bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Groundwater Storage Change in the Great Artesian Basin Using GRACE and Groundwater Budgets
Authors: Castellazzi P. , Ransley T. , McPherson A. , Slatter E. , Frost A. , Shokri A. , Wallace L. , Crosbie R. , Janardhanan S. , Kilgour P. , Raiber M. , Vizy J. , Rollet N. 
Published: November 2024

AbstractLarge, confined aquifer systems play a vital role in sustaining human settlements and industries in many regions. Understanding the sustainability of these water resources requires the evaluation of groundwater storage change. Direct in‐situ observation of groundwater storage is limited by the distribution and availability of groundwater level and aquifer storativity data. Here, we use and compare two auxiliary methods, applied at basin and sub‐basin scales, to assess groundwater storage changes in the Great Artesian Basin (GAB), one of the World's largest confined aquifer systems. The first, the groundwater budget, derives storage change as the residual of fluxes in and out of the GAB, assuming they are all accounted for and accurately estimated. The second uses time‐variable gravity data from GRACE satellites to estimate temporal changes in groundwater mass, assuming that all other components of the terrestrial water mass change detected by GRACE are correctly subtracted. Despite the depletion observed during the 20th century, groundwater storage is mostly stable during 2002–2022. An increase in storage is detected in the Surat sub‐basin, a major recharge area. This increase is attributed to an over‐representation of large recharge events during the study period and/or storage recovery following rehabilitation of free‐flowing bores. The approach consisting in disaggregating GRACE data assumes that water storage changes in confined aquifers is dominated by changes in the GAB, and as such, it may overestimate the increase in the GAB by incorrectly attributing the increase occurring in overlying aquifers to the GAB. In contrast, the recharge estimates used in the groundwater budgets do not account for flood recharge and might underestimate storage increase in the GAB.
Estimation of Terrestrial Water Storage Changes in Brazil From the Joint Inversion of GRACE‐Based Geopotential Difference and GNSS Vertical Displacement Data
Authors: Zhong Bo , Li Xianpao , Chen Jianli , Li Jiancheng , Xu Hongyi 
Published: November 2024

AbstractGravity Recovery and Climate Experiment (GRACE) satellite gravimetry and Global Navigation Satellite System (GNSS) surface displacement measurements offer complementary advantages for monitoring terrestrial water storage (TWS) changes. We propose a new joint inversion model based on the combination of GRACE‐based geopotential difference (GPD) observations using the mascon method and GNSS vertical displacements through the Green's function method to obtain reliable TWS changes in Brazil. The performance of the jointly inverted TWS changes is assessed through closed‐loop simulations and comparisons with hydrometeorological data (precipitation‐P, evapotranspiration‐ET, and runoff‐R) using water budget closure (P‐ET‐R) and river water level observations from satellite altimetry. The simulation results indicate that the joint inversion results exhibit higher accuracy and reliability than GRACE GPD‐based mascon (GPD‐mascon) and GNSS solutions, and the standard deviations (STDs) of joint results decrease by ∼6.98 and ∼37.5 mm compared to those from GPD‐mascon and GNSS solutions. The joint inversion of real GRACE and GNSS data demonstrates notably lower uncertainty than that of GPD‐mascon solutions and exhibits significant improvement than GNSS‐only solutions. The STDs and correlation coefficients between monthly R time series derived from three inversion methods (joint inversion, GPD‐mascon and GNSS solutions, combined with P and ET through water budget closure) and in situ observations are 19.607 mm and 0.912, 20.879 mm and 0.904, and 31.370 mm and 0.778, respectively. The joint estimates also yield better correlation with river water level observations compared to GPD‐mascon and GNSS solutions. Furthermore, at the weekly time scale, the joint inversion results show better consistency with P‐ET‐R data than those from GPD‐mascon and GNSS solutions.
Mechanistic Simulation of Salt‐Affected Soil‐Plant‐Atmosphere Continuum Dynamics in Seasonally Frozen Regions
Authors: Xun Yihao , Xu Xu , Kurylyk Barret , Li Xinhu , Mu Danning , Huang Guanhua 
Published: November 2024

