about their spatial variability and temporal evolution, and how these impact upper ocean biogeochemistry. Here we investigate these using observations of a cyclonic eddy carried out along four sequential transects. Consistent with previous observations of cyclonic eddies, the eddy core had doming isopycnals, bringing elevated nutrient waters nearer to the surface. However, we also found that the upper layer of the eddy above the nutricline had significantly lower phosphate concentrations within its core relative to its edge. We attributed this to elevated N2 fixation within the eddy core, which was likely driven by enhanced subsurface iron supply, ultimately resulting in increased phosphate consumption. Eddy‐enhanced N2 fixation was additionally supported by the elevation of nitrate + nitrite to phosphate ratios below the euphotic zone. Moreover, we observed that while the upward displacement of isopycnals within the eddy core led to an increase in phytoplankton biomass in the lower euphotic zone, there was no significant increase in total phytoplankton biomass across the entire euphotic zone. Cyclonic eddies in the subtropical North Pacific are projected to be becoming more frequent, implying that such dynamics could become increasingly important for regulating nutrient biogeochemistry and ultimately productivity of the region.
Communication Distance and Bayesian Inference in Non‐Perennial Streams
Authors: Aho Ken , Derryberry Dewayne , Godsey Sarah E. , Ramos Rob , Warix Sara R. , Zipper Samuel 
Published: November 2023

AbstractNon‐perennial streams are receiving increased attention from researchers, however, suitable methods for measuring their hydrologic connectivity remain scarce. To address this deficiency, we developed Bayesian statistical approaches for measuring both average active stream length, and a new metric called average communication distance. Average communication distance is a theoretical increasedeffective distancethat stream‐borne materials must travel, given non‐continuous streamflow. Because it is the product of the inverse probability of surface water presence and stream length, the average communication distance of a non‐perennial stream segment will be greater than its actual physical length. As an application we considered Murphy Creek, a simple non‐perennial stream network in southwestern Idaho, USA. We used surface water presence/absence data obtained in 2019, and priors for the probability of surface water, based on predictions from an existing regional United States Geological Survey model. Average communication distance posterior distributions revealed locations where effective stream lengths increased dramatically due to flow rarity. We also found strong seasonal (spring, summer, fall) differences in network‐level posterior distributions of both average stream length and average communication distance. Our work demonstrates the unique perspectives concerning network drying provided by communication distance, and demonstrates the general usefulness of Bayesian approaches in the analysis of non‐perennial streams.
Kinesin family member 18B activates mTORC1 signaling via actin gamma 1 to promote the recurrence of human hepatocellular carcinoma
Authors: Li Qian , Sun Mengqing , Meng Yao , Feng Mengqing , Wang Menglan , Chang Cunjie , Dong Heng , Bu Fangtian , Xu Chao , Liu Jing , Ling Qi , Qiao Yiting , Chen Jianxiang 
Published: November 2023

AbstractThe mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway is frequently reported to be hyperactivated in hepatocellular carcinoma (HCC) and contributes to HCC recurrence. However, the underlying regulatory mechanisms of mTORC1 signaling in HCC are not fully understood. In the present study, we found that the expression of kinesin family member 18B (KIF18B) was positively correlated with mTORC1 signaling in HCC, and the upregulation of KIF18B and p-mTOR was associated with a poor prognosis and HCC recurrence. Utilizing in vitro and in vivo assays, we showed that KIF18B promoted HCC cell proliferation and migration through activating mTORC1 signaling. Mechanistically, we identified Actin gamma 1 (γ-Actin) as a binding partner of KIF18B. KIF18B and γ-Actin synergistically modulated lysosome positioning, promoted mTORC1 translocation to lysosome membrane, and prohibited p70 S6K from entering lysosomes for degradation, which finally led to the enhancement of mTORC1 signaling transduction. Moreover, we found that KIF18B was a direct target of Forkhead box M1, which explains the potential mechanism of KIF18B overexpression in HCC. Our study highlights the potential of KIF18B as a therapeutic target for the treatment of HCC.
Evolving treatment patterns and improved outcomes in relapsed/refractory mantle cell lymphoma: a prospective cohort study
Authors: Bock Allison M. , Gile Jennifer J. , Larson Melissa C. , Poonsombudlert Kittika , Tawfiq Reema K. , Maliske Seth , Maurer Matthew J. , Kabat Brian F. , Paludo Jonas , Inwards David J. , Ayyappan Sabarish , Link Brian K. , Ansell Stephen M. , Habermann Thomas M. , Witzig Thomas E. , Nowakowski Grzegorz S. , Cerhan James R. , Farooq Umar , Wang Yucai 
Published: November 2023

