bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human‐Induced Impacts
Authors: Yu Jiang , Tian Yong , Wang Xiaoli , Sun Taotao , Lancia Michele , Andrews Charles B. , Zheng Chunmiao 
Published: August 2024

AbstractCurrent integrated modeling frameworks for simulating nutrient sources and dynamics are inadequate for large regional watersheds dominated by groundwater‐surface water interactions due to their simplistic representations of groundwater. In this study, we develop a coupled model that integrates comprehensive surface water, 3‐D groundwater, soil erosion, and nutrient processes. The model is intended to enhance the understanding of nutrient dynamics and sources in the Pearl River Basin (PRB). The model exhibits satisfactory performance in simulating streamflow and sediment transport patterns, capturing essential seasonal variations in water quality indicators. Hydrological budget assessments from 2002 to 2020 in the PRB reveal that 54% of precipitation drains into the South China Sea as surface water, while groundwater discharge as baseflow accounts for 18% of the streamflow. The nutrient budget for the PRB indicates that non‐point sources are the dominant contributors to both nitrogen (N) and phosphorus (P), ranging between 64% and 90%. Improved sewage collection and treatment have reduced point source nutrient contributions over the evaluation period. Groundwater remains a significant and consistent source of N, contributing between 11% and 19%. Natural disturbances and fertilization have led to an upward trend in river N inputs, while afforestation and sewage reduction efforts have resulted in a downward trend in river P inputs. Increased fertilization emerges as a central concern for the PRB, suggesting cost‐effective mitigation of fertilizer usage a pragmatic solution. The coupled simulation model developed in this study offers a novel systems approach for basin‐wide nutrient analysis and pollution control strategies, considering both natural and human‐induced disturbances.
Tertiary lymphoid structures in diseases: immune mechanisms and therapeutic advances
Authors: Zhao Lianyu , Jin Song , Wang Shengyao , Zhang Zhe , Wang Xuan , Chen Zhanwei , Wang Xiaohui , Huang Shengyun , Zhang Dongsheng , Wu Haiwei 
Published: August 2024

AbstractTertiary lymphoid structures (TLSs) are defined as lymphoid aggregates formed in non-hematopoietic organs under pathological conditions. Similar to secondary lymphoid organs (SLOs), the formation of TLSs relies on the interaction between lymphoid tissue inducer (LTi) cells and lymphoid tissue organizer (LTo) cells, involving multiple cytokines. Heterogeneity is a distinguishing feature of TLSs, which may lead to differences in their functions. Growing evidence suggests that TLSs are associated with various diseases, such as cancers, autoimmune diseases, transplant rejection, chronic inflammation, infection, and even ageing. However, the detailed mechanisms behind these clinical associations are not yet fully understood. The mechanisms by which TLS maturation and localization affect immune function are also unclear. Therefore, it is necessary to enhance the understanding of TLS development and function at the cellular and molecular level, which may allow us to utilize them to improve the immune microenvironment. In this review, we delve into the composition, formation mechanism, associations with diseases, and potential therapeutic applications of TLSs. Furthermore, we discuss the therapeutic implications of TLSs, such as their role as markers of therapeutic response and prognosis. Finally, we summarize various methods for detecting and targeting TLSs. Overall, we provide a comprehensive understanding of TLSs and aim to develop more effective therapeutic strategies.
Silicon ion radiation as a viable surrogate for emulating neutron radiation damage in silicates
Authors: Polavaram Krishna C. , Evani Sai Kalyan , Drewry Sean M. , Rodriguez Elena Tajuelo , Alnaggar Mohammed G. , Wetteland Christopher J. , Page Katharine , Popovics John S. , Sickafus Kurt E. , Le Pape Yann , Garg Nishant 
Published: August 2024

