bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerating Subglacial Hydrology for Ice Sheet Models With Deep Learning Methods
Authors: Verjans Vincent , Robel Alexander 
Published: January 2024

AbstractSubglacial drainage networks regulate the response of ice sheet flow to surface meltwater input to the subglacial environment. Simulating subglacial hydrology evolution is critical to projecting ice sheet sensitivity to climate, and contribution to sea‐level change. However, current numerical subglacial hydrology models are computationally expensive, and, consequently, evolving subglacial hydrology is neglected in large‐scale ice sheet simulations. We present a deep learning emulator of a state‐of‐the‐art subglacial hydrology model, trained at multiple Greenland glaciers. Our emulator performs strongly in both temporal (R2 > 0.99) and spatial (R2 > 0.95) generalization, offers high computational savings, and can be used to force numerical ice sheet models. This will enable century‐ and large‐scale ice sheet model simulations, including interactions between ice flow and increased meltwater input to the subglacial environment. Generally, our work demonstrates that machine learning can further improve ice sheet models, reduce computational bottlenecks, and exploit information from high‐fidelity models and novel observational platforms.
Inferring Whistler‐Mode Chorus Wave Source Regions in the Martian Mini‐Magnetospheres
Authors: Cheng Sanwei , Su Zhenpeng , Wu Zhiyong , Wang Yuming 
Published: January 2024

AbstractMartian mini‐magnetospheres contain whistler‐mode chorus waves potentially contributing to atmospheric escape, analogous to the Earth's inner magnetosphere. At Earth, the chorus waves have been found to originate from the near‐equatorial region spanning approximately 2% of the entire magnetic field line length. However, because of the lack of wave Poynting flux measurements, the Martian chorus source region remains unclear. By comparing the frequency dependence between observed wave power and modeled linear growth rates, we present the first attempt to explore the chorus wave source distribution along the Martian mini‐magnetospheric field lines. Our data‐to‐model comparisons support that these waves are not generated by a single source tightly confined near the magnetic strength minimal location but by intermittent or continuous sources spanning up to 40% of the entire field line length. These results imply that the Martian mini‐magnetospheres could have more active energy transfer processes mediated by whistler‐mode chorus waves than the expectation.
Flow and Turbulence Due To Wood Contribute to Declogging of Gravel Bed
Authors: Schalko I. , Ponce M. , Lassar S. , Schwindt S. , Haun S. , Nepf H. 
Published: January 2024

AbstractThe placement of wood in rivers is a common restoration method used to locally affect hydraulic and morphologic conditions to create habitat. Laboratory experiments demonstrated that wood placements can also promote surface declogging, that is, removal of fine sediment from a gravel bed, thereby restoring spawning grounds for fish. Logs of different size and submergence level were placed on a gravel bed clogged with fines. Surface declogging was observed in regions of elevated turbulence in the log wake and elevated velocity adjacent to the log. A criteria for declogging was identified based on a modified non‐dimensional Shields parameter combining mean and turbulent velocity at the bed. The footprint of declogged bed scaled with log dimensions. Emergent logs produced a larger declogging footprint compared to submerged logs of the same length, due to their stronger influence on the flow field. Logs were also shown to prevent clogging over similar areas.
Impacts of Reclamation on Hydrodynamic and Suspended Sediment Transport in the Bohai Sea
Authors: Liu Siyu , Li Guangxue , Liu Shidong , Xing Lvyang , Pan Yufeng , Yu Di 
Published: January 2024