AbstractOver the last two decades, the frontline therapy for mantle cell lymphoma (MCL) has evolved. However, the impact of subsequent lines of therapy on survival outcomes has not been well characterized. In this study, we investigated the treatment patterns and survival outcomes in patients with relapsed/refractory (R/R) MCL treated with second-line (2 L) therapy. Adult patients with newly diagnosed MCL from 2002 to 2015 were enrolled in a prospective cohort study. Clinical characteristics, 2 L treatment details, and outcomes were compared between patients who received 2 L treatment between 2003–2009 (Era 1), 2010–2014 (Era 2), and 2015–2021 (Era 3). 2 L treatment was heterogenous in all eras, and there was a substantial shift in the pattern of 2 L therapy over time. The estimated 2-year EFS rate was 21% (95% CI, 13–35), 40% (95% CI, 30–53), and 51% (95% CI, 37–68) in Era 1–3 respectively, and the 5-year OS rate was 31% (95% CI, 21–45), 37% (95% CI, 27–50), and 67% (95% CI, 54–83) in Era 1–3, respectively. These results provide real-world evidence on evolving treatment patterns of 2 L therapy based on the era of relapse. The changes in 2 L treatment correlated with improved EFS and OS, suggesting that treatment advances are associated with improved outcomes in patients with R/R MCL.
UBE4B interacts with the ITCH E3 ubiquitin ligase to induce Ku70 and c-FLIPL polyubiquitination and enhanced neuroblastoma apoptosis
Authors: Le Clorennec Christophe , Subramonian Divya , Huo Yuchen , Zage Peter E. 
Published: November 2023

AbstractExpression of the UBE4B ubiquitin ligase is strongly associated with neuroblastoma patient outcomes, but the functional roles of UBE4B in neuroblastoma pathogenesis are not known. We evaluated interactions of UBE4B with the E3 ubiquitin ligase ITCH/AIP4 and the effects of UBE4B expression on Ku70 and c-FLIPL ubiquitination and proteasomal degradation by co-immunoprecipitation and Western blots. We also evaluated the role of UBE4B in apoptosis induced by histone deacetylase (HDAC) inhibition using Western blots. UBE4B binding to ITCH was mediated by WW domains in the ITCH protein. ITCH activation led to ITCH-UBE4B complex formation and recruitment of Ku70 and c-FLIPL via ITCH WW domains, followed by Ku70 and c-FLIPL Lys48/Lys63 branched polyubiquitination and proteasomal degradation. HDAC inhibition induced Ku70 acetylation, leading to release of c-FLIPL and Bax from Ku70, increased Ku70 and c-FLIPL Lys48/Lys63 branched polyubiquitination via the ITCH-UBE4B complex, and induction of apoptosis. UBE4B depletion led to reduced polyubiquitination and increased levels of Ku70 and c-FLIPL and to reduced apoptosis induced by HDAC inhibition via stabilization of c-FLIPL and Ku70 and inhibition of caspase 8 activation. Our results have identified novel interactions and novel targets for UBE4B ubiquitin ligase activity and a direct role for the ITCH-UBE4B complex in responses of neuroblastoma cells to HDAC inhibition, suggesting that the ITCH-UBE4B complex plays a critical role in responses of neuroblastoma to therapy and identifying a potential mechanism underlying the association of UBE4B expression with neuroblastoma patient outcomes.
CLOOME: contrastive learning unlocks bioimaging databases for queries with chemical structures
Authors: Sanchez-Fernandez Ana , Rumetshofer Elisabeth , Hochreiter Sepp , Klambauer Günter 
Published: November 2023

AbstractThe field of bioimage analysis is currently impacted by a profound transformation, driven by the advancements in imaging technologies and artificial intelligence. The emergence of multi-modal AI systems could allow extracting and utilizing knowledge from bioimaging databases based on information from other data modalities. We leverage the multi-modal contrastive learning paradigm, which enables the embedding of both bioimages and chemical structures into a unified space by means of bioimage and molecular structure encoders. This common embedding space unlocks the possibility of querying bioimaging databases with chemical structures that induce different phenotypic effects. Concretely, in this work we show that a retrieval system based on multi-modal contrastive learning is capable of identifying the correct bioimage corresponding to a given chemical structure from a database of ~2000 candidate images with a top-1 accuracy >70 times higher than a random baseline. Additionally, the bioimage encoder demonstrates remarkable transferability to various further prediction tasks within the domain of drug discovery, such as activity prediction, molecule classification, and mechanism of action identification. Thus, our approach not only addresses the current limitations of bioimaging databases but also paves the way towards foundation models for microscopy images.
Mitigating stimulated Brillouin scattering in multimode fibers with focused output via wavefront shaping
Authors: Chen Chun-Wei , Nguyen Linh V. , Wisal Kabish , Wei Shuen , Warren-Smith Stephen C. , Henderson-Sapir Ori , Schartner Erik P. , Ahmadi Peyman , Ebendorff-Heidepriem Heike , Stone A. Douglas , Ottaway David J. , Cao Hui 
Published: November 2023