AbstractNuclear power plants are aging around the world, and a precise assessment of irradiation damage in their components is needed. One key component, concrete, and specifically the silicates in its aggregates, can undergo significant expansion upon neutron radiation, which can lead to cracking and, ultimately, structural failure. However, assessing and predicting the extent of damage via neutron radiation is challenging due to reasons such as residual radioactivity and, most importantly, the high time involved. Here, we evaluate whether ion radiation can be a viable surrogate. Specifically, by employing Si2+ ion radiations and a comprehensive multi-modal imaging protocol, we report mineral-specific responses for key silicates such as quartz, albite, anorthite, and microcline. We find that 10 MeV Si2+ ions result in mineral expansions that are remarkably comparable to neutron radiation equivalent expansions (R2 = 0.86, RMSE = 1.29%), opening up pathways towards rapid assessment of silicates subject to irradiation.
Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts
Authors: Ramsköld Daniel , Hendriks Gert-Jan , Larsson Anton J. M. , Mayr Juliane V. , Ziegenhain Christoph , Hagemann-Jensen Michael , Hartmanis Leonard , Sandberg Rickard 
Published: August 2024

AbstractAnalyses of transcriptional bursting from single-cell RNA-sequencing data have revealed patterns of variation and regulation in the kinetic parameters that could be inferred. Here we profiled newly transcribed (4-thiouridine-labelled) RNA across 10,000 individual primary mouse fibroblasts to more broadly infer bursting kinetics and coordination. We demonstrate that inference from new RNA profiles could separate the kinetic parameters that together specify the burst size, and that the synthesis rate (and not the transcriptional off rate) controls the burst size. Importantly, transcriptome-wide inference of transcriptional on and off rates provided conclusive evidence that RNA polymerase II transcribes genes in bursts. Recent reports identified examples of transcriptional co-bursting, yet no global analyses have been performed. The deep new RNA profiles we generated with allelic resolution demonstrated that co-bursting rarely appears more frequently than expected by chance, except for certain gene pairs, notably paralogues located in close genomic proximity. Altogether, new RNA single-cell profiling critically improves the inference of transcriptional bursting and provides strong evidence for independent transcriptional bursting of mammalian genes.
Spatially clustered type I interferon responses at injury borderzones
Authors: Ninh V. K. , Calcagno D. M. , Yu J. D. , Zhang B. , Taghdiri N. , Sehgal R. , Mesfin J. M. , Chen C. J. , Kalhor K. , Toomu A. , Duran J. M. , Adler E. , Hu J. , Zhang K. , Christman K. L. , Fu Z. , Bintu B. , King K. R. 
Published: August 2024

AbstractSterile inflammation after myocardial infarction is classically credited to myeloid cells interacting with dead cell debris in the infarct zone1,2. Here we show that cardiomyocytes are the dominant initiators of a previously undescribed type I interferon response in the infarct borderzone. Using spatial transcriptomics analysis in mice and humans, we find that myocardial infarction induces colonies of interferon-induced cells (IFNICs) expressing interferon-stimulated genes decorating the borderzone, where cardiomyocytes experience mechanical stress, nuclear rupture and escape of chromosomal DNA. Cardiomyocyte-selective deletion of Irf3 abrogated IFNIC colonies, whereas mice lacking Irf3 in fibroblasts, macrophages, neutrophils or endothelial cells, Ccr2-deficient mice or plasmacytoid-dendritic-cell-depleted mice did not. Interferons blunted the protective matricellular programs and contractile function of borderzone fibroblasts, and increased vulnerability to pathological remodelling. In mice that died after myocardial infarction, IFNIC colonies were immediately adjacent to sites of ventricular rupture, while mice lacking IFNICs were protected from rupture and exhibited improved survival3. Together, these results reveal a pathological borderzone niche characterized by a cardiomyocyte-initiated innate immune response. We suggest that selective inhibition of IRF3 activation in non-immune cells could limit ischaemic cardiomyopathy while avoiding broad immunosuppression.
AI generates covertly racist decisions about people based on their dialect
Authors: Hofmann Valentin , Kalluri Pratyusha Ria , Jurafsky Dan , King Sharese 
Published: August 2024

