bluuebunny/crossref_metadata_2025_split huggingface dataset:
CON-FOLD Explainable Machine Learning with Confidence
Authors: MCGINNESS LACHLAN , BAUMGARTNER PETER 
Published: October 2024

AbstractFOLD-RM is an explainable machine learning classification algorithm that uses training data to create a set of classification rules. In this paper, we introduce CON-FOLD which extends FOLD-RM in several ways. CON-FOLD assigns probability-based confidence scores to rules learned for a classification task. This allows users to know how confident they should be in a prediction made by the model. We present a confidence-based pruning algorithm that uses the unique structure of FOLD-RM rules to efficiently prune rules and prevent overfitting. Furthermore, CON-FOLD enables the user to provide preexisting knowledge in the form of logic program rules that are either (fixed) background knowledge or (modifiable) initial rule candidates. The paper describes our method in detail and reports on practical experiments. We demonstrate the performance of the algorithm on benchmark datasets from the UCI Machine Learning Repository. For that, we introduce a new metric, Inverse Brier Score, to evaluate the accuracy of the produced confidence scores. Finally, we apply this extension to a real-world example that requires explainability: marking of student responses to a short answer question from the Australian Physics Olympiad.
The Election of an ‘Outsider’ Archbishop
Authors: Porter Muriel 
Published: October 2024

Abstract
The 1984 election of David Penman as Anglican Archbishop of Melbourne was surprising, coming at the end of a controversial process in which two better-known candidates had consistently been the front runners. His election disrupted the longstanding power base of Melbourne Diocese represented by the two men passed over. But his election disrupted more than that – it disrupted the stalemate preventing the ordination of women in the Anglican Church of Australia. His election was crucial to the struggle to have women ordained in the Australian church. As Melbourne Diocesan Synod prepares to elect its next archbishop in 2025, it is timely to re-visit the 1984 election.
Groundwaterscapes: A Global Classification and Mapping of Groundwater's Large‐Scale Socioeconomic, Ecological, and Earth System Functions
Authors: Huggins Xander , Gleeson Tom , Villholth Karen G. , Rocha Juan C. , Famiglietti James S. 
Published: October 2024

AbstractGroundwater is a dynamic component of the global water cycle with important social, economic, ecological, and Earth system functions. We present a new global classification and mapping of groundwater systems, which we call groundwaterscapes, that represent predominant configurations of large‐scale groundwater system functions. We identify and map 15 groundwaterscapes which offer a new lens to conceptualize, study, model, and manage groundwater. Groundwaterscapes are derived using a novel application of sequenced self‐organizing maps that capture patterns in groundwater system functions at the grid cell level (∼10 km), including groundwater‐dependent ecosystem type and density, storage capacity, irrigation, safe drinking water access, and national governance. All large aquifer systems of the world are characterized by multiple groundwaterscapes, highlighting the pitfalls of treating these groundwater bodies as lumped systems in global assessments. We evaluate the distribution of Global Groundwater Monitoring Network wells across groundwaterscapes and find that industrial agricultural regions are disproportionately monitored, while several groundwaterscapes have next to no monitoring wells. This disparity undermines the ability to understand system dynamics across the full range of settings that characterize groundwater systems globally. We argue that groundwaterscapes offer a conceptual and spatial tool to guide model development, hypothesis testing, and future data collection initiatives to better understand groundwater's embeddedness within social‐ecological systems at the global scale.
Poroelastic Response of a Fractured Rock to Hydrostatic Pressure Oscillations
Authors: Chapman Samuel , Lissa Simón , Fortin Jerome , Quintal Beatriz 
Published: October 2024

