bluuebunny/crossref_metadata_2025_split huggingface dataset:
Source, Migration Pathways, and Atmospheric Release of Geologic Methane Associated With the Complex Permafrost Regimes of the Outer Mackenzie River Delta, Northwest Territories, Canada
Authors: Dallimore Scott R. , Lapham Laura L. , Côté Michelle M. , Bowen Robert , MacLeod Roger , McIntosh Marcek Hadley A. , Wheat C. Geoff , Collett Timothy S. 
Published: June 2024

AbstractSources and fluxes of methane to the atmosphere from permafrost are significant but poorly constrained in global climate models. We present data collected from the variable permafrost setting of the outer Mackenzie River Delta, including observations of aquatic methane seepage, core determinations of in situ methane occurrence and seep gas isotope geochemistry. The sources and locations of in situ geologic methane occurrence and aquatic and atmospheric gas release appear to be controlled by the regional geology and permafrost conditions. Where permafrost is >250 m thick, thermogenic gas deposits at depth are isolated by laterally continuous, low permeability ice‐bearing sediments with few through‐going thawed taliks. Thus, the observed in situ methane and aquatic gas seepage appears to be dominated by microbial methane. In contrast, where permafrost is <80 m thick, taliks are more likely to be through‐going, providing permeable conduits from depth and migration pathways for both thermogenic and biogenic gas. Continuous annual fluid sampling of two lakes and a river channel documents aquatic methane flux from microbial sources, more deeply buried thermogenic sources, and mixtures of both. Using estimates of in situ methane concentration from deep core samples and observations of in situ free gas occurrences, we conclude that the reservoir of in situ geologic methane within ice bonded permafrost is substantial and that this methane is presently migrating with ongoing atmospheric release. It is our assessment that the permafrost setting, and processes described are sensitive to future climate change as the permafrost warms.
Forest Treatment Effects on Watershed Responses Under Warming
Authors: Cederstrom Charles J. , Vivoni Enrique R. , Mascaro Giuseppe , Svoma Bohumil 
Published: June 2024

AbstractThe effects of forest treatments on watershed hydrology have often been studied in isolation from climate change. Consequently, under a warming climate, it is unclear how forest thinning will impact snowpacks, evapotranspiration, and streamflow availability. In this study, we used a distributed hydrologic model to provide insight into the effects of warming and forest treatment on the hydrologic response of the Beaver Creek watershed (∼1,100 km2) of central Arizona. Prior to the numerical experiments, confidence in the hydrologic model performance was established by comparisons to long‐term observations (2003–2018) of snow water equivalent and streamflow using station observations and through spatially distributed estimates. Results indicated that warming during the 21st century could increase mean annual streamflow by 1.5% for warming levels up to +1°C, followed by a −29% decrease for continued warming up to +6°C, due to the varying effects of warming on snow sublimation, soil evaporation, and plant transpiration. On average, forest thinning increased streamflow by +12% (or 7 mm/yr) through lower plant transpiration by −19% (or −18 mm/yr), while also increasing the change in soil water storage by +42% (or 11 mm/yr). Forest thinning delayed the detrimental effects of warming on streamflow until +4°C, as compared to +2°C without forest treatment. Furthermore, model results suggested that forest cover reductions laterally displace water availability and evapotranspiration to downstream sites. These model‐derived mechanisms provide insights on the potential for water resilience toward warming effects afforded through treatment projects in southwestern US ponderosa pine forests.
Time‐And‐Space Averaging Applied to Intermittent Multiphase Flow Experiments
Authors: Wang Tingting , McClure James E. , Da Wang Ying , Berg Steffen , Chen Cheng , Mostaghimi Peyman , Armstrong Ryan T. 
Published: June 2024

