bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing Urban Thermal Environment and Energy Sustainability With Temperature‐Adaptive Radiative Roofs
Authors: Zhang Keer , Zhao Lei , Oleson Keith , Li Xinchang “Cathy” , Lee Xuhui 
Published: January 2025

AbstractUrban overheating presents significant challenges to public health and energy sustainability. Conventional radiative cooling strategies, such as cool roofs with high albedo, lead to undesired winter cooling and increased space heating demand for cities with cold winters, a phenomenon known as heating energy penalty. A novel roof coating with high albedo and temperature‐adaptive emissivity (TAE)—low emissivity during cold conditions and high emissivity during hot conditions—has the potential to mitigate winter heating energy penalty. In this study, we implement this roof coating in a global climate model to evaluate its impact on air temperature and building energy demand for space heating and cooling in global cities. Adopting roofs with TAE increases global urban air temperature by up to +0.54°C in the winter (99th percentile; mean change +0.16°C) but has negligible effects on summer urban air temperature (mean change +0.05°C). Combining TAE with high albedo effectively provides summer cooling and does not increase building energy demand in the winter, particularly for mid‐latitude cities. Sensitivities of air temperature to changes in emissivity and albedo are associated with local “apparent” net longwave radiation and incoming solar radiation, respectively. We propose a simple parameterization of air temperature responses to emissivity and albedo to facilitate the development of city‐specific radiative mitigation strategies. This study emphasizes the necessity of developing mitigation approaches specific to local cloudiness.
Heat and Drought Events Alter Biogenic Capacity to Balance CO2 Budget in South‐Western Europe
Authors: Segura‐Barrero R. , Lauvaux T. , Lian J. , Ciais P. , Badia A. , Ventura S. , Bazzi H. , Abbessi E. , Fu Z. , Xiao J. , Li X. , Villalba G. 
Published: January 2025

AbstractHeat and drought events are increasing in frequency and intensity, posing significant risks to natural and agricultural ecosystems with uncertain effects on the net ecosystem CO2 exchange (NEE). The current Vegetation Photosynthesis and Respiration Model (VPRM) was adjusted to include soil moisture impacts on the gross ecosystem exchange (GEE) and respiration (RECO) fluxes to assess the temporal variability of NEE over south‐western Europe for 2001–2022. Warming temperatures lengthen growing seasons, causing an increase in GEE, which is mostly compensated by a similar increment in RECO. As a result, there is a modest increase in the net carbon sink of 0.69 gC m−2 yr−1 but with high spatial and annual variability. The heatwave of 2022 reduced net carbon uptake by 91.7 TgC, a 26.4% decrease from the mean. The interannual variability of NEE is more influenced by drought in temperate humid regions than in Mediterranean semi‐arid regions. These results emphasize the vulnerability of the net carbon sink as drying trends could revert the NEE trends, as it is happening for croplands in the French Central Massif.
An Investigation Into Far‐Flank Magnetic Reconnection at Earth's Magnetopause
Authors: Sullivan K. M. , Fuselier S. A. , Trattner K. J. , Petrinec S. M. , Burch J. L. , Gershman D. J. 
Published: January 2025

AbstractMagnetospheric Multiscale (MMS) observations have revealed that reconnection occurs along the flanks of Earth's magnetopause, near and past the terminator when the interplanetary magnetic field is southward. However, the question remains how common this reconnection is. Previous research has indicated that reconnection may be suppressed in the far‐flank regions due to the high velocity shear between the plasma in the magnetosheath and the plasma in the magnetosphere. This study investigates far‐flank reconnection by looking for evidence of reconnection in crossings of the far‐flank magnetopause. Forty‐one magnetopause crossing events were found that satisfied certain criteria and 35 of these events showed identifiable signs of reconnection. Based on these findings, reconnection is not suppressed along the magnetospheric flanks due to the velocity shear during southward IMF.
Barotropic Trends Through the Barents Sea Opening for the Period 1975–2021
Authors: Jahanmard Vahidreza , Löptien Ulrike , Sandø Anne Britt , Gierisch Andrea M. U. , Dietze Heiner , Lien Vidar , Delpeche‐Ellmann Nicole , Hordoir Robinson 
Published: January 2025