AbstractPoroelastic coupling between fractures and the surrounding rock is important to numerous applications in geosciences. We measure the in‐situ fluid pressure and local strain response of a fractured carbonate sample to hydrostatic pressure oscillations. A linear poroelastic model that represents the rock sample is parameterized using X‐ray imaging and ultrasonic wave transmission measurements. The numerical solution, based on Biot's quasistatic equations, is consistent with the measured frequency dependent dispersion of the apparent bulk modulus of the background matrix and the in‐situ pore pressure response, which is caused by fluid pressure diffusion from the compliant fractures into the stiffer matrix. The observed fluid pressure diffusion is causally related to the numerically quantified intrinsic attenuation at seismic frequencies, which is a major contributor to the dissipation of seismic waves. Our analysis supports the use of a simple approximation of fractures as compliant and planar inclusions in numerical simulations based on linear poroelasticity.
What Distinguishes Summer Extreme Precipitation From Non‐Extreme Precipitation Over the Tibetan Plateau?
Authors: Ding Zhiyuan , Ha Yao , Huangfu Jingliang , Zhong Zhong 
Published: October 2024

AbstractThis study focuses on the primary synoptic‐scale patterns and precursors of extreme and non‐extreme precipitation over the Tibetan Plateau (TP). Atmospheric circulation anomalies and their precursors associated with regional extreme precipitation events (REPE) demonstrate distinct precursor wave train and heightened intensity than regional non‐extreme precipitation events (non‐REPE). Specifically, REPE over the northwestern TP (NWTP) exhibits a geopotential height anomaly induced by a latitudinal propagating Rossby wave train along 40°N. In contrast, over the southeastern TP (SETP), REPE is characterized by a geopotential height anomaly caused by a northwest‐southeastward propagating Rossby wave train. The ascending motion anomalies of REPE over both NWTP and SETP are primarily attributed to the geostrophic zonal temperature advection, which is significantly stronger during REPE compared to non‐REPE. This finding provides valuable insights for forecasting summer extreme precipitation over TP.
Self‐Potential Tomography Preconditioned by Particle Swarm Optimization—Application to Monitoring Hyporheic Exchange in a Bedrock River
Authors: Ikard Scott J. , Carroll Kenneth C. , Brooks Scott C. , Rucker Dale F. , Smith‐Vega Gladisol , Elwes Aubrey 
Published: October 2024

AbstractA self‐potential (SP) data‐inversion algorithm was developed and tested on an analytical model of electrical‐potential profile data attributed to single and multiple polarized electrical sources. The developed algorithm was then validated by an application to SP‐monitoring field data measured on the floodplain of East Fork Poplar Creek, Oak Ridge, Tennessee, to image electrical sources in areas conducive to preferential flow into the flood plain from the bedrock‐lined riverbed. The algorithm combined stochastic source‐localization by particle‐swarm‐optimization (PSO) of electrical sources characterized by simplified geometries with source tomography by regularized weighted least‐squares minimization of a quadratic objective function. Prior information was incorporated by preconditioning the tomography algorithm by PSO results. Variable percentages of random noise were added to analytical‐model data to evaluate the algorithm performance. Results indicated that true parameters of single‐source models were inverted and approximated with small residual error, whereas inversion of analytical‐model data representing multiple electrical sources accurately approximated the locations of the sources but miscalculated some parameters because of the non‐uniqueness of the inverse‐model solution. Source tomography applied to analytical model data during testing produced a spatially continuous parameter field that identified the locations of point‐scale synthetic dipole sources of electrical current flow with varying degrees of accuracy depending on the prior information incorporated into the tomography. When applied to SP‐monitoring field data, the algorithm imaged electrical sources within a known fault that intersects the bedrock riverbed and flood plain of East Fork Poplar Creek and depicted dynamic electrical conditions attributed to hyporheic exchange.
Long-range enhancement for fluorescence and Raman spectroscopy using Ag nanoislands protected with column-structured silica overlayer
Authors: Minamikawa Takeo , Sakaguchi Reiko , Harada Yoshinori , Tanioka Hiroki , Inoue Sota , Hase Hideharu , Mori Yasuo , Takamatsu Tetsuro , Yamasaki Yu , Morimoto Yukihiro , Kawasaki Masahiro , Kawasaki Mitsuo 
Published: October 2024