AbstractVarious researchers have studied fluctuations in pore‐scale phase occupancy during multiphase flow in porous media using synchrotron‐based X‐ray microcomputed tomography (micro‐CT). However, the impact of these fluctuations on the concept of a representative volume is not yet fully understood. In this study, we performed spatial and temporal averaging of multiphase flow experiments visualized with synchrotron‐based micro‐CT, focusing on oil saturation as the key parameter to determine a representative time‐and‐space average. Our findings revealed that a saturation value representative of both time and space was achieved during fractional flow experiments in drainage mode with fractional flows of 0.8, 0.5, and 0.3. Furthermore, we computed a range of relative permeabilities on the basis of whether momentaneous saturation or time‐and‐space averaged saturation was utilized for direct simulation. Our results highlighted the importance of time‐and‐space averaging in determining a representative relative permeability and indicated that the temporal and spatial scales covered in a typical micro‐CT flow experiment were sufficient to obtain a representative saturation value for sandstone rock under intermittent flow conditions.
Data Assimilation Informed Model Structure Improvement (DAISI) for Robust Prediction Under Climate Change: Application to 201 Catchments in Southeastern Australia
Authors: Lerat Julien , Chiew Francis , Robertson David , Andréassian Vazken , Zheng Hongxing 
Published: June 2024

AbstractThis paper presents a method to analyze and improve the set of equations constituting a rainfall‐runoff model structure based on a combination of a data assimilation algorithm and polynomial updates to the state equations. The method, which we have called “Data Assimilation Informed model Structure Improvement” (DAISI) is generic, modular, and demonstrated with an application to the GR2M model and 201 catchments in South‐East Australia. Our results show that the updated model generated with DAISI generally performed better for all metrics considered included Kling‐Gupta Efficiency, NSE on log transform flow and flow duration curve bias. In addition, the elasticity of modeled runoff to rainfall is higher in the updated model, which suggests that the structural changes could have a significant impact on climate change simulations. Finally, the DAISI diagnostic identified a reduced number of update configurations in the GR2M structure with distinct regional patterns in three sub‐regions of the modeling domain (Western Victoria, central region, and Northern New South Wales). These configurations correspond to specific polynomials of the state variables that could be used to improve equations in a revised model. Several potential improvements of DAISI are proposed including the use of additional observed variables such as actual evapotranspiration to better constrain internal model fluxes.
Detrital Input Sustains Diatom Production off a Glaciated Arctic Coast
Authors: Ng Hong Chin , Hendry Katharine R. , Ward Rachael , Woodward E. M. S. , Leng Melanie J. , Pickering Rebecca A. , Krause Jeffrey W. 
Published: June 2024

AbstractIn the Arctic and subarctic oceans, the relatively low supply of silicon (compared to other nutrients) can make it limiting for the growth of diatoms, a fundamental building block of the oceanic food web. Glaciers release large quantities of dissolved silicon and dissolvable solid amorphous silica phases into high‐latitude estuaries (fjords), but the role of these glacially‐derived silica phases in sustaining diatom growth in the coastal and open‐water sectors remains unknown. Here we show how stable and radiogenic silicon isotopes can be used together to address this question, using southwest Greenland as a case study. This study finds enhanced levels of detrital (i.e., mineral) amorphous silica, likely glacially‐sourced, sustaining a large portion of diatom growth observed off the coast, revealing how the phytoplankton community can function during high‐meltwater periods.
Atmospheric and Ionospheric Responses to Orographic Gravity Waves Prior to the December 2022 Cold Air Outbreak
Authors: Inchin P. A. , Bhatt A. , Bramberger M. , Chakraborty S. , Debchoudhury S. , Heale C. 
Published: June 2024

AbstractMountain waves are known sources of fluctuations in the upper atmosphere. However, their effects over the Continental United States (CONUS) are considered modest as compared to hot spots such as the Southern Andes. Here, we present an observation‐guided case study examining the dynamics of gravity waves (GWs) and their impacts on the ionosphere over the CONUS prior to the cold air outbreak in December 2022, which resulted from a significant distortion of the tropospheric polar vortex. The investigation relies on MERRA‐2 and ERA5 reanalysis data sets for the climatological contextualization, analysis of GWs based on National Aeronautics and Space Administration Aqua satellite's Atmospheric Infrared Sounder, 557.7 and 630.0 nm airglow emission observations, and the measurements of ionospheric disturbances retrieved from Global Navigation Satellite System signal‐based total electron content (TEC) and Super Dual Auroral Radar Network observations. We demonstrate that the tropospheric polar jet stream shifted toward the Rocky Mountains, generated large amplitude GWs (up to 11 K of brightness temperature), which, aided by winter‐time winds over mid‐latitudes, could propagate to mesospheric heights. The breaking of GWs plausibly led to the generation of a plethora of secondary acoustic and GWs that eventually emerged as the sources of extensive ionospheric fluctuations of ∼3–30 min periods and up to 0.7 TECu, observed across the entire CONUS for several days. This case offers a valuable demonstration of the interplay between tropospheric circulation and the ionosphere over CONUS, pointing to the need for a better understanding of wave‐driven deep‐atmosphere coupled dynamics.
MAL2 reprograms lipid metabolism in intrahepatic cholangiocarcinoma via EGFR/SREBP-1 pathway based on single-cell RNA sequencing
Authors: Huang Tian , Cao Hengsong , Liu Chuan , Sun Xiaohu , Dai Shipeng , Liu Li , Wang Yuliang , Guo Cheng , Wang Xuehao , Gao Yun , Tang Weiwei , Xia Yongxiang 
Published: June 2024