AbstractWe analyze the output of a regional ocean model that comprises the North Atlantic and the Arctic Ocean for the period 1975–2021. We focus on the flow through the cross sections closing the Nordic Sea basin. The simulated flow at Barents Sea Opening (BSO) shows a clear positive trend. To understand the origin of this trend, we reconstruct the BSO flow based on wind time series over the Nordic Seas using deep learning. To explore potential links between the results from this reconstruction and the major atmospheric modes, we perform a suite of idealized experiments where the ocean model is forced with wind field anomalies that refer to known changes in the leading modes of atmospheric circulation over the North Atlantic and Arctic Oceans. Known changes in the major atmospheric wind patterns over the North Atlantic have a weak impact on the simulated BSO flow, and the sign is not consistent with the overall trend of the full simulation. The latter holds as well for the known temporal changes in the intensity of the Arctic dipole mode. The weak temporal changes in the Arctic oscillation are consistent with the trend in the BSO flow but could not explain its amplitude. Ultimately, we could not establish a clear link between the BSO flow trend and changes in the major atmospheric modes. We conclude that the atmospheric pattern responsible for the BSO flow trend does not project directly on the leading modes of atmospheric variability over the North Atlantic and the Arctic.
Modeling Spatial Distributions of Salt Marsh Blue Carbon Using Morphometric Parameters From Lidar
Authors: Turek B. , Teng W. , Yu Q. , Yellen B. , Woodruff J. 
Published: January 2025

AbstractSalt marshes sequester large amounts of carbon, mainly within their deep soils. Several nationwide assessments have indicated that spatial variability of marsh soil carbon is minimal, however there's a need to further reduce carbon stock uncertainties by exploring finer‐scale variation using a process‐based modeling approach. Marsh soil properties vary spatially with several parameters, including marsh platform elevation, which controls inundation depth, and proximity to the marsh edge and tidal creek network, which control variability in relative sediment supply. We used lidar to extract these morphometric parameters from salt marshes to map soil organic carbon across a marsh at the meter scale. Soil samples were collected in 2021 from four northeast U.S. salts marshes with distinctive geomorphologies. Tidal creeks were delineated from 1‐m resolution topobathy lidar data using a semi‐automated workflow in GIS. Log‐linear multivariate regression models were developed to predict soil organic matter, bulk density, and carbon density as a function of predictive metrics at each site and across sites. Distance from tidal creeks was the most significant model predictor. Modeling marsh soil characteristics worked best in marshes with single channel hydrology. Addition of distance to the inlet and tidal range as regional metrics significantly improved cross‐site modeling. Our mechanistic approach reveals important meter‐level variation in soil characteristics across a marsh and provides motivation to continue rigorous mapping of soil carbon at fine spatial resolutions. Furthermore, carbon density values used to calculate total marsh carbon stocks should be carefully selected depending on project scale, marsh geomorphology, and desired accuracy.
Real‐Time Flood Inundation Modeling With Flow Resistance Parameter Learning
Authors: Young Alexander , Albertson John D. , Moretti Giovanni , Orlandini Stefano 
Published: January 2025