AbstractWe demonstrate long-range enhancement of fluorescence and Raman scattering using a dense random array of Ag nanoislands (AgNIs) coated with column-structured silica (CSS) overlayer of over 100 nm thickness, namely, remote plasmonic-like enhancement (RPE). The CSS layer provides physical and chemical protection, reducing the impact between analyte molecules and metal nanostructures. RPE plates are fabricated with high productivity using sputtering and chemical immersion in gold(I)/halide solution. The RPE plate significantly enhances Raman scattering and fluorescence, even without proximity between analyte molecules and metal nanostructures. The maximum enhancement factors are 107-fold for Raman scattering and 102-fold for fluorescence. RPE is successfully applied to enhance fluorescence biosensing of intracellular signalling dynamics in HeLa cells and Raman histological imaging of oesophagus tissues. Our findings present an interesting deviation from the conventional near-field enhancement theory, as they cannot be readily explained within its framework. However, based on the phenomenological aspects we have demonstrated, the observed enhancement is likely associated with the remote resonant coupling between the localised surface plasmon of AgNIs and the molecular transition dipole of the analyte, facilitated through the CSS structure. Although further investigation is warranted to fully understand the underlying mechanisms, the RPE plate offers practical advantages, such as high productivity and biocompatibility, making it a valuable tool for biosensing and biomolecular analysis in chemistry, biology, and medicine. We anticipate that RPE will advance as a versatile analytical tool for enhanced biosensing using Raman and fluorescence analysis in various biological contexts.
Movable surface acoustic wave tweezers: a versatile toolbox for micromanipulation
Authors: Qin Xianming , Liu Xianglian , Liu Shuo , Zhang Chuanyu , Bai Ningning , Li Xue , Wang Weidong , Liu Dan , Yang Qiqi , Yang Ruiguo , Shen Yajing , Wei Xueyong 
Published: October 2024

AbstractSurface acoustic wave (SAW) tweezers are a promising multifunctional micromanipulation method that controls microscale targets via patterned acoustic fields. Owing to their device structure and bonding process, most SAW tweezers have limitations in terms of controlling the position and motion of the acoustic traps, as they generate an acoustic field with a fixed region and adjust the manipulation effects via signal modulation. To address this challenge, we propose movable SAW tweezers with a multilayer structure, achieving dynamic control of their wave field and acoustic trap positions; we demonstrate their precise manipulation functions, such as translation, in-plane rotation, out-of-plane rotation, and cluster formation, on a wide spectrum of samples, including particles, bubbles, droplets, cells, and microorganisms. Our method not only improves the degree of freedom and working range of SAW tweezers but also allows for precise and selective manipulation of microtargets via microtools and localized wavefields. Owing to their flexibility, versatility, and biocompatibility, the movable SAW tweezers can be a practical platform for achieving arbitrary manipulation of microscale targets and have the potential to play significant roles in biomedical microrobotics.
Role of glia in delirium: proposed mechanisms and translational implications
Authors: Heffernan Áine Bríd , Steinruecke Moritz , Dempsey Georgia , Chandran Siddharthan , Selvaraj Bhuvaneish T. , Jiwaji Zoeb , Stavrou Maria 
Published: October 2024