AbstractIntrahepatic cholangiocarcinoma (ICC) is a highly aggressive cancer characterized by a poor prognosis and resistance to chemotherapy. In this study, utilizing scRNA-seq, we discovered that the tetra-transmembrane protein mal, T cell differentiation protein 2 (MAL2), exhibited specific enrichment in ICC cancer cells and was strongly associated with a poor prognosis. The inhibition of MAL2 effectively suppressed cell proliferation, invasion, and migration. Transcriptomics and metabolomics analyses suggested that MAL2 promoted lipid accumulation in ICC by stabilizing EGFR membrane localization and activated the PI3K/AKT/SREBP-1 axis. Molecular docking and Co-IP proved that MAL2 interacted directly with EGFR. Based on constructed ICC organoids, the downregulation of MAL2 enhanced apoptosis and sensitized ICC cells to cisplatin. Lastly, we conducted a virtual screen to identify sarizotan, a small molecule inhibitor of MAL2, and successfully validated its ability to inhibit MAL2 function. Our findings highlight the tumorigenic role of MAL2 and its involvement in cisplatin sensitivity, suggesting the potential for novel combination therapeutic strategies in ICC.
A unified framework for estimating country-specific cumulative incidence for 18 diseases stratified by polygenic risk
Authors: Jermy Bradley , Läll Kristi , Wolford Brooke N. , Wang Ying , Zguro Kristina , Cheng Yipeng , Kanai Masahiro , Kanoni Stavroula , Yang Zhiyu , Hartonen Tuomo , Monti Remo , Wanner Julian , Youssef Omar ,   Estonian Biobank research team,   FinnGen, Lippert Christoph , van Heel David , Okada Yukinori , McCartney Daniel L. , Hayward Caroline , Marioni Riccardo E. , Furini Simone , Renieri Alessandra , Martin Alicia R. , Neale Benjamin M. , Hveem Kristian , Mägi Reedik , Palotie Aarno , Heyne Henrike , Mars Nina , Ganna Andrea , Ripatti Samuli 
Published: June 2024

AbstractPolygenic scores (PGSs) offer the ability to predict genetic risk for complex diseases across the life course; a key benefit over short-term prediction models. To produce risk estimates relevant to clinical and public health decision-making, it is important to account for varying effects due to age and sex. Here, we develop a novel framework to estimate country-, age-, and sex-specific estimates of cumulative incidence stratified by PGS for 18 high-burden diseases. We integrate PGS associations from seven studies in four countries (N = 1,197,129) with disease incidences from the Global Burden of Disease. PGS has a significant sex-specific effect for asthma, hip osteoarthritis, gout, coronary heart disease and type 2 diabetes (T2D), with all but T2D exhibiting a larger effect in men. PGS has a larger effect in younger individuals for 13 diseases, with effects decreasing linearly with age. We show for breast cancer that, relative to individuals in the bottom 20% of polygenic risk, the top 5% attain an absolute risk for screening eligibility 16.3 years earlier. Our framework increases the generalizability of results from biobank studies and the accuracy of absolute risk estimates by appropriately accounting for age- and sex-specific PGS effects. Our results highlight the potential of PGS as a screening tool which may assist in the early prevention of common diseases.
Transient growth factor expression via mRNA in lipid nanoparticles promotes hepatocyte cell therapy in mice
Authors: Smith Anna R. , Rizvi Fatima , Everton Elissa , Adeagbo Anisah , Wu Susan , Tam Ying , Muramatsu Hiromi , Pardi Norbert , Weissman Drew , Gouon-Evans Valerie 
Published: June 2024

