bluuebunny/crossref_metadata_2025_split huggingface dataset:
Land Surface Modeling as a Tool to Explore Sustainable Irrigation Practices in Mediterranean Fruit Orchards
Authors: Dombrowski O. , Brogi C. , Hendricks Franssen H.‐J. , Pisinaras V. , Panagopoulos A. , Swenson S. , Bogena H. 
Published: July 2024

AbstractIrrigation strongly influences land‐atmosphere processes from regional to global scale. Therefore, an accurate representation of irrigation is crucial to understand these interactions and address water resources issues. While irrigation schemes are increasingly integrated into land surface models, their evaluation and further development remains challenging due to data limitations. This study assessed the representation of field‐scale irrigation using the Community Land Model version 5 (CLM5) through comparison of observed and simulated soil moisture, transpiration and crop yield. Irrigation was simulated by (a) adjusting the current irrigation routine and (b) by implementing a novel irrigation data stream that allows to directly use observed irrigation amounts and schedules. In a following step, the effect of different irrigation scenarios at the regional scale was simulated by using this novel data stream. At the plot scale, the novel irrigation data stream performed better in representing observed SM dynamics compared to the current irrigation routine. Nonetheless, simplifications in crop and irrigation representation and uncertainty in the relation between water stress and yield currently limit the ability of CLM5 for field‐scale irrigation scheduling. Still, the simulations revealed valuable insights into model performance that can inform and improve the modeling beyond the field scale. At regional scale, the simulations identified irrigation priorities and potential water savings. Furthermore, application of LSMs such as CLM5 can help to study the effects of irrigation beyond water availability, for example, on energy fluxes and climate, thus providing a powerful tool to assess the broader implications of irrigation at larger scale.
Quartz Dissolution Effects on Flow Channelization and Transport Behavior in Three‐Dimensional Fracture Networks
Authors: Hyman Jeffrey D. , Navarre‐Sitchler Alexis , Sweeney Matthew R. , Pachalieva Aleksandra , Carey James W. , Viswanathan Hari S. 
Published: July 2024

AbstractWe perform a set of reactive transport simulations in three‐dimensional fracture networks to characterize the impact of geochemical reactions on flow channelization. Flow channelization, a frequently observed phenomenon in porous and fractured subsurface rock formations, results from the spatially variable hydraulic resistance offered by a geological structure. In addition to geo‐structural features such as network connectivity, geometry, and hydraulic resistance, geochemical reactions, for example, dissolution and precipitation, can dynamically inhibit or enhance flow channelization. These geochemical processes can change the fracture permeability leading to increased flow channelization, which are localized connected regions of high volumetric flow rates that are seemingly ubiquitous in the subsurface. In our simulations, fractures partially filled with quartz are gradually dissolved until quasi‐steady state conditions are obtained. We compare the flow field's initial unreacted and final dissolved states in terms of flow and transport observations. We observe that the dissolved fracture networks provide less resistance to flow and exhibit increased flow channelization when compared to their unreacted counterparts. However, there is substantial variability in the magnitude of these changes which implies that the channelization strongly depends on the network structure. In turn, we identify the interplay between the particular network structure and the impact of geochemical dissolution on flow channelization. The presented results indicate that geological systems that have been weathering or reactive for longer times in older landscapes are likely to have increased flow channelization compared to their equivalent but younger counterparts, which implies a time dependence on flow channelization in fractured media.
Southwest Pacific Ocean Warming Driven by Circulation Changes
Authors: Sutton P. J. H. , Rickard G. J. , Roemmich D. H. 
Published: July 2024

AbstractAn area of ocean centered on 179°E, 46°S has warmed to full depth since 2006, with surface warming around 5 times the global rate. This Subtropical Front area is associated with a confluence of warm, salty, subtropical water from the north carried in a western boundary current and cold, fresh, subantarctic water from the south carried in the northernmost branch of the Antarctic Circumpolar Current. Temperature and salinity changes observed from Argo floats indicate that the Subtropical Frontal Zone has moved west ∼120 km, creating this area of strong warming analogous to changes in extension regions of other western boundary currents. The warming is a result of changes in the local flows of subantarctic water, evident in satellite altimeter data and 1,000 m Argo trajectories, which in turn likely result from changes in meridional ocean heat content and winds. The warming has placed this biologically‐significant region in almost perpetual marine heatwave conditions.
Unexpected Global Structure of Quasi‐4‐Day Wave With Westward Zonal Wavenumber 2 During the February 2023 Unusual Major Sudden Stratospheric Warming With Elevated Stratopause
Authors: Qin Yusong , Gu Sheng‐Yang , Dou Xiankang , Wei Yafei 
Published: July 2024