Abstract
Delirium is a common acute onset neurological syndrome characterised by transient fluctuations in cognition. It affects over 20% of medical inpatients and 50% of those critically ill. Delirium is associated with morbidity and mortality, causes distress to patients and carers, and has significant socioeconomic costs in ageing populations. Despite its clinical significance, the pathophysiology of delirium is understudied, and many underlying cellular mechanisms remain unknown. There are currently no effective pharmacological treatments which directly target underlying disease processes. Although many studies focus on neuronal dysfunction in delirium, glial cells, primarily astrocytes, microglia, and oligodendrocytes, and their associated systems, are increasingly implicated in delirium pathophysiology. In this review, we discuss current evidence which implicates glial cells in delirium, including biomarker studies, post-mortem tissue analyses and pre-clinical models. In particular, we focus on how astrocyte pathology, including aberrant brain energy metabolism and glymphatic dysfunction, reactive microglia, blood-brain barrier impairment, and white matter changes may contribute to the pathogenesis of delirium. We also outline limitations in this body of work and the unique challenges faced in identifying causative mechanisms in delirium. Finally, we discuss how established neuroimaging and single-cell techniques may provide further mechanistic insight at pre-clinical and clinical levels.
The link between amyloid β and ferroptosis pathway in Alzheimer’s disease progression
Authors: Majerníková Naďa , Marmolejo-Garza Alejandro , Salinas Casandra Salinas , Luu Minh D. A. , Zhang Yuequ , Trombetta-Lima Marina , Tomin Tamara , Birner-Gruenberger Ruth , Lehtonen Šárka , Koistinaho Jari , Wolters Justina C. , Ayton Scott , den Dunnen Wilfred F. A. , Dolga Amalia M. 
Published: October 2024

AbstractAlzheimer’s disease (AD) affects millions of people worldwide and represents the most prevalent form of dementia. Treatment strategies aiming to interfere with the formation of amyloid β (Aβ) plaques and neurofibrillary tangles (NFTs), the two major AD hallmarks, have shown modest or no effect. Recent evidence suggests that ferroptosis, a type of programmed cell death caused by iron accumulation and lipid peroxidation, contributes to AD pathogenesis. The existing link between ferroptosis and AD has been largely based on cell culture and animal studies, while evidence from human brain tissue is limited. Here we evaluate if Aβ is associated with ferroptosis pathways in post-mortem human brain tissue and whether ferroptosis inhibition could attenuate Aβ-related effects in human brain organoids. Performing positive pixel density scoring on immunohistochemically stained post-mortem Brodmann Area 17 sections revealed that the progression of AD pathology was accompanied by decreased expression of nuclear receptor co-activator 4 and glutathione peroxidase 4 in the grey matter. Differentiating between white and grey matter, allowed for a more precise understanding of the disease’s impact on different brain regions. In addition, ferroptosis inhibition prevented Aβ pathology, decreased lipid peroxidation and restored iron storage in human AD iPSCs-derived brain cortical organoids at day 50 of differentiation. Differential gene expression analysis of RNAseq of AD organoids compared to isogenic controls indicated activation of the ferroptotic pathway. This was also supported by results from untargeted proteomic analysis revealing significant changes between AD and isogenic brain organoids. Determining the causality between the development of Aβ plaques and the deregulation of molecular pathways involved in ferroptosis is crucial for developing potential therapeutic interventions.
Proteomic profiling reveals CEACAM6 function in driving gallbladder cancer aggressiveness through integrin receptor, PRKCD and AKT/ERK signaling
Authors: Sugiyanto Raisatun Nisa , Metzger Carmen , Inal Aslihan , Truckenmueller Felicia , Gür Kira , Eiteneuer Eva , Huth Thorben , Fraas Angelika , Heinze Ivonne , Kirkpatrick Joanna , Sticht Carsten , Albrecht Thomas , Goeppert Benjamin , Poth Tanja , Pusch Stefan , Mehrabi Arianeb , Schirmacher Peter , Ji Junfang , Ori Alessandro , Roessler Stephanie 
Published: October 2024