AbstractPrimary human hepatocyte (PHH) transplantation is a promising alternative to liver transplantation, whereby liver function could be restored by partial repopulation of the diseased organ with healthy cells. However, currently PHH engraftment efficiency is low and benefits are not maintained long-term. Here we refine two male mouse models of human chronic and acute liver diseases to recapitulate compromised hepatocyte proliferation observed in nearly all human liver diseases by overexpression of p21 in hepatocytes. In these clinically relevant contexts, we demonstrate that transient, yet robust expression of human hepatocyte growth factor and epidermal growth factor in the liver via nucleoside-modified mRNA in lipid nanoparticles, whose safety was validated with mRNA-based COVID-19 vaccines, drastically improves PHH engraftment, reduces disease burden, and improves overall liver function. This strategy may overcome the critical barriers to clinical translation of cell therapies with primary or stem cell-derived hepatocytes for the treatment of liver diseases.
CRIMP: a CRISPR/Cas9 insertional mutagenesis protocol and toolkit
Authors: Miles Lee B. , Calcinotto Vanessa , Oveissi Sara , Serrano Rita J. , Sonntag Carmen , Mulia Orlen , Lee Clara , Bryson-Richardson Robert J. 
Published: June 2024

AbstractSite-directed insertion is a powerful approach for generating mutant alleles, but low efficiency and the need for customisation for each target has limited its application. To overcome this, we developed a highly efficient targeted insertional mutagenesis system, CRIMP, and an associated plasmid toolkit, CRIMPkit, that disrupts native gene expression by inducing complete transcriptional termination, generating null mutant alleles without inducing genetic compensation. The protocol results in a high frequency of integration events and can generate very early targeted insertions, during the first cell division, producing embryos with expression in one or both halves of the body plan. Fluorescent readout of integration events facilitates selection of successfully mutagenized fish and, subsequently, visual identification of heterozygous and mutant animals. Together, these advances greatly improve the efficacy of generating and studying mutant lines. The CRIMPkit contains 24 ready-to-use plasmid vectors to allow easy and complete mutagenesis of any gene in any reading frame without requiring custom sequences, modification, or subcloning.
Morphology shapes community dynamics in early animal ecosystems
Authors: Stephenson Nile P. , Delahooke Katie M. , Barnes Nicole , Rideout Benjamin W. T. , Kenchington Charlotte G. , Manica Andrea , Mitchell Emily G. 
Published: June 2024

AbstractThe driving forces behind the evolution of early metazoans are not well understood, but key insights into their ecology and evolution can be gained through ecological analyses of the in situ, sessile communities of the Avalon assemblage in the Ediacaran (~565 million years ago). Community structure in the Avalon is thought to be underpinned by epifaunal tiering and ecological succession, which we investigate in this study in 18 Avalon communities. Here we found that Avalon communities form four distinctive Community Types irrespective of succession processes, which are instead based on the dominance of morphologically distinct taxa, and that tiering is prevalent in three of these Community Types. Our results are consistent with emergent neutrality, whereby ecologically specialized morphologies evolve as a consequence of neutral (stochastic or reproductive) processes within niches, leading to generalization within the frond-dominated Community Type. Our results provide an ecological signature of the first origination and subsequent loss of disparate morphologies, probably as a consequence of community restructuring in response to ecological innovation. This restructuring led to the survival of non-tiered frondose generalists over tiered specialists, even into the youngest Ediacaran assemblages. Such frondose body plans also survive beyond the Ediacaran–Cambrian transition, perhaps due to the greater resilience afforded to them by their alternative ecological strategies.
Fox Insight at 5 years - a cohort of 54,000 participants contributing longitudinal patient-reported outcome, genetic, and microbiome data relating to Parkinson’s disease
Authors: Gottesman Joshua , Karim Yasir , Forbes Jodie , Kirsch Leslie , Stagman Keaton , Korell Monica , Tanner Caroline 
Published: June 2024