AbstractDuring February 2023, the quasi‐4‐day wave (Q4DW) with westward zonal wavenumber 2 (W2) reached its largest amplitude of ∼400 m in the Southern Hemisphere (SH) geopotential height observations since 2004, which occurred simultaneously with an Arctic major sudden stratospheric warming (SSW) with an elevated stratopause (ES). However, the Q4DW‐W2 perturbations in the Northern Hemisphere (NH) were unexpectedly suppressed despite the unstable Arctic stratosphere and mesosphere during the 2023 ES‐SSW. Diagnostic analysis shows that the westward winds at ∼54°N–70°N in the upper stratosphere of ∼‐79 m/s during the 2023 ES‐SSW were the strongest during boreal winters over the past two decades, which benefited from the onset of a preceding minor SSW at the end of January. The strongest westward wind generated a wave geometry configuration of full reflection for Q4DW‐W2 in the NH, while the Q4DW‐W2 enhancement in the SH was induced by the in‐situ amplification of the surviving seeding perturbations.
Antarctic Bottom Water Warming, Freshening, and Contraction in the Eastern Bellingshausen Basin
Authors: Johnson Gregory C. , Mahmud A. K. M. Sadman , Macdonald Alison M. , Twining Benjamin S. 
Published: July 2024

AbstractAntarctic Bottom Water has been warming in recent decades throughout most of the oceans and freshening in regions close to its Indian and Pacific sector sources. We assess warming rates on isobars in the eastern Pacific sector of the Southern Ocean using CTD data collected from shipboard surveys from the early 1990s through the late 2010s together with CTD data collected from Deep Argo floats deployed in the region in January 2023. We show cooling and freshening in the temperature‐salinity relation for water colder than ∼0.4°C. We further find a recent acceleration in the regional bottom water warming rate vertically averaged for pressures exceeding 3,700 dbar, with the 2017/18 to 2023/24 trend of 7.5 (±0.9) m°C yr−1 nearly triple the 1992/95 to 2023/24 trend of 2.8 (±0.2) m°C yr−1. The 0.2°C isotherm descent rate for these same time periods nearly quadruples from 7.8 to 28 m yr−1.
SHARP Shock Database
Authors: Ganushkina N. Y. , van de Kamp M. , Hoppe T. , Dubyagin S. , Gedalin M. , Dimmock A. , Lalti A. , Khotyaintsev Y. V. , Graham D. B. , Vink J. , Russell C. T. 
Published: July 2024

AbstractDespite more than half a century of Collisionless shock (CS) research, our understanding of the processes of the shock energy dissipation into the charge particle heating and acceleration remains incomplete. To help to address the problem of the rate of the data analysis on CSs being well below of the rate of the data acquisition, an open‐source high‐level database of shocks and a centralized source of advanced tools for the purpose of analyzing shock structure and dynamics have been developed. The database is called SHARP shock database by the name of the project SHARP (Shocks: structure, AcceleRation, dissiPation) funded by the European Union's Horizon 2020 program. The SHARP shock database contains shock crossings and corresponding parameters obtained from Cluster and MMS (Magnetospheric Multiscale) missions for terrestrial bow shocks, THEMIS (Time History of Events and Macroscale Interactions during Substorms)/ARTEMIS (Acceleration, Reconnection, Turbulence and Electrodynamics of the Moon's Interaction with the Sun) missions for interplanetary shocks, and MAVEN (Mars Atmosphere and Volatile EvolutioN) and VEX (Venus Express) missions for shocks at non‐magnetized planets. The SHARP shock database can be accessed via https://sharp.fmi.fi/shock‐database/.
Seasonal Carbon Dioxide Concentrations and Fluxes Throughout Denmark's Stream Network
Authors: Martinsen Kenneth Thorø , Sand‐Jensen Kaj , Bergmann Victor , Skjærlund Tobias , Kjær Johan Emil , Koch Julian 
Published: July 2024