AbstractSince the 1970s, extensive land reclamation has been carried out in the Bohai Sea. However, reclamation activities were prohibited in 2018. Using the MIKE3 numerical model, this study selected 1976 and 2018 as representative years before and after reclamation, respectively, and developed a highly accurate three‐dimensional hydrodynamic and sediment transport model for the Bohai Sea. The model was employed to access the effects of reclamation on tidal waves, tidal prism, residual current, tidal flux (TF), and suspended sediment flux (SSF). The results revealed that after reclamation, the amphidromic points of M2 and S2 shifted southward near Qinhuangdao, and eastward near the Yellow River estuary. The M2 amplitude in the Bohai Bay exhibited a maximum increase of 30 cm. In the Bohai Sea, the tidal prism decreased by 3.95%, suggesting a decrease in water exchange capacity. The TF in the Bohai Sea and Laizhou Bay decreased by 0.7% and 12%, respectively, while increasing by 16% in Bohai Bay and 12% in Liaodong Bay, primarily due to the variations in tidal waves. Furthermore, SSF decreased by 6% in the Bohai Sea, but increased by 125% in Bohai Bay and 114% in Laizhou Bay. The significant increase in SSF in Bohai Bay and Laizhou Bay was mainly attributed to the higher suspended sediment concentrations and the stronger residual current velocities near the Yellow River estuary. This study provides comprehensive insights into the impacts of reclamation on TF and SSF in the Bohai Sea, which could contribute to marine resource development and the planning of environmental restoration projects.
Consistent Modeling of Transport Processes and Travel Times—Coupling Soil Hydrologic Processes With StorAge Selection Functions
Authors: Schwemmle Robin , Weiler Markus 
Published: January 2024

AbstractUnderstanding the transport processes and travel times of pollutants in the subsurface is crucial for an effective management of drinking water resources. Transport processes and soil hydrologic processes are inherently linked to each other. In order to account for this link, we couple the process‐based hydrologic model RoGeR with StorAge Selection (SAS) functions. We assign to each hydrological process a specific SAS function (e.g., power law distribution function). To represent different transport mechanisms, we combined a specific set of SAS functions into four transport model structures: complete‐mixing, piston flow, advection‐dispersion and advection‐dispersion with time‐variant parameters. In this study, we conduct modeling experiments at the Rietholzbach lysimeter, Switzerland. All modeling experiments are benchmarked with HYDRUS‐1D. We compare our simulations to the measured hydrologic variables (percolation and evapotranspiration fluxes and soil water storage dynamics) and the measured water stable isotope signal (18O) in the lysimeter seepage for a period of ten years (1997–2007). An additional virtual bromide tracer experiment was used to benchmark the models. Additionally, we carried out a sensitivity analysis and provided Sobol indices for hydrologic model parameters and SAS parameters. Our results indicate that the advection‐dispersion transport model produces the best results. And thus, advective‐dispersive transport processes play a dominant role at Rietholzbach lysimeter. Our modeling approach provides the capability to test hypotheses of different transport mechanisms and to improve process understanding and predictions of transport processes. Overall, the combined model allows a very effective simulation of combined flux and transport processes at various temporal and spatial scales.
Integrated genomic and transcriptomic analysis reveals the activation of PI3K signaling pathway in HPV-independent cervical cancers
Authors: Wang Yi , He Misi , He Tiancong , Ouyang Xueyan , Shen Xuxia , Shi Wanling , Huang Shengling , Xiang Libing , Zou Dongling , Jiang Wei , Yang Huijuan 
Published: January 2024

Abstract
Background
HPV-independent cervical cancers (HPV-ind CCs) are uncommon with worse prognosis and poorly understood. This study investigated the molecular characteristics of HPV-ind CCs, aiming to explore new strategies for HPV-ind CCs.

Methods
HPV status of 1010 cervical cancer patients were detected by RT-PCR, PCR and RNA-sequencing (RNA-seq). Whole exome sequencing (WES) and RNA-seq were performed in identified HPV-ind CCs. The efficacy of PI3Kα inhibitor BYL719 in HPV-ind CCs was evaluated in cell lines, patient-derived organoids (PDOs) and patient-derived xenografts (PDXs).

Results
Twenty-five CCs were identified as HPV-ind, which were more common seen in older, adenocarcinoma patients and exhibited poorer prognosis as well as higher tumor mutation burden compared to HPV-associated CCs. HPV-ind CCs were featured with highly activated PI3K/AKT signaling pathway, particularly, PIK3CA being the most predominant genomic alteration (36%). BYL719 demonstrated superior tumor suppression in vitro and in vivo. Furthermore, HPV-ind CCs were classified into two subtypes according to distinct prognosis by gene expression profiles, the metabolism subtype and immune subtype.