AbstractFox Insight is an online, longitudinal study of over 54,000 people with and without Parkinson’s disease, facilitating discovery, validation, and reproducibility in Parkinson’s disease research. The study administers routine longitudinal assessments, one-time questionnaires on an array of topics such as environmental exposure or COVID-19, plus genetic and microbiome data collection. Researchers can explore and download patient-reported outcomes data and Parkinson’s disease related genetic variants upon completing a Data Use Agreement. The full genetic data set, including approximately 650,000 single nucleotide polymorphisms for over 10,000 participants, and the microbiome data set for over 650 participants, can be requested with a heightened level of access. Since the first Fox Insight data descriptor was published in 2020, the data captured has been extended significantly, so this paper supersedes the previous one. Since then, the number of participants has increased by more than 20,000; an additional 1,747,729 surveys were completed; 130 gigabytes of genetic data were released; responses from 16 new one-time surveys were collected; and, data from one additional sub-study was made available.
GLAMOUR: GLobAl building MOrphology dataset for URban hydroclimate modelling
Authors: Li Ruidong , Sun Ting , Ghaffarian Saman , Tsamados Michel , Ni Guangheng 
Published: June 2024

AbstractUnderstanding building morphology is crucial for accurately simulating interactions between urban structures and hydroclimate dynamics. Despite significant efforts to generate detailed global building morphology datasets, there is a lack of practical solutions using publicly accessible resources. In this work, we present GLAMOUR, a dataset derived from open-source Sentinel imagery that captures the average building height and footprint at a resolution of 0.0009° across urbanized areas worldwide. Validated in 18 cities, GLAMOUR exhibits superior accuracy with median root mean square errors of 7.5 m and 0.14 for building height and footprint estimations, indicating better overall performance against existing published datasets. The GLAMOUR dataset provides essential morphological information of 3D building structures and can be integrated with other datasets and tools for a wide range of applications including 3D building model generation and urban morphometric parameter derivation. These extended applications enable refined hydroclimate simulation and hazard assessment on a broader scale and offer valuable insights for researchers and policymakers in building sustainable and resilient urban environments prepared for future climate adaptation.
Predictive biomarkers of intra-ocular pressure decrease after cataract surgery associated with trabecular washout in patients with pseudo exfoliative glaucoma
Authors: Vallée Rodolphe , Meduri Enrico , Vallée Jean-Noël , Lallouette Athena , Haffane Zakarya , Paillard Archibald , Mansouri Kaweh , Mermoud André 
Published: June 2024

AbstractTo investigate biomarkers of intra-ocular pressure (IOP) decrease after cataract surgery with trabecular washout in pseudo-exfoliative (PEX) glaucoma. A single-center observational prospective study in PEX glaucoma patients undergoing cataract surgery with trabecular washout (Goniowash) was performed from 2018 to 2021. Age, gender, visual acuity, IOP, endothelial cell count, central corneal thickness, medications, were collected over 16-month follow-up. Multivariable binomial regression models were implemented. 54 eyes (35 subjects) were included. Mean preoperative IOP (IOPBL) was 15.9 ± 3.5 mmHg. Postoperative IOP reduction was significant at 1-month and throughout follow-up (p < 0.01, respectively). IOPBL was a predictive biomarker inversely correlated to IOP decrease throughout follow-up (p < 0.001). At 1 and 12 months of follow-up, IOP decrease concerned 31 (57.4%) and 34 (63.0%) eyes with an average IOP decrease of 17.5% (from 17.6 ± 3.1 to 14.3 ± 2.2 mmHg) and 23.0% (from 17.7 ± 2.8 to 13.5 ± 2.6 mmHg), respectively. Performance (AUC) of IOPBL was 0.85 and 0.94 (p < 0.0001, respectively), with IOPBL threshold ≥ 15 mmHg for 82.1% and 96.8% sensitivity, 84.2% and 75.0% specificity, 1.84 and 3.91 IOP decrease odds-ratio, respectively. All PEX glaucoma patients with IOPBL greater than or equal to the average general population IOP were likely to achieve a significant sustainable postoperative IOP decrease.