AbstractEmergency response to flood plain inundations requires real‐time forecasts of flow depth, velocity, and arrival time. Detailed and rapid flood inundation forecasts can be obtained from numerical solution of 2D unsteady flow equations based on high‐resolution topographic data and geomorphologically informed unstructured meshes. However, flow resistance parameters representing the effects of land surface topography unresolved by digital terrain model data remain uncertain. In the present study, flow resistance parameters representing the effects of roughness, vegetation, and buildings are determined hydraulically in real‐time using flow depth observations. A detailed numerical reproduction of a real flood has been largely corroborated by observations and subsequently used as a surrogate of the ground truth target. In synthetic numerical experiments, flow depth observations are obtained from a network of in‐situ flow depth sensors assigned to hydraulically relevant locations in the flood plain. Starting from a generic resistance parameter set, the capability of a tandem 2D surface flow model and Bayesian optimization technique to achieve convergence to the target resistance parameter set is tested. Convergence to the target resistance parameter set was obtained with 50 or fewer tandem flow + optimization iterations for each forecasting cycle in which the difference between simulated and observed flow depths is minimized. The flood arrival time errors across a 52 flood plain inundation area were reduced by 3.13 hr with respect to results obtained without optimization from a fixed range of flow resistance parameters. Performance metrics like critical success index and probability of detection reach values above 90% across the flood plain.
Exposure to childhood maltreatment is associated with specific epigenetic patterns in sperm
Authors: Tuulari Jetro J. , Bourgery Matthieu , Iversen Jo , Koefoed Thomas Gade , Ahonen Annukka , Ahmedani Ammar , Kataja Eeva-Leena , Karlsson Linnea , Barrès Romain , Karlsson Hasse , Kotaja Noora 
Published: January 2025

AbstractChildhood maltreatment exposure (CME) increases the risk of adverse long-term health consequences for the exposed individual. Animal studies suggest that CME may also influence the health and behaviour in the next generation offspring through CME-driven epigenetic changes in the germ line. Here we investigated the associated between early life stress on the epigenome of sperm in humans with history of CME. We measured paternal CME using the Trauma and Distress Scale (TADS) questionnaire and mapped sperm-borne sncRNAs expression by small RNA sequencing (small RNA-seq) and DNA methylation (DNAme) in spermatozoa by reduced-representation bisulfite sequencing (RRBS-seq) in males from the FinnBrain Birth Cohort Study. The study design was a (nested) case-control study, high-TADS (TADS ≥ 39, n = 25 for DNAme and n = 14 for small RNA-seq) and low-TADS (TADS ≤ 10, n = 30 for DNAme and n = 16 for small RNA-seq). We identified 3 genomic regions with differential methylation between low and high-TADS and 68 tRNA-derived small RNAs (tsRNAs) and miRNAs with different levels in males with high CME (False discovery rate, FDR corrected p < 0.05). Of potential interest, we identified differential expression of miRNA hsa-mir-34c-5p and differential methylation levels near the CRTC1 and GBX2 genes, which are documented to control brain development. Our results provide further evidence that early life stress influences the paternal germline epigenome and supports a possible effect in modulating the development of the central nervous system of the next generation.
Dynamic tracking of objects in the macaque dorsomedial frontal cortex
Authors: Rajalingham Rishi , Sohn Hansem , Jazayeri Mehrdad 
Published: January 2025

AbstractA central tenet of cognitive neuroscience is that humans build an internal model of the external world and use mental simulation of the model to perform physical inferences. Decades of human experiments have shown that behaviors in many physical reasoning tasks are consistent with predictions from the mental simulation theory. However, evidence for the defining feature of mental simulation – that neural population dynamics reflect simulations of physical states in the environment – is limited. We test the mental simulation hypothesis by combining a naturalistic ball-interception task, large-scale electrophysiology in non-human primates, and recurrent neural network modeling. We find that neurons in the monkeys’ dorsomedial frontal cortex (DMFC) represent task-relevant information about the ball position in a multiplexed fashion. At a population level, the activity pattern in DMFC comprises a low-dimensional neural embedding that tracks the ball both when it is visible and invisible, serving as a neural substrate for mental simulation. A systematic comparison of different classes of task-optimized RNN models with the DMFC data provides further evidence supporting the mental simulation hypothesis. Our findings provide evidence that neural dynamics in the frontal cortex are consistent with internal simulation of external states in the environment.
Tuning the selectivity of NH3 oxidation via cooperative electronic interactions between platinum and copper sites
Authors: Chen Lu , Guan Xuze , Fei Zhaofu , Asakura Hiroyuki , Zhang Lun , Wang Zhipeng , Su Xinlian , Yao Zhangyi , Keenan Luke L. , Hayama Shusaku , van Spronsen Matthijs A. , Karagoz Burcu , Held Georg , Allen Christopher S. , Hopkinson David G. , Decarolis Donato , Callison June , Dyson Paul J. , Wang Feng Ryan 
Published: January 2025