AbstractThe salt‐affected Soil‐Plant‐Atmosphere Continuum (SPAC) is a dynamic, interactive system that is particularly complex in seasonally frozen regions where salt transport, precipitation‐dissolution, and soil freeze‐thaw processes play crucial, interrelated roles. Understanding these coupled processes and representing them with mathematical models is critical for effective management of SPAC systems. This study presents a new mechanistic approach and an improved model that integrates a chemical equilibrium module within a mechanistic‐based transport computational module (modified SHAW model). The chemical equilibrium module determines salt precipitation‐dissolution using thermodynamic theory and explains the effects of efflorescence and subflorescence on system dynamics. The model enables simultaneous solutions for heat, water, and salt transport with chemical equilibrium throughout non‐freezing and freezing seasons, as well as plant growth dynamics. Assessment of the model using laboratory experiments and field studies showed good performance, with coefficient of determination values exceeding 0.65 for simulated and measured evaporation rate, leaf area index, soil water content, salt content, and temperature. Furthermore, a comparison between simulation results considering and neglecting the impact of salt precipitation‐dissolution highlights potential inaccuracies in soil heat‐water‐salt dynamics and plant water use resulting from the omission of this process in mechanistic models.
Multi-omics reveal immune microenvironment alterations in multiple myeloma and its precursor stages
Authors: Cheng Yan , Sun Fumou , Alapat Daisy V. , Wanchai Visanu , Mery David , Siegel Eric R. , Xu Hongwei , Johnson Sarah , Guo Wancheng , Bailey Clyde , Ashby Cody , Bauer Michael Anton , Hadidi Samer Al , Schinke Carolina , Thanendrarajan Sharmilan , Zangari Maurizio , van Rhee Frits , Tricot Guido , Shaughnessy John D. , Zhan Fenghuang 
Published: November 2024

AbstractTumor immune microenvironmental alterations occur early in multiple myeloma (MM) development. In this study, we aim to systematically characterize the tumor immune microenvironment (TME) and the tumor-immune interactions from precursor stages, i.e., monoclonal gammopathy of undetermined significance (MGUS) and smoldering MM (SMM), to newly diagnosed MM, comparing these to healthy donors. Using CIBERSORT, mass cytometry (CyTOF), and single-cell RNA sequencing (scRNA-Seq), we examined innate and adaptive immune changes across these stages. We found a decrease in granulocytes in the TME predicts MM outcomes. HLA-DR is reduced in CD16+ monocytes and plasmacytoid dendritic cells, while myeloid dendritic cells show decreased expression of stress and immune-response genes. NK cells and CD8+ T cells shift from a GZMK+ to a GZMB+ cytotoxic phenotype in the TME, with increased inhibitory markers TIM3 and TIGIT. In paired samples, the proportion and gene expression pattern in patient-specific GZMB+CD8+ T cells remain largely unchanged despite MM progression. Our findings provide a comprehensive immune landscape of MM and its precursors, offering insights into therapeutic strategies. Enhancing neutrophil and NK cell cytotoxicity, tumor antigen presentation, and CD8+ T cell versatility in precursor stages may prevent MM progression.
Cardiotoxicity following thoracic radiotherapy for lung cancer
Authors: Walls Gerard M. , Bergom Carmen , Mitchell Joshua D. , Rentschler Stacey L. , Hugo Geoffrey D. , Samson Pamela P. , Robinson Clifford G. 
Published: November 2024

Abstract
Radiotherapy is the standard of care treatment for unresectable NSCLC, combined with concurrent chemotherapy and adjuvant immunotherapy. Despite technological advances in radiotherapy planning and delivery, the risk of damage to surrounding thoracic tissues remains high. Cardiac problems, including arrhythmia, heart failure and ischaemic events, occur in 20% of patients with lung cancer who undergo radiotherapy. As survival rates improve incrementally for this cohort, minimising the cardiovascular morbidity of RT is increasingly important. Problematically, the reporting of cardiac endpoints has been poor in thoracic radiotherapy clinical trials, and retrospective studies have been limited by the lack of standardisation of nomenclature and endpoints. How baseline cardiovascular profile and cardiac substructure radiation dose distribution impact the risk of cardiotoxicity is incompletely understood. As Thoracic Oncology departments seek to expand the indications for radiotherapy, and as the patient cohort becomes older and more comorbid, there is a pressing need for cardiotoxicity to be comprehensively characterised with sophisticated oncology, physics and cardio-oncology evaluations. This review synthesises the evidence base for cardiotoxicity in conventional radiotherapy, focusing on lung cancer, including current data, unmet clinical needs, and future scientific directions.
Scaling whole-chip QAOA for higher-order ising spin glass models on heavy-hex graphs
Authors: Pelofske Elijah , Bärtschi Andreas , Cincio Lukasz , Golden John , Eidenbenz Stephan 
Published: November 2024