AbstractStreams are important freshwater habitats in large‐scale carbon budgets because of their high CO2 fluxes which are driven by high CO2 concentrations and surface‐water turbulence. High CO2 concentrations are promoted by terrestrial carbon inputs, groundwater flow, and internal respiration, all of which vary greatly across space and time. We used environmental monitoring data to calculate CO2 concentrations along with a wide range of predictor variables including outputs from a national hydrological model and trained machine learning models to predict spatially distributed seasonal CO2 concentrations in Danish streams. We found that streams were supersaturated in dissolved CO2 (mean = 118 μM) and higher during autumn and winter than during spring and summer. The best model, a Random Forest model, scored R2 = 0.46, MAE = 46.0 μM, and ⍴ = 0.72 on a test set. The most important predictor variables were catchment slope, seasonality, height above nearest drainage, and depth to groundwater, highlighting the importance of landscape morphometry and soil‐groundwater‐stream connectivity. Stream CO2 fluxes determined from the predicted concentrations and gas transfer velocities estimated using empirical relationships averaged 253 mmol m−2 d−1, and the annual emissions were 513 Gg CO2 from the national stream network (area = 139 km2). Our analysis presents a framework for modeling seasonal CO2 concentrations and estimating fluxes at a national scale by means of large‐scale hydrological model outputs. Future efforts should consider further improving the temporal resolution, direct measurements of fluxes and gas transfer velocities, and seasonal variation in stream surface area.
PARP inhibition with rucaparib alone followed by combination with atezolizumab: Phase Ib COUPLET clinical study in advanced gynaecological and triple-negative breast cancers
Authors: Kristeleit Rebecca , Leary Alexandra , Oaknin Ana , Redondo Andres , George Angela , Chui Stephen , Seiller Aicha , Liste-Hermoso Mario , Willis Jenna , Shemesh Colby S. , Xiao Jim , Lin Kevin K. , Molinero Luciana , Guan Yinghui , Ray-Coquard Isabelle , Mileshkin Linda 
Published: July 2024

Abstract
Background
Combining PARP inhibitors (PARPis) with immune checkpoint inhibitors may improve clinical outcomes in selected cancers. We evaluated rucaparib and atezolizumab in advanced gynaecological or triple-negative breast cancer (TNBC).

Methods
After identifying the recommended dose, patients with PARPi-naive BRCA-mutated or homologous recombination-deficient/loss-of-heterozygosity-high platinum-sensitive ovarian cancer or TNBC received rucaparib plus atezolizumab. Tumour biopsies were collected pre-treatment, during single-agent rucaparib run-in, and after starting combination therapy.

Results
The most common adverse events with rucaparib 600 mg twice daily and atezolizumab 1200 mg on Day 1 every 3 weeks were gastrointestinal effects, fatigue, liver enzyme elevations, and anaemia. Responding patients typically had BRCA-mutated tumours and higher pre-treatment tumour levels of PD-L1 and CD8 + T cells. Markers of DNA damage repair decreased during rucaparib run-in and combination treatment in responders, but typically increased in non-responders. Apoptosis signature expression showed the reverse. CD8 + T-cell activity and STING pathway activation increased during rucaparib run-in, increasing further with atezolizumab.

Conclusions
In this small study, rucaparib plus atezolizumab demonstrated acceptable safety and activity in BRCA-mutated tumours. Increasing anti-tumour immunity and inflammation might be a key mechanism of action for clinical benefit from the combination, potentially guiding more targeted development of such regimens.

Clinical trial registration
ClinicalTrials.gov (NCT03101280).
The effect of four loading intravitreal aflibercept injections on macular fluid in treatment-naïve neovascular age-related macular degeneration
Authors: Chandra Shruti , Raimondi Raffaele , Lim Alicia , Mohan Amy , Melmane Sneha , Menon Geeta , Chandran Manju , Sivaprasad Sobha , Burton Benjamin J. L. , Kotagiri Ajay 
Published: July 2024

Abstract
Purpose
To evaluate the effect of four versus three loading aflibercept injections on macular fluid resolution and visual acuity (VA) in exudative neovascular AMD (nAMD).

Methods
Multicentre, retrospective cohort study of treatment naïve nAMD eyes undergoing 3 versus 4 loading doses of aflibercept. Change in VA and fluid resolution on optical coherence tomography (OCT), were evaluated at 8 weeks post loading. The primary outcome was proportion of patients with no intraretinal (IRF) and/or subretinal (SRF) fluid at central 1 mm and whole macula at 8 weeks after loading. Data were summarised with mean ± SD for continuous variables, and n (%) for categorical variables.