AbstractHundreds of millions of people now interact with language models, with uses ranging from help with writing1,2 to informing hiring decisions3. However, these language models are known to perpetuate systematic racial prejudices, making their judgements biased in problematic ways about groups such as African Americans4–7. Although previous research has focused on overt racism in language models, social scientists have argued that racism with a more subtle character has developed over time, particularly in the United States after the civil rights movement8,9. It is unknown whether this covert racism manifests in language models. Here, we demonstrate that language models embody covert racism in the form of dialect prejudice, exhibiting raciolinguistic stereotypes about speakers of African American English (AAE) that are more negative than any human stereotypes about African Americans ever experimentally recorded. By contrast, the language models’ overt stereotypes about African Americans are more positive. Dialect prejudice has the potential for harmful consequences: language models are more likely to suggest that speakers of AAE be assigned less-prestigious jobs, be convicted of crimes and be sentenced to death. Finally, we show that current practices of alleviating racial bias in language models, such as human preference alignment, exacerbate the discrepancy between covert and overt stereotypes, by superficially obscuring the racism that language models maintain on a deeper level. Our findings have far-reaching implications for the fair and safe use of language technology.
Sympathetic neuropeptide Y protects from obesity by sustaining thermogenic fat
Authors: Zhu Yitao , Yao Lu , Gallo-Ferraz Ana L. , Bombassaro Bruna , Simões Marcela R. , Abe Ichitaro , Chen Jing , Sarker Gitalee , Ciccarelli Alessandro , Zhou Linna , Lee Carl , Sidarta-Oliveira Davi , Martínez-Sánchez Noelia , Dustin Michael L. , Zhan Cheng , Horvath Tamas L. , Velloso Licio A. , Kajimura Shingo , Domingos Ana I. 
Published: August 2024

AbstractHuman mutations in neuropeptide Y (NPY) have been linked to high body mass index but not altered dietary patterns1. Here we uncover the mechanism by which NPY in sympathetic neurons2,3 protects from obesity. Imaging of cleared mouse brown and white adipose tissue (BAT and WAT, respectively) established that NPY+ sympathetic axons are a smaller subset that mostly maps to the perivasculature; analysis of single-cell RNA sequencing datasets identified mural cells as the main NPY-responsive cells in adipose tissues. We show that NPY sustains the proliferation of mural cells, which are a source of thermogenic adipocytes in both BAT and WAT4–6. We found that diet-induced obesity leads to neuropathy of NPY+ axons and concomitant depletion of mural cells. This defect was replicated in mice with NPY abrogated from sympathetic neurons. The loss of NPY in sympathetic neurons whitened interscapular BAT, reducing its thermogenic ability and decreasing energy expenditure before the onset of obesity. It also caused adult-onset obesity of mice fed on a regular chow diet and rendered them more susceptible to diet-induced obesity without increasing food consumption. Our results indicate that, relative to central NPY, peripheral NPY produced by sympathetic nerves has the opposite effect on body weight by sustaining energy expenditure independently of food intake.
A population code for spatial representation in the zebrafish telencephalon
Authors: Yang Chuyu , Mammen Lorenz , Kim Byoungsoo , Li Meng , Robson Drew N. , Li Jennifer M. 
Published: August 2024

AbstractSpatial learning in teleost fish requires an intact telencephalon1, a brain region that contains putative analogues to components of the mammalian limbic system (for example, hippocampus)2–4. However, cells fundamental to spatial cognition in mammals—for example, place cells (PCs)5,6—have yet to be established in any fish species. In this study, using tracking microscopy to record brain-wide calcium activity in freely swimming larval zebrafish7, we compute the spatial information content8 of each neuron across the brain. Strikingly, in every recorded animal, cells with the highest spatial specificity were enriched in the zebrafish telencephalon. These PCs form a population code of space from which we can decode the animal’s spatial location across time. By continuous recording of population-level activity, we found that the activity manifold of PCs refines and untangles over time. Through systematic manipulation of allothetic and idiothetic cues, we demonstrate that zebrafish PCs integrate multiple sources of information and can flexibly remap to form distinct spatial maps. Using analysis of neighbourhood distance between PCs across environments, we found evidence for a weakly preconfigured network in the telencephalon. The discovery of zebrafish PCs represents a step forward in our understanding of spatial cognition across species and the functional role of the early vertebrate telencephalon.
Carbon emissions from the 2023 Canadian wildfires
Authors: Byrne Brendan , Liu Junjie , Bowman Kevin W. , Pascolini-Campbell Madeleine , Chatterjee Abhishek , Pandey Sudhanshu , Miyazaki Kazuyuki , van der Werf Guido R. , Wunch Debra , Wennberg Paul O. , Roehl Coleen M. , Sinha Saptarshi 
Published: August 2024