Conclusions
This study reveals the prevalence, clinicopathology, and molecular features of HPV-ind CCs and emphasizes the importance of PIK3CA mutations and PI3K pathway activation in tumorigenesis, which suggests the potential significance of PI3Kα inhibitors in HPV-ind CC patients.
Divergent immune microenvironments in two tumor nodules from a patient with mismatch repair-deficient prostate cancer
Authors: Bergom Hannah E. , Sena Laura A. , Day Abderrahman , Miller Benjamin , Miller Carly D. , Lozada John R. , Zorko Nicholas , Wang Jinhua , Shenderov Eugene , Lobo Francisco Pereira , Caramella-Pereira Fernanda , Marchionni Luigi , Drake Charles G. , Lotan Tamara , De Marzo Angelo M. , Hwang Justin , Antonarakis Emmanuel S. 
Published: January 2024

AbstractPatients with prostate cancer (PC) generally do not respond favorably to immune checkpoint inhibitors, which may be due to a low abundance of tumor-infiltrating lymphocytes even when mutational load is high. Here, we identified a patient who presented with high-grade primary prostate cancer with two adjacent tumor nodules. While both nodules were mismatch repair-deficient (MMRd), exhibited pathogenicMSH2andMSH6alterations, had a high tumor mutational burden (TMB), and demonstrated high microsatellite instability (MSI), they had markedly distinct immune phenotypes. The first displayed a dense infiltrate of lymphocytes (“hot nodule”), while the second displayed significantly fewer infiltrating lymphocytes (“cold nodule”). Whole-exome DNA analysis found that both nodules shared many identical mutations, indicating that they were derived from a single clone. However, the cold nodule appeared to be sub-clonal relative to the hot nodule, suggesting divergent evolution of the cold nodule from the hot nodule. Whole-transcriptome RNA analysis found that the cold nodule demonstrated lower expression of genes related to antigen presentation (HLA) and, paradoxically, classical tumor immune tolerance markers such as PD-L1 (CD274) and CTLA-4. Immune cell deconvolution suggested that the hot nodule was enriched not only in CD8+ and CD4 + T lymphocytes, but also in M1 macrophages, activated NK cells, and γδ T cells compared to the cold nodule. This case highlights that MMRd/TMB-high PC can evolve to minimize an anti-tumor immune response, and nominates downregulation of antigen presentation machinery (HLA loss) as a potential mechanism of adaptive immune evasion in PC.
Theoretical guarantees for permutation-equivariant quantum neural networks
Authors: Schatzki Louis , Larocca Martín , Nguyen Quynh T. , Sauvage Frédéric , Cerezo M. 
Published: January 2024

AbstractDespite the great promise of quantum machine learning models, there are several challenges one must overcome before unlocking their full potential. For instance, models based on quantum neural networks (QNNs) can suffer from excessive local minima and barren plateaus in their training landscapes. Recently, the nascent field of geometric quantum machine learning (GQML) has emerged as a potential solution to some of those issues. The key insight of GQML is that one should design architectures, such as equivariant QNNs, encoding the symmetries of the problem at hand. Here, we focus on problems with permutation symmetry (i.e., symmetry group Sn), and show how to build Sn-equivariant QNNs We provide an analytical study of their performance, proving that they do not suffer from barren plateaus, quickly reach overparametrization, and generalize well from small amounts of data. To verify our results, we perform numerical simulations for a graph state classification task. Our work provides theoretical guarantees for equivariant QNNs, thus indicating the power and potential of GQML.
Quantum LOSR networks cannot generate graph states with high fidelity
Authors: Wang Yi-Xuan , Xu Zhen-Peng , Gühne Otfried 
Published: January 2024

AbstractQuantum networks lead to novel notions of locality and correlations and an important problem concerns the question of which quantum states can be experimentally prepared with a given network structure and devices and which not. We prove that all multi-qubit graph states arising from a connected graph cannot originate from any quantum network with bipartite sources, as long as feed-forward and quantum memories are not available. Moreover, the fidelity of a multi-qubit graph state and any network state cannot exceed 9/10. Similar results can also be established for a large class of multi-qudit graph states.
Inferring chemical disequilibrium biosignatures for Proterozoic Earth-like exoplanets
Authors: Young Amber V. , Robinson Tyler D. , Krissansen-Totton Joshua , Schwieterman Edward W. , Wogan Nicholas F. , Way Michael J. , Sohl Linda E. , Arney Giada N. , Reinhard Christopher T. , Line Michael R. , Catling David C. , Windsor James D. 
Published: January 2024