AbstractSelective catalytic oxidation (SCO) of NH3 to N2 is one of the most effective methods used to eliminate NH3 emissions. However, achieving high conversion over a wide operating temperature range while avoiding over-oxidation to NOx remains a significant challenge. Here, we report a bi-metallic surficial catalyst (PtSCuO/Al2O3) with improved Pt atom efficiency that overcomes the limitations of current catalysts. It achieves full NH3 conversion at 250 °C with a weight hourly space velocity of 600 ml NH3·h−1·g−1, which is 50 °C lower than commercial Pt/Al2O3, and maintains high N2 selectivity through a wide temperature window. Operando XAFS studies reveal that the surface Pt atoms in PtSCuO/Al2O3 enhance the redox properties of the Cu species, thus accelerating the Cu2+ reduction rate and improving the rate of the NH3-SCO reaction. Moreover, a synergistic effect between Pt and Cu sites in PtSCuO/Al2O3 contributes to the high selectivity by facilitating internal selective catalytic reduction.
Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics
Authors: Biggs George S. , Cawood Emma E. , Vuorinen Aini , McCarthy William J. , Wilders Harry , Riziotis Ioannis G. , van der Zouwen Antonie J. , Pettinger Jonathan , Nightingale Luke , Chen Peiling , Powell Andrew J. , House David , Boulton Simon J. , Skehel J. Mark , Rittinger Katrin , Bush Jacob T. 
Published: January 2025

Abstract
Identifying pharmacological probes for human proteins represents a key opportunity to accelerate the discovery of new therapeutics. High-content screening approaches to expand the ligandable proteome offer the potential to expedite the discovery of novel chemical probes to study protein function. Screening libraries of reactive fragments by chemoproteomics offers a compelling approach to ligand discovery, however, optimising sample throughput, proteomic depth, and data reproducibility remains a key challenge. We report a versatile, label-free quantification proteomics platform for competitive profiling of cysteine-reactive fragments against the native proteome. This high-throughput platform combines SP4 plate-based sample preparation with rapid chromatographic gradients. Data-independent acquisition performed on a Bruker timsTOF Pro 2 consistently identified ~23,000 cysteine sites per run, with a total of ~32,000 cysteine sites profiled in HEK293T and Jurkat lysate. Crucially, this depth in cysteinome coverage is met with high data completeness, enabling robust identification of liganded proteins. In this study, 80 reactive fragments were screened in two cell lines identifying >400 ligand-protein interactions. Hits were validated through concentration-response experiments and the platform was utilised for hit expansion and live cell experiments. This label-free platform represents a significant step forward in high-throughput proteomics to evaluate ligandability of cysteines across the human proteome.
Genome-wide characterization of 54 urinary metabolites reveals molecular impact of kidney function
Authors: Valo Erkka , Richmond Anne , Mutter Stefan , Dahlström Emma H. , Campbell Archie , Porteous David J. , Wilson James F. ,   FinnDiane Study Group, Mutter Stefan , Groop Per-Henrik , Hayward Caroline , Sandholm Niina 
Published: January 2025

AbstractDissecting the genetic mechanisms underlying urinary metabolite concentrations can provide molecular insights into kidney function and open possibilities for causal assessment of urinary metabolites with risk factors and disease outcomes. Proton nuclear magnetic resonance metabolomics provides a high-throughput means for urinary metabolite profiling, as widely applied for blood biomarker studies. Here we report a genome-wide association study meta-analysed for 3 European cohorts comprising 8,011 individuals, covering both people with type 1 diabetes and general population settings. We identify 54 associations (p < 9.3 × 10−10) for 19 of 54 studied metabolite concentrations. Out of these, 33 were not reported previously for relevant urinary or blood metabolite traits. Subsequent two-sample Mendelian randomization analysis suggests that estimated glomerular filtration rate causally affects 13 urinary metabolite concentrations whereas urinary ethanolamine, an initial precursor for phosphatidylcholine and phosphatidylethanolamine, was associated with higher eGFR lending support for a potential protective role. Our study provides a catalogue of genetic associations for 53 metabolites, enabling further investigation on how urinary metabolites are linked to human health.
Degradation bottlenecks and resource competition in transiently and stably engineered mammalian cells
Authors: Gabrielli Jacopo , Di Blasi Roberto , Kontoravdi Cleo , Ceroni Francesca 
Published: January 2025