Results
Data from 995 patients was analysed (355 patients − 4 loading doses and 640–3 loading doses). At 8 weeks post 4 loading doses proportion of eyes with neither IRF nor SRF, no IRF and no SRF were 62.8%, 88.7% and 79.2% at fovea versus 56.1%, 87.9% and 69.9% in the whole macula, respectively. Fluid resolution at both fovea and macula were significantly higher in eyes with 4 loading injections versus 3 (p = 0.0001). The mean VA change was +4.0 (±11.3) and +5.4(±13.3) letters for 3 and 4 loading doses groups (p = 0.09).

Conclusion
Four loading dose injections of aflibercept results in higher proportion of eyes with total fluid resolution in the central subfield and total macular scan when compared to those receiving 3 loading dose injections at 8 weeks post loading phase. However, the better drying effect of 4th loading dose does not translate into better short-term VA outcomes.
Human navigation strategies and their errors result from dynamic interactions of spatial uncertainties
Authors: Kessler Fabian , Frankenstein Julia , Rothkopf Constantin A. 
Published: July 2024

AbstractGoal-directed navigation requires continuously integrating uncertain self-motion and landmark cues into an internal sense of location and direction, concurrently planning future paths, and sequentially executing motor actions. Here, we provide a unified account of these processes with a computational model of probabilistic path planning in the framework of optimal feedback control under uncertainty. This model gives rise to diverse human navigational strategies previously believed to be distinct behaviors and predicts quantitatively both the errors and the variability of navigation across numerous experiments. This furthermore explains how sequential egocentric landmark observations form an uncertain allocentric cognitive map, how this internal map is used both in route planning and during execution of movements, and reconciles seemingly contradictory results about cue-integration behavior in navigation. Taken together, the present work provides a parsimonious explanation of how patterns of human goal-directed navigation behavior arise from the continuous and dynamic interactions of spatial uncertainties in perception, cognition, and action.
An in-situ peptide-antibody self-assembly to block CD47 and CD24 signaling enhances macrophage-mediated phagocytosis and anti-tumor immune responses
Authors: Zhang Weiqi , Zeng Yinghua , Xiao Qiuqun , Wu Yuanyuan , Liu Jiale , Wang Haocheng , Luo Yuting , Zhan Jie , Liao Ning , Cai Yanbin 
Published: July 2024

AbstractTargeted immunomodulation for reactivating innate cells, especially macrophages, holds great promise to complement current adaptive immunotherapy. Nevertheless, there is still a lack of high-performance therapeutics for blocking macrophage phagocytosis checkpoint inhibitors in solid tumors. Herein, a peptide-antibody combo-supramolecular in situ assembled CD47 and CD24 bi-target inhibitor (PAC-SABI) is described, which undergoes biomimetic surface propagation on cancer cell membranes through ligand-receptor binding and enzyme-triggered reactions. By simultaneously blocking CD47 and CD24 signaling, PAC-SABI enhances the phagocytic ability of macrophages in vitro and in vivo, promoting anti-tumor responses in breast and pancreatic cancer mouse models. Moreover, building on the foundation of PAC-SABI-induced macrophage repolarization and increased CD8+ T cell tumor infiltration, sequential anti-PD-1 therapy further suppresses 4T1 tumor progression, prolonging survival rate. The in vivo construction of PAC-SABI-based nano-architectonics provides an efficient platform for bridging innate and adaptive immunity to maximize therapeutic potency.
Chemically tailored block copolymers for highly reliable sub-10-nm patterns by directed self-assembly
Authors: Maekawa Shinsuke , Seshimo Takehiro , Dazai Takahiro , Sato Kazufumi , Hatakeyama-Sato Kan , Nabae Yuta , Hayakawa Teruaki 
Published: July 2024

AbstractWhile block copolymer (BCP) lithography is theoretically capable of printing features smaller than 10 nm, developing practical BCPs for this purpose remains challenging. Herein, we report the creation of a chemically tailored, highly reliable, and practically applicable block copolymer and sub-10-nm line patterns by directed self-assembly. Polystyrene-block-[poly(glycidyl methacrylate)-random-poly(methyl methacrylate)] (PS-b-(PGMA-r-PMMA) or PS-b-PGM), which is based on PS-b-PMMA with an appropriate amount of introduced PGMA (10–33 mol%) is quantitatively post-functionalized with thiols. The use of 2,2,2-trifluoroethanethiol leads to polymers (PS-b-PGFMs) with Flory–Huggins interaction parameters (χ) that are 3.5–4.6-times higher than that of PS-b-PMMA and well-defined higher-order structures with domain spacings of less than 20 nm. This study leads to the smallest perpendicular lamellar domain size of 12.3 nm. Furthermore, thin-film lamellar domain alignment and vertical orientation are highly reliably and reproducibly obtained by directed self-assembly to yield line patterns that correspond to a 7.6 nm half-pitch size.
Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response
Authors: Coulton Alexander , Murai Jun , Qian Danwen , Thakkar Krupa , Lewis Claire E. , Litchfield Kevin 
Published: July 2024