AbstractWe show that the quantum approximate optimization algorithm (QAOA) for higher-order, random coefficient, heavy-hex compatible spin glass Ising models has strong parameter concentration across problem sizes from 16 up to 127 qubits for p = 1 up to p = 5, which allows for computationally efficient parameter transfer of QAOA angles. Matrix product state (MPS) simulation is used to compute noise-free QAOA performance. Hardware-compatible short-depth QAOA circuits are executed on ensembles of 100 higher-order Ising models on noisy IBM quantum superconducting processors with 16, 27, and 127 qubits using QAOA angles learned from a single 16-qubit instance using the JuliQAOA tool. We show that the best quantum processors find lower energy solutions up to p = 2 or p = 3, and find mean energies that are about a factor of two off from the noise-free distribution. We show that p = 1 QAOA energy landscapes remain very similar as the problem size increases using NISQ hardware gridsearches with up to a 414 qubit processor.
A cellular basis for mapping behavioural structure
Authors: El-Gaby Mohamady , Harris Adam Loyd , Whittington James C. R. , Dorrell William , Bhomick Arya , Walton Mark E. , Akam Thomas , Behrens Timothy E. J. 
Published: November 2024

AbstractTo flexibly adapt to new situations, our brains must understand the regularities in the world, as well as those in our own patterns of behaviour. A wealth of findings is beginning to reveal the algorithms that we use to map the outside world1–6. However, the biological algorithms that map the complex structured behaviours that we compose to reach our goals remain unknown. Here we reveal a neuronal implementation of an algorithm for mapping abstract behavioural structure and transferring it to new scenarios. We trained mice on many tasks that shared a common structure (organizing a sequence of goals) but differed in the specific goal locations. The mice discovered the underlying task structure, enabling zero-shot inferences on the first trial of new tasks. The activity of most neurons in the medial frontal cortex tiled progress to goal, akin to how place cells map physical space. These ‘goal-progress cells’ generalized, stretching and compressing their tiling to accommodate different goal distances. By contrast, progress along the overall sequence of goals was not encoded explicitly. Instead, a subset of goal-progress cells was further tuned such that individual neurons fired with a fixed task lag from a particular behavioural step. Together, these cells acted as task-structured memory buffers, implementing an algorithm that instantaneously encoded the entire sequence of future behavioural steps, and whose dynamics automatically computed the appropriate action at each step. These dynamics mirrored the abstract task structure both on-task and during offline sleep. Our findings suggest that schemata of complex behavioural structures can be generated by sculpting progress-to-goal tuning into task-structured buffers of individual behavioural steps.
Central pattern generator control of a vertebrate ultradian sleep rhythm
Authors: Fenk Lorenz A. , Riquelme Juan Luis , Laurent Gilles 
Published: November 2024

AbstractThe mechanisms underlying the mammalian ultradian sleep rhythm—the alternation of rapid-eye-movement (REM) and slow-wave (SW) states—are not well understood but probably depend, at least in part, on circuits in the brainstem1–6. Here, we use perturbation experiments to probe this ultradian rhythm in sleeping lizards (Pogona vitticeps)7–9 and test the hypothesis that it originates in a central pattern generator10,11—circuits that are typically susceptible to phase-dependent reset and entrainment by external stimuli12. Using light pulses, we find that Pogona’s ultradian rhythm8 can be reset in a phase-dependent manner, with a critical transition from phase delay to phase advance in the middle of SW. The ultradian rhythm frequency can be decreased or increased, within limits, by entrainment with light pulses. During entrainment, Pogona REM (REMP) can be shortened but not lengthened, whereas SW can be dilated more flexibly. In awake animals, a few alternating light/dark epochs matching natural REMP and SW durations entrain a sleep-like brain rhythm, suggesting the transient activation of an ultradian rhythm generator. In sleeping animals, a light pulse delivered to a single eye causes an immediate ultradian rhythm reset, but only of the contralateral hemisphere; both sides resynchronize spontaneously, indicating that sleep is controlled by paired rhythm-generating circuits linked by functional excitation. Our results indicate that central pattern generators of a type usually known to control motor rhythms may also organize the ultradian sleep rhythm in a vertebrate.
Evaluation of uranium migration during the maturation of hydrocarbon source rocks
Authors: Wang Junxian , Li Ziying , He Feng , Bai Fengtian , Qiu Linfei , Guo Jian , Zhang Chuang 
Published: November 2024