AbstractDegradation tags, otherwise known as degrons, are portable sequences that can be used to alter protein stability. Here, we report that degron-tagged proteins compete for cellular degradation resources in engineered mammalian cells leading to coupling of the degradation rates of otherwise independently expressed proteins when constitutively targeted human degrons are adopted. We show the effect of this competition to be dependent on the context of the degrons. By considering different proteins, degron position and cellular hosts, we highlight how the impact of the degron on both degradation strength and resource coupling changes, with identification of orthogonal combinations. By adopting inducible bacterial and plant degrons we also highlight how controlled uncoupling of synthetic construct degradation from the native machinery can be achieved. We then build a genomically integrated capacity monitor tagged with different degrons and confirm resource competition between genomic and transiently expressed DNA constructs. This work expands the characterisation of resource competition in engineered mammalian cells to protein degradation also including integrated systems, providing a framework for the optimisation of heterologous expression systems to advance applications in fundamental and applied biological research.
The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron
Authors: Rüttiger Ann-Sophie , Ryan Daniel , Spiga Luisella , Lamm-Schmidt Vanessa , Prezza Gianluca , Reichardt Sarah , Langford Madison , Barquist Lars , Faber Franziska , Zhu Wenhan , Westermann Alexander J. 
Published: January 2025

AbstractParamount to human health, symbiotic bacteria in the gastrointestinal tract rely on the breakdown of complex polysaccharides to thrive in this sugar-deprived environment. Gut Bacteroides are metabolic generalists and deploy dozens of polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. The expression of the multi-protein PUL complexes is tightly regulated at the transcriptional level. However, how PULs are orchestrated at translational level in response to the fluctuating levels of their cognate substrates is unknown. Here, we identify the RNA-binding protein RbpB and a family of noncoding RNAs as key players in post-transcriptional PUL regulation. We demonstrate that RbpB interacts with numerous cellular transcripts, including a paralogous noncoding RNA family comprised of 14 members, the FopS (family of paralogous sRNAs). Through a series of in-vitro and in-vivo assays, we reveal that FopS sRNAs repress the translation of SusC-like glycan transporters when substrates are limited—an effect antagonized by RbpB. Ablation of RbpB in Bacteroides thetaiotaomicron compromises colonization in the mouse gut in a diet-dependent manner. Together, this study adds to our understanding of RNA-coordinated metabolic control as an important factor contributing to the in-vivo fitness of predominant microbiota species in dynamic nutrient landscapes.
A Y chromosome-linked genome editor for efficient population suppression in the malaria vector Anopheles gambiae
Authors: Tolosana Ignacio , Willis Katie , Gribble Matthew , Phillimore Lee , Burt Austin , Nolan Tony , Crisanti Andrea , Bernardini Federica 
Published: January 2025

AbstractGenetic control – the deliberate introduction of genetic traits to control a pest or vector population – offers a powerful tool to augment conventional mosquito control tools that have been successful in reducing malaria burden but that are compromised by a range of operational challenges. Self-sustaining genetic control strategies have shown great potential in laboratory settings, but hesitancy due to their invasive and persistent nature may delay their implementation. Here, instead, we describe a self-limiting strategy, designed to have geographically and temporally restricted effect, based on a Y chromosome-linked genome editor (YLE). The YLE comprises a CRISPR-Cas9 construct that is always inherited by males yet generates an autosomal dominant mutation that is transmitted to over 90% of the offspring and results in female-specific sterility. To our knowledge, our system represents a pioneering approach in the engineering of the Y chromosome to generate a genetic control strain for mosquitoes. Mathematical modelling shows that this YLE technology is up to seven times more efficient for population suppression than optimal versions of other self-limiting strategies, such as the widely used Sterile Insect Technique or the Release of Insects carrying a Dominant Lethal gene.