AbstractThe paradigm for macrophage characterization has evolved from the simple M1/M2 dichotomy to a more complex model that encompasses the broad spectrum of macrophage phenotypic diversity, due to differences in ontogeny and/or local stimuli. We currently lack an in-depth pan-cancer single cell RNA-seq (scRNAseq) atlas of tumour-associated macrophages (TAMs) that fully captures this complexity. In addition, an increased understanding of macrophage diversity could help to explain the variable responses of cancer patients to immunotherapy. Our atlas includes well established macrophage subsets as well as a number of additional ones. We associate macrophage composition with tumour phenotype and show macrophage subsets can vary between primary and metastatic tumours growing in sites like the liver. We also examine macrophage-T cell functional cross talk and identify two subsets of TAMs associated with T cell activation. Analysis of TAM signatures in a large cohort of immune checkpoint inhibitor-treated patients (CPI1000 + ) identify multiple TAM subsets associated with response, including the presence of a subset of TAMs that upregulate collagen-related genes. Finally, we demonstrate the utility of our data as a resource and reference atlas for mapping of novel macrophage datasets using projection. Overall, these advances represent an important step in both macrophage classification and overcoming resistance to immunotherapies in cancer.
Using real-time modelling to inform the 2017 Ebola outbreak response in DR Congo
Authors: Thompson R. , Hart W. , Keita M. , Fall I. , Gueye A. , Chamla D. , Mossoko M. , Ahuka-Mundeke S. , Nsio-Mbeta J. , Jombart T. , Polonsky J. 
Published: July 2024

AbstractImportant policy questions during infections disease outbreaks include: i) How effective are particular interventions?; ii) When can resource-intensive interventions be removed? We used mathematical modelling to address these questions during the 2017 Ebola outbreak in Likati Health Zone, Democratic Republic of the Congo (DRC). Eight cases occurred before 15 May 2017, when the Ebola Response Team (ERT; co-ordinated by the World Health Organisation and DRC Ministry of Health) was deployed to reduce transmission. We used a branching process model to estimate that, pre-ERT arrival, the reproduction number was$$R=1.49$$R=1.49(95% credible interval$$({{{{\mathrm{0.67,2.81}}}}})$$(0.67, 2.81)). The risk of further cases occurring without the ERT was estimated to be 0.97 (97%). However, no cases materialised, suggesting that the ERT’s measures were effective. We also estimated the risk of withdrawing the ERT in real-time. By the actual ERT withdrawal date (2 July 2017), the risk of future cases without the ERT was only 0.01, indicating that the ERT withdrawal decision was safe. We evaluated the sensitivity of our results to the estimated$$R$$Rvalue and considered different criteria for determining the ERT withdrawal date. This research provides an extensible modelling framework that can be used to guide decisions about when to relax interventions during future outbreaks.
Water quality management could halve future water scarcity cost-effectively in the Pearl River Basin
Authors: Baccour Safa , Goelema Gerwin , Kahil Taher , Albiac Jose , van Vliet Michelle T. H. , Zhu Xueqin , Strokal Maryna 
Published: July 2024

AbstractReducing water scarcity requires both mitigation of the increasing water pollution and adaptation to the changing availability and demand of water resources under global change. However, state-of-the-art water scarcity modeling efforts often ignore water quality and associated biogeochemical processes in the design of water scarcity reduction measures. Here, we identify cost-effective options for reducing future water scarcity by accounting for water quantity and quality in the highly water stressed and polluted Pearl River Basin in China under various socio-economic and climatic change scenarios based on the Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs). Our modeling approach integrates a nutrient model (MARINA-Nutrients) with a cost-optimization procedure, considering biogeochemistry and human activities on land in a spatially explicit way. Results indicate that future water scarcity is expected to increase by a factor of four in most parts of the Pearl River Basin by 2050 under the RCP8.5-SSP5 scenario. Results also show that water quality management options could half future water scarcity in a cost-effective way. Our analysis could serve as an example of water scarcity assessment for other highly water stressed and polluted river basins around the world and inform the design of cost-effective measures to reduce water scarcity.