AbstractChemical disequilibrium quantified using the available free energy has previously been proposed as a potential biosignature. However, researchers remotely sensing exoplanet biosignatures have not yet investigated how observational uncertainties impact the ability to infer a life-generated available free energy. We pair an atmospheric retrieval tool to a thermodynamics model to assess the detectability of chemical disequilibrium signatures of Earth-like exoplanets, focusing on the Proterozoic eon when the atmospheric abundances of oxygen–methane disequilibrium pairs may have been relatively high. Retrieval model studies applied across a range of gas abundances revealed that order-of-magnitude constraints on the disequilibrium energy are achieved with simulated reflected-light observations for the high-abundance scenario and high signal-to-noise ratios (50), whereas weak constraints are found for moderate signal-to-noise ratios (20–30) and medium- to low-abundance cases. Furthermore, the disequilibrium-energy constraints are improved by using the modest thermal information encoded in water vapour opacities at optical and near-infrared wavelengths. These results highlight how remotely detecting chemical disequilibrium biosignatures can be a useful and metabolism-agnostic approach to biosignature detection.
Transnational conservation to anticipate future plant shifts in Europe
Authors: Chauvier-Mendes Yohann , Pollock Laura J. , Verburg Peter H. , Karger Dirk N. , Pellissier Loïc , Lavergne Sébastien , Zimmermann Niklaus E. , Thuiller Wilfried 
Published: January 2024

AbstractTo meet the COP15 biodiversity framework in the European Union (EU), one target is to protect 30% of its land by 2030 through a resilient transnational conservation network. The European Alps are a key hub of this network hosting some of the most extensive natural areas and biodiversity hotspots in Europe. Here we assess the robustness of the current European reserve network to safeguard the European Alps’ flora by 2080 using semi-mechanistic simulations. We first highlight that the current network needs strong readjustments as it does not capture biodiversity patterns as well as our conservation simulations. Overall, we predict a strong shift in conservation need through time along latitudes, and from lower to higher elevations as plants migrate upslope and shrink their distribution. While increasing species, trait and evolutionary diversity, migration could also threaten 70% of the resident flora. In the face of global changes, the future European reserve network will need to ensure strong elevation and latitudinal connections to complementarily protect multifaceted biodiversity beyond national borders.
Shoreline classification maps and ground truth data for the Neuse River Estuary, North Carolina
Authors: Sirianni Hannah , Richter Jessica , Sirianni Matthew J. , Pettyjohn Sarah 
Published: January 2024

AbstractEstuaries provide essential ecosystem services and economic value but are facing widespread degradation due to changing anthropogenic and climatic factors. In North Carolina, coastal structures, like bulkheads and riprap, are widely used by property owners throughout the Albemarle-Pamlico estuary to stop erosion and reclaim lost land following storm events. While coastal development is tightly governed, limited historical and no up-to-date data report on the spatial distribution of coastal structures throughout the Albemarle-Pamlico estuary. Here we describe the development of a dataset that classifies and catalogues 67 km of shoreline type along the Neuse River Estuary (NRE), a large tributary of the Albemarle-Pamlico. We used available LiDAR digital elevation models (DEMs), aerial imagery, and a ground truthing field campaign to determine shoreline type present along the NRE as of 2020. We validated these results using an intensive manual editing procedure that comparatively examines DEMs, LiDAR derived slope, aerial imagery, and ground truth photography of the shoreline. This dataset is available for public download.
Molecular dynamics simulations of displacement cascades in LiAlO2 and LiAl5O8 ceramics
Authors: Roy Ankit , Casella Andrew M. , Senor David J. , Jiang Weilin , Devanathan Ram 
Published: January 2024