AbstractThe 2023 Canadian forest fires have been extreme in scale and intensity with more than seven times the average annual area burned compared to the previous four decades1. Here, we quantify the carbon emissions from these fires from May to September 2023 on the basis of inverse modelling of satellite carbon monoxide observations. We find that the magnitude of the carbon emissions is 647 TgC (570–727 TgC), comparable to the annual fossil fuel emissions of large nations, with only India, China and the USA releasing more carbon per year2. We find that widespread hot–dry weather was a principal driver of fire spread, with 2023 being the warmest and driest year since at least 19803. Although temperatures were extreme relative to the historical record, climate projections indicate that these temperatures are likely to be typical during the 2050s, even under a moderate climate mitigation scenario (shared socioeconomic pathway, SSP 2–4.5)4. Such conditions are likely to drive increased fire activity and suppress carbon uptake by Canadian forests, adding to concerns about the long-term durability of these forests as a carbon sink5–8.
Mating proximity blinds threat perception
Authors: Cazalé-Debat Laurie , Scheunemann Lisa , Day Megan , Fernandez-d.V. Alquicira Tania , Dimtsi Anna , Zhang Youchong , Blackburn Lauren A. , Ballardini Charles , Greenin-Whitehead Katie , Reynolds Eric , Lin Andrew C. , Owald David , Rezaval Carolina 
Published: August 2024

AbstractRomantic engagement can bias sensory perception. This ‘love blindness’ reflects a common behavioural principle across organisms: favouring pursuit of a coveted reward over potential risks1. In the case of animal courtship, such sensory biases may support reproductive success but can also expose individuals to danger, such as predation2,3. However, how neural networks balance the trade-off between risk and reward is unknown. Here we discover a dopamine-governed filter mechanism in male Drosophila that reduces threat perception as courtship progresses. We show that during early courtship stages, threat-activated visual neurons inhibit central courtship nodes via specific serotonergic neurons. This serotonergic inhibition prompts flies to abort courtship when they see imminent danger. However, as flies advance in the courtship process, the dopaminergic filter system reduces visual threat responses, shifting the balance from survival to mating. By recording neural activity from males as they approach mating, we demonstrate that progress in courtship is registered as dopaminergic activity levels ramping up. This dopamine signalling inhibits the visual threat detection pathway via Dop2R receptors, allowing male flies to focus on courtship when they are close to copulation. Thus, dopamine signalling biases sensory perception based on perceived goal proximity, to prioritize between competing behaviours.
Sodium chloride in the tumor microenvironment enhances T cell metabolic fitness and cytotoxicity
Authors: Soll Dominik , Chu Chang-Feng , Sun Shan , Lutz Veronika , Arunkumar Mahima , Gachechiladze Mariam , Schäuble Sascha , Alissa-Alkhalaf Maha , Nguyen Trang , Khalil Michelle-Amirah , Garcia-Ribelles Ignacio , Mueller Michael , Buder Katrin , Michalke Bernhard , Panagiotou Gianni , Ziegler-Martin Kai , Benz Pascal , Schatzlmaier Philipp , Hiller Karsten , Stockinger Hannes , Luu Maik , Schober Kilian , Moosmann Carolin , Schamel Wolfgang W. , Huber Magdalena , Zielinski Christina E. 
Published: August 2024

AbstractThe efficacy of antitumor immunity is associated with the metabolic state of cytotoxic T cells, which is sensitive to the tumor microenvironment. Whether ionic signals affect adaptive antitumor immune responses is unclear. In the present study, we show that there is an enrichment of sodium in solid tumors from patients with breast cancer. Sodium chloride (NaCl) enhances the activation state and effector functions of human CD8+ T cells, which is associated with enhanced metabolic fitness. These NaCl-induced effects translate into increased tumor cell killing in vitro and in vivo. Mechanistically, NaCl-induced changes in CD8+ T cells are linked to sodium-induced upregulation of Na+/K+-ATPase activity, followed by membrane hyperpolarization, which magnifies the electromotive force for T cell receptor (TCR)-induced calcium influx and downstream TCR signaling. We therefore propose that NaCl is a positive regulator of acute antitumor immunity that might be modulated for ex vivo conditioning of therapeutic T cells, such as CAR T cells.
Health and economic impacts of Lassa vaccination campaigns in West Africa
Authors: Smith David R. M. , Turner Joanne , Fahr Patrick , Attfield Lauren A. , Bessell Paul R. , Donnelly Christl A. , Gibb Rory , Jones Kate E. , Redding David W. , Asogun Danny , Ayodeji Oladele Oluwafemi , Azuogu Benedict N. , Fischer William A. , Jan Kamji , Olayinka Adebola T. , Wohl David A. , Torkelson Andrew A. , Dinkel Katelyn A. , Nixon Emily J. , Pouwels Koen B. , Hollingsworth T. Déirdre 
Published: August 2024