AbstractGallbladder cancer (GBC) presents as an aggressive malignancy with poor patient outcome. Like other epithelial cancers, the mechanisms of GBC cancer progression remain vague and efforts in finding targeted therapies fall below expectations. This study combined proteomic analysis of formalin-fixed paraffin-embedded (FFPE) GBC samples, functional and molecular characterization of potential oncogenes and identification of potential therapeutic strategies for GBC. We identified Carcinoembryonic Antigen-related Cell Adhesion Molecule 6 (CEACAM6) as one of the significantly most upregulated proteins in GBC. CEACAM6 overexpression has been observed in other cancer entities but the molecular function remains unclear. Our functional analyses in vitro and in vivo mouse models revealed that CEACAM6 supported the initial steps of cancer progression and metastasis by decreasing cell adhesion and promoting migration and invasion of GBC cells. Conversely, CEACAM6 knockdown abolished GBC aggressiveness by increasing cell adhesion while reducing cell migration, cell proliferation, and colony formation. BirA-BioID followed by mass-spectrometry revealed Integrin Beta-1 (ITGB1) and Protein Kinase C Delta (PRKCD) as direct molecular and functional partners of CEACAM6 supporting GBC cell migration. ERK and AKT signaling and their downstream target genes were regulated by CEACAM6 and thus the treatment with AKT inhibitor capivasertib or ERK inhibitor ulixertinib mitigated the CEACAM6-induced migration. These findings demonstrate that CEACAM6 is crucially involved in gallbladder cancer progression by promoting migration and inhibiting cell adhesion through ERK and AKT signaling providing specific options for treatment of CEACAM6-positive cancers.
Xanthohumol overcomes osimertinib resistance via governing ubiquitination-modulated Ets-1 turnover
Authors: Ma Ying , Wang Ruirui , Liao Jinzhuang , Guo Pengfei , Wang Qiang , Li Wei 
Published: October 2024

AbstractNon-small cell lung cancer (NSCLC) is a prevalent and fatal malignancy with a significant global impact. Recent advancements have introduced targeted therapies like tyrosine kinase inhibitors (TKIs) such as osimertinib, which have improved patient outcomes, particularly in those with EGFR mutations. Despite these advancements, acquired resistance to TKIs remains a significant challenge. Hence, one of the current research priorities is understanding the resistance mechanisms and identifying new therapeutic targets to improve therapeutic efficacy. Herein, we identified high expression of c-Met in osimertinib-resistant NSCLC cells, and depletion of c-Met significantly inhibited the proliferation of osimertinib-resistant cells and prolonged survival in mice, suggesting c-Met as an attractive therapeutic target. To identify effective anti-tumor agents targeting c-Met, we screened a compound library containing 641 natural products and found that only xanthohumol exhibited potent inhibitory effects against osimertinib-resistant NSCLC cells. Moreover, combination treatment with xanthohumol and osimertinib sensitized osimertinib-resistant NSCLC cells to osimertinib both in vitro and in vivo. Mechanistically, xanthohumol disrupted the interaction between USP9X and Ets-1, and inhibited the phosphorylation of Ets-1 at Thr38, promoting its degradation, thereby targeting the Ets-1/c-Met signaling axis and inducing intrinsic apoptosis in osimertinib-resistant NSCLC cells. Overall, the research highlights the critical role of targeting c-Met to address osimertinib resistance in NSCLC. By demonstrating the efficacy of xanthohumol in overcoming resistance and enhancing therapeutic outcomes, this study provides valuable insights and potential new strategies for improving the clinical management of NSCLC.
Extended magenta aurora as revealed by citizen science
Authors: Kataoka Ryuho , Reddy Sachin Alexander , Nakano Shinya , Pettit Joshua , Nakamura Yuki 
Published: October 2024

AbstractDuring large geomagnetic storms, red auroras are typically observed from low-latitude countries such as Japan. The color arises from a specific emission line of oxygen atoms at high altitudes. However, during the May 10-11th 2024 superstorm, magenta auroras were observed above Japan instead of the typical red. In this study, we demonstrate that the magenta hue is created by a mixture of red (O) and a blue (N2+) aurora at extremely high altitudes. The blue color originates from the N2+ first negative emission band caused by both resonant scattering of the upwelling molecular ions and heavy particle precipitation during the storm. This study is primarily driven by observations from citizen scientists, and confirmed and quantified with observations from spacecraft and modeling techniques. Additionally, we show that high solar activity, terrestrial season, and the preheating of the atmosphere all contribute to the occurrence of magenta aurora. This study showcases the value and richness of citizen science, and we anticipate that such approaches will become increasingly important in the future.