AbstractThe key challenge for high-power delivery through optical fibers is overcoming nonlinear optical effects. To keep a smooth output beam, most techniques for mitigating optical nonlinearities are restricted to single-mode fibers. Moving out of the single-mode paradigm, we show experimentally that wavefront-shaping of coherent input light to a highly multimode fiber can increase the power threshold for stimulated Brillouin scattering (SBS) by an order of magnitude, whilst simultaneously controlling the output beam profile. The SBS suppression results from an effective broadening of the Brillouin spectrum under multimode excitation, without broadening of transmitted light. Strongest suppression is achieved with selective mode excitation that gives the broadest Brillouin spectrum. Our method is efficient, robust, and applicable to continuous waves and pulses. This work points toward a promising route for mitigating detrimental nonlinear effects in optical fibers, enabling further power scaling of high-power fiber systems for applications to directed energy, remote sensing, and gravitational-wave detection.
Local membrane source gathering by p62 body drives autophagosome formation
Authors: Feng Xuezhao , Sun Daxiao , Li Yanchang , Zhang Jinpei , Liu Shiyu , Zhang Dachuan , Zheng Jingxiang , Xi Qing , Liang Haisha , Zhao Wenkang , Li Ying , Xu Mengbo , He Jiayu , Liu Tong , Hasim Ayshamgul , Ma Meisheng , Xu Ping , Mi Na 
Published: November 2023

AbstractAutophagosomes are double-membrane vesicles generated intracellularly to encapsulate substrates for lysosomal degradation during autophagy. Phase separated p62 body plays pivotal roles during autophagosome formation, however, the underlying mechanisms are still not fully understood. Here we describe a spatial membrane gathering mode by which p62 body functions in autophagosome formation. Mass spectrometry-based proteomics reveals significant enrichment of vesicle trafficking components within p62 body. Combining cellular experiments and biochemical reconstitution assays, we confirm the gathering of ATG9 and ATG16L1-positive vesicles around p62 body, especially in Atg2ab DKO cells with blocked lipid transfer and vesicle fusion. Interestingly, p62 body also regulates ATG9 and ATG16L vesicle trafficking flux intracellularly. We further determine the lipid contents associated with p62 body via lipidomic profiling. Moreover, with in vitro kinase assay, we uncover the functions of p62 body as a platform to assemble ULK1 complex and invigorate PI3KC3-C1 kinase cascade for PI3P generation. Collectively, our study raises a membrane-based working model for multifaceted p62 body in controlling autophagosome biogenesis, and highlights the interplay between membraneless condensates and membrane vesicles in regulating cellular functions.
The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter
Authors: Mirón Gonzalo Díaz , Semelak Jonathan A. , Grisanti Luca , Rodriguez Alex , Conti Irene , Stella Martina , Velusamy Jayaramakrishnan , Seriani Nicola , Došlić Nadja , Rivalta Ivan , Garavelli Marco , Estrin Dario A. , Kaminski Schierle Gabriele S. , González Lebrero Mariano C. , Hassanali Ali , Morzan Uriel N. 
Published: November 2023

AbstractChallenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.
Evidence for charge delocalization crossover in the quantum critical superconductor CeRhIn5
Authors: Wang Honghong , Park Tae Beom , Kim Jihyun , Jang Harim , Bauer Eric D. , Thompson Joe D. , Park Tuson 
Published: November 2023

AbstractThe nature of charge degrees-of-freedom distinguishes scenarios for interpreting the character of a second order magnetic transition at zero temperature, that is, a magnetic quantum critical point (QCP). Heavy-fermion systems are prototypes of this paradigm, and in those, the relevant question is where, relative to a magnetic QCP, does the Kondo effect delocalize their f-electron degrees-of-freedom. Herein, we use pressure-dependent Hall measurements to identify a finite-temperature scale Eloc that signals a crossover from f-localized to f-delocalized character. As a function of pressure, Eloc(P) extrapolates smoothly to zero temperature at the antiferromagnetic QCP of CeRhIn5 where its Fermi surface reconstructs, hallmarks of Kondo-breakdown criticality that generates critical magnetic and charge fluctuations. In 4.4% Sn-doped CeRhIn5, however, Eloc(P) extrapolates into its magnetically ordered phase and is decoupled from the pressure-induced magnetic QCP, which implies a spin-density-wave (SDW) type of criticality that produces only critical fluctuations of the SDW order parameter. Our results demonstrate the importance of experimentally determining Eloc to characterize quantum criticality and the associated consequences for understanding the pairing mechanism of superconductivity that reaches a maximum Tc in both materials at their respective magnetic QCP.