AbstractThe source of uranium is an important research topic related to the exploration of sandstone-type uranium deposits, and potential uranium sources in deep basins are often overlooked. Black organic-rich shale is a common uranium-bearing rock in deep sedimentary basins. However, relatively few studies have investigated the migration of uranium during hydrocarbon generation in and release from uranium-rich shale. In this study, the uranium-rich shale in the Chang 7 member of the Yanchang Formation of the Upper Triassic in the Ordos Basin was selected to investigate the migration of uranium and other trace elements during the thermal maturation of uranium-rich shale via a semiopen pyrolysis simulation system. The gas and liquid products as well as the solid residue were thoroughly analysed by means of multiple instruments. The results showed that uranium significantly migrated before hydrocarbon generation (Ro < 0.61%), with a leaching rate between 12.1% and 18.8%. The leaching rate of uranium during the hydrocarbon generation stage (0.63% < Ro < 1.35%) was relatively low, ranging from 0 to 7.2%. Cu, Pb, Zn, Mo, and other trace elements also migrated considerably during the early stage of thermal evolution, with leaching rates ranging from 2.9 ~ 11.6%. The yield of low-molecular-weight organic acids (LOAs) was the highest in the early stage of thermal maturity, and the LOA yield exhibited a good correlation with the leaching rates of Cu, Pb, Zn, Co, Mo, etc. The generation of LOAs from source rocks was conducive to the leaching and migration of trace elements. Moreover, according to a statistical analysis of published geochemical data, the total organic carbon (TOC) content, uranium content, and U/TOC ratio in shale decreased significantly with increasing burial depth, indicating that uranium migrated significantly upon kerogen hydrocarbon generation during thermal evolution. Therefore, uranium-rich shale is an important deep uranium source in sedimentary basins.
Synchronous photocatalytic benzimidazole formation and olefin reduction by magnetic separable visible-light-driven Pd-g-C3N4-Vanillin@γ-Fe2O3-TiO2 Nanocomposite
Authors: Jafarpour Maasoumeh , Rezaeifard Abdolreza , Pourmorteza Narges , Kudeyani Maryam Ghanbari 
Published: November 2024

AbstractA visible light-responsive magnetically separable photocatalyst Pd-g-C3N4-Vanillin@γ-Fe2O3-TiO2 is fabricated using vanillin as a natural junction under ultrasonic agitation. Structural, morphological, optical, thermal, and magnetic assessments of the as-prepared catalyst are carried out. The photocatalyst successfully drives the simultaneous benzimidazole formation, and olefin hydrogenation with high atom economy under blue LED light and mild conditions. The photocatalytic activity of Pd-g-C3N4-Vanillin@γ-Fe2O3-TiO2 is significantly affected by the γ-Fe2O3:TiO2 weight ratio. PL spectra revealed the effective separation of carriers in the fabricated catalyst promoting its photocatalytic activity. The action spectra using the apparent quantum efficiency (AQE) exhibited the maximum AQEs at 520 and 750 nm in which the highest performance for styrene hydrogenation is observed. The title magnetically separable heterogeneous photocatalyst provides high yields of products under perfectly safe visible light, produces low/zero waste, and avoids using an external high-pressure hydrogen gas source, harmful solvents, undesirable additives, and reducing agents rendering green conditions for chemical reactions.
Quantification of cavitating flows with neutron imaging
Authors: Karathanassis I. K. , Heidari-Koochi M. , Koukouvinis F. , Weiss L. , Trtik P. , Spivey D. , Wensing M. , Gavaises M. 
Published: November 2024