AbstractLassa fever is a zoonotic disease identified by the World Health Organization (WHO) as having pandemic potential. This study estimates the health-economic burden of Lassa fever throughout West Africa and projects impacts of a series of vaccination campaigns. We also model the emergence of ‘Lassa-X’—a hypothetical pandemic Lassa virus variant—and project impacts of achieving 100 Days Mission vaccination targets. Our model predicted 2.7 million (95% uncertainty interval: 2.1–3.4 million) Lassa virus infections annually, resulting over 10 years in 2.0 million (793,800–3.9 million) disability-adjusted life years (DALYs). The most effective vaccination strategy was a population-wide preventive campaign primarily targeting WHO-classified ‘endemic’ districts. Under conservative vaccine efficacy assumptions, this campaign averted $20.1 million ($8.2–$39.0 million) in lost DALY value and $128.2 million ($67.2–$231.9 million) in societal costs (2021 international dollars ($)). Reactive vaccination in response to local outbreaks averted just one-tenth the health-economic burden of preventive campaigns. In the event of Lassa-X emerging, spreading throughout West Africa and causing approximately 1.2 million DALYs within 2 years, 100 Days Mission vaccination averted 22% of DALYs given a vaccine 70% effective against disease and 74% of DALYs given a vaccine 70% effective against both infection and disease. These findings suggest how vaccination could alleviate Lassa fever’s burden and assist in pandemic preparedness.
Planktonic ciliate communities along an environmental gradient in the Nile Delta (Damietta region, Egypt)
Authors: El-Tohamy Wael S. , Hopcroft Russell R. 
Published: August 2024

AbstractThe spatial patterns of planktonic ciliate communities were studied from May to June 2019 in the Nile Delta’s Damietta region, southeastern Mediterranean. The ciliate communities were sampled from twenty-five sites of five stressed domains with spatial gradients of environmental status. A total of 32 ciliate taxa with six dominant species were identified, comprising 21 tintinnids and 11 aloricate ciliates. The abundance and richness of each ciliate group varied geographically and were most strongly influenced by salinity variations; tintinnid ciliates attained high abundance and richness at high salinity sites in the harbour and coastal region and decreased within the estuary upstream. Aloricate ciliates were poorly represented at most sites but were a substantial proportion of upstream estuarine sites. Multivariate/univariate analyses demonstrated that spatial patterns of the ciliate communities were significantly correlated with environmental variables, especially salinity, chlorophyll-a, and nutrients, either alone or in combination with one another. These results indicate that the ciliates can be useful bioindicators in stressed environments while also allowing the detection of impacts on short time scales by rapidly responding to environmental variations.
Short-term exposure to fine particulate pollution and elderly mortality in Chile
Authors: Busch Pablo , Rocha Paulo , Lee Kyung Jin , Cifuentes Luis Abdón , Tai Xiao Hui 
Published: August 2024

AbstractExposure to fine particulate matter (PM2.5) is known to cause adverse health outcomes. Most of the evidence has been derived from developed countries, with lower pollution levels and different demographics and comorbidities from the rest of the world. Here we leverage new satellite-based measurements of PM2.5, combined with comprehensive public records in Chile, to study the effect of PM2.5pollution on elderly mortality. We find that a 10μg/m3monthly increase in PM2.5exposure is associated with a 1.7% increase (95% C.I.: 1.1–2.4%) in all-cause mortality for individuals aged 75+. Satellite-based measurements allow us to comprehensively investigate heterogeneous effects. We find remarkably similar effect sizes across baseline exposure, rural and urban areas, income, and over time, demonstrating consistency in the evidence on mortality effects of PM2.5exposure. The most notable source of heterogeneity is geographical, with effects closer to 5% in the center-south and in the metropolitan area.