AbstractMolecular dynamics was employed to investigate the radiation damage due to collision cascades in LiAlO2 and LiAl5O8, the latter being a secondary phase formed in the former during irradiation. Atomic displacement cascades were simulated by initiating primary knock-on atoms (PKA) with energy values = 5, 10 and 15 keV and the damage was quantified by the number of Frenkel pairs formed for each species: Li, Al and O. The primary challenges of modeling an ionic system with and without a core–shell model for oxygen atoms were addressed and new findings on the radiation resistance of these ceramics are presented. The working of a variable timestep function and the kinetics in the background of the simulations have been elaborated to highlight the novelty of the simulation approach. More importantly, the key results indicated that LiAlO2 experiences much more radiation damage than LiAl5O8, where the number of Li Frenkel pairs in LiAlO2 was 3–5 times higher than in LiAl5O8 while the number of Frenkel pairs for Al and O in LiAlO2 are ~ 2 times higher than in LiAl5O8. The primary reason is high displacement threshold energies (Ed) in LiAl5O8 for Li cations. The greater Ed for Li imparts higher resistance to damage during the collision cascade and thus inhibits amorphization in LiAl5O8. The presented results suggest that LiAl5O8 is likely to maintain structural integrity better than LiAlO2 in the irradiation conditions studied in this work.
A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison
Authors: Wehrenberg Gerrit , Tokarska Małgorzata , Cocchiararo Berardino , Nowak Carsten 
Published: January 2024

AbstractThe European bison was saved from the brink of extinction due to considerable conservation efforts since the early twentieth century. The current global population of > 9500 individuals is the result of successful ex situ breeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96 markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in further Bos species with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world’s first studbook of a threatened species.
Interaction of designed cationic antimicrobial peptides with the outer membrane of gram-negative bacteria
Authors: He Shelley , Deber Charles M. 
Published: January 2024

AbstractThe outer membrane (OM) is a hallmark feature of gram-negative bacteria that provides the species with heightened resistance against antibiotic threats while cationic antimicrobial peptides (CAPs) are natural antibiotics broadly recognized for their ability to disrupt bacterial membranes. It has been well-established that lipopolysaccharides present on the OM are among major targets of CAP activity against gram-negative species. Here we investigate how the relative distribution of charged residues along the primary peptide sequence, in conjunction with its overall hydrophobicity, affects such peptide-OM interactions in the natural CAP Ponericin W1. Using a designed peptide library derived from Ponericin W1, we determined that the consecutive placement of Lys residues at the peptide N- or C-terminus (ex. “PonN”: KKKKKKWLGSALIGALLPSVVGLFQ) enhances peptide binding affinity to OM lipopolysaccharides compared to constructs where Lys residues are interspersed throughout the primary sequence (ex. “PonAmp”: WLKKALKIGAKLLPSVVKLFKGSGQ). Antimicrobial activity against multidrug resistant strains of Pseudomonas aeruginosa was similarly found to be highest among Lys-clustered sequences. Our findings suggest that while native Ponericin W1 exerts its initial activity at the OM, Lys-clustering may be a promising means to enhance potency towards this interface, thereby augmenting peptide entry and activity at the IM, with apparent advantage against multidrug-resistant species.
Pneumonia detection based on RSNA dataset and anchor-free deep learning detector
Authors: Wu Linghua , Zhang Jing , Wang Yilin , Ding Rong , Cao Yueqin , Liu Guiqin , Liufu Changsheng , Xie Baowei , Kang Shanping , Liu Rui , Li Wenle , Guan Furen 
Published: January 2024

AbstractPneumonia is a highly lethal disease, and research on its treatment and early screening tools has received extensive attention from researchers. Due to the maturity and cost reduction of chest X-ray technology, and with the development of artificial intelligence technology, pneumonia identification based on deep learning and chest X-ray has attracted attention from all over the world. Although the feature extraction capability of deep learning is strong, existing deep learning object detection frameworks are based on pre-defined anchors, which require a lot of tuning and experience to guarantee their excellent results in the face of new applications or data. To avoid the influence of anchor settings in pneumonia detection, this paper proposes an anchor-free object detection framework and RSNA dataset based on pneumonia detection. First, a data enhancement scheme is used to preprocess the chest X-ray images; second, an anchor-free object detection framework is used for pneumonia detection, which contains a feature pyramid, two-branch detection head, and focal loss. The average precision of 51.5 obtained by Intersection over Union (IoU) calculation shows that the pneumonia detection results obtained in this paper can surpass the existing classical object detection framework, providing an idea for future research and exploration.