AbstractThe current experimental investigation demonstrates the capability of neutron imaging to quantify cavitation, in terms of vapour content, within an orifice of an abruptly constricting geometry. The morphology of different cavitation regimes setting in was properly visualised owing to the high spatial resolution of 16 μm achieved, given the extensive field of view of 12.9 × 12.9 mm2 offered by the imaging set-up. At a second step, the method was proven capable of highlighting subtle differences between fluids of different rheological properties. More specifically, a reference liquid was comparatively assessed against a counterpart additised with a Quaternary Ammonium Salt (QAS) agent, thus obtaining a viscoelastic behaviour. In accordance with previous studies, it was verified, yet in a quantifiable manner, that the presence of viscoelastic additives affects the overall cavitation topology by promoting the formation of more localised vortical cavities rather than cloud-like structures occupying a larger portion of the orifice core. To the authors’ best knowledge, the present work is the first to demonstrate that neutron imaging is suitable for quantifying in-nozzle cavitating flow at the micrometre level, consequently elucidating the distinct forms of vaporous structures that arise. The potential of incorporating neutron irradiation for the quantification of two-phase flows in metallic microfluidics devices has been established.
Exploring the limits of hierarchical world models in reinforcement learning
Authors: Schiewer Robin , Subramoney Anand , Wiskott Laurenz 
Published: November 2024

AbstractHierarchical model-based reinforcement learning (HMBRL) aims to combine the sample efficiency of model-based reinforcement learning with the abstraction capability of hierarchical reinforcement learning. While HMBRL has great potential, the structural and conceptual complexities of current approaches make it challenging to extract general principles, hindering understanding and adaptation to new use cases, and thereby impeding the overall progress of the field. In this work we describe a novel HMBRL framework and evaluate it thoroughly. We construct hierarchical world models that simulate the environment at various levels of temporal abstraction. These models are used to train a stack of agents that communicate top-down by proposing goals to their subordinate agents. A significant focus of this study is the exploration of a static and environment agnostic temporal abstraction, which allows concurrent training of models and agents throughout the hierarchy. Unlike most goal-conditioned H(MB)RL approaches, it also leads to comparatively low dimensional abstract actions. Although our HMBRL approach did not outperform traditional methods in terms of final episode returns, it successfully facilitated decision-making across two levels of abstraction. A central challenge in enhancing our method’s performance, as uncovered through comprehensive experimentation, is model exploitation on the abstract level of our world model stack. We provide an in depth examination of this issue, discussing its implications and suggesting directions for future research to overcome this challenge. By sharing these findings, we aim to contribute to the broader discourse on refining HMBRL methodologies.
Specific human gene expression in response to infection is an effective marker for diagnosis of latent and active tuberculosis
Authors: Nakiboneka Ritah , Walbaum Natasha , Musisi Emmanuel , Nevels Michael , Nyirenda Tonney , Nliwasa Marriott , Msefula Chisomo L. , Sloan Derek , Sabiiti Wilber 
Published: November 2024

AbstractRNA sequencing and microarray analysis revealed transcriptional markers expressed in whole blood can differentiate active pulmonary TB (ATB) from other respiratory diseases (ORDs), and latent TB infection (LTBI) from healthy controls (HC). Here we describe a streamlined reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay that could be applied at near point-of-care for diagnosing and distinguishing ATB from ORDs and LTBI from HC. A literature review was undertaken to identify the most plausible host-gene markers (HGM) of TB infection. Primers, and dual labelled hydrolysis probes were designed and analytically evaluated for accuracy in an in-vitro model of infection using a lung fibroblast cell-line. Best performing genes were multiplexed into panels of 2–4 targets and taken forward for clinical evaluation. Mycobacteria Growth Indicator Tube and QuantiFERON-TB Gold Plus were used as reference tests for ATB and LTBI respectively. A total of 16 HGM were selected and incorporated into five multiplex RT-qPCR panels. PCR assay efficiency of all evaluated targets was ≥ 90% with a median analytical sensitivity of 292 copies/µl [IQR: 215.0-358.3 copies/µl], and a median limit of quantification of 61.7 copies/µl [IQR: 29.4-176.3 copies/µl]. Clinically, ATB was characterised by higher gene expression than ORDs, while LTBI was associated with lower gene expression than HC, Kruskal-Wallis p < 0.0001. Crucially, BATF2, CD64, GBP5, C1QB, GBP6, DUSP3, and GAS6 exhibited high differentiative ability for ATB from ORDs, LTBI or HC while KLF2, PTPRC, NEMF, ASUN, and ZNF296 independently discriminated LTBI from HC. Our results show that different HGM maybe required for ATB and LTBI differentiation from ORDs or HC respectively and demonstrate the feasibility of host gene-based RT-qPCR to diagnose ATB and LTBI at near point-of-care.