bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two Small Volcanoes, One Inside the Other: Geophysical and Drilling Investigation of Bažina Maar in Western Eger Rift
Authors: Hrubcová Pavla , Fischer Tomáš , Rapprich Vladislav , Valenta Jan , Tábořík Petr , Mrlina Jan , Dahm Torsten , Vylita Tomáš , Beránek Roman , Klanica Radek , Vlček Josef , Turjaková Veronika 
Published: August 2023

AbstractMaar‐diatreme volcanoes are small volcanic structures with a funnel‐shaped crater surrounded by a tephra‐ring. They are usually formed by the explosive phreatomagmatic eruptions when groundwater comes into the contact with magma. We focus on such a structure in the geodynamically active western Eger Rift (Czech Republic) and present results from multidisciplinary geophysical investigation calibrated by drilling in the newly discovered Pleistocene Bažina maar. We evaluated morphological (LiDAR‐based DEM) data and confirmed the existence of a maar‐diatreme structure by combined geophysical methods. In the map view, they revealed circular negative gravity anomaly, funnel‐shape low‐resistivity anomaly, and strong magnetic anomaly. These results allowed for the optimal location of two boreholes in the maar crater, which evinced its contact with country rocks and lithologies of the maar‐diatreme filling. The drilling revealed coherent volcanic rocks and volcaniclastic deposits, moreover, it revealed a presence of a pyroclastic cone with the olivine nephelinite feeding conduit. Further investigations disclosed maar structure and subsequent pyroclastic cone(s) with several generations of eruptions and systematic decrease of water influence on the eruption style. Different eruption styles suggest a unique evolution of two volcanoes, one inside the other. The age of the Bažina maar eruption, estimated from the reverse polarity of the detected magnetic anomaly, implies that the effusion and solidification of the lava during the eruption must be older than 0.78 Ma (Pleistocene). This points to an active volcanism in the western Eger Rift in a span of ∼0.5 Ma, where Bažina represents the oldest (maybe opening) phase.
Sub‐Grid Representation of Vegetation Cover in Land Surface Schemes Improves the Modeling of How Climate Responds to Deforestation
Authors: Qin Yingzuo , Wang Dashan , Cao Ye’er , Cai Xitian , Liang Shijing , Beck Hylke E. , Zeng Zhenzhong 
Published: August 2023

AbstractUnderstanding the regional climate response to land cover change requires a realistic sub‐grid representation of vegetation cover in the land surface scheme (LSS) of climate models. The Community Land Model (CLM) is considered one of the most advanced LSSs; however, when coupled with the Weather Research and Forecasting (WRF) model, the tiling vegetation cover approach was deactivated. Here, we reactivated the theoretical sub‐grid vegetation cover representation in WRF‐CLM and applied it to assess the impacts of deforestation on regional climate in the Southeast Asian Massif region. We found that CLM‐tiling performs more accurate simulations of surface air temperature and precipitation compared to other LSSs using the in situ observations. Importantly, CLM‐tiling successfully captures the theoretical sensitivity of evapotranspiration (ET) and temperature to sub‐grid deforestation, aligning with Noah‐mosaic, and it substantially improves the spatial pattern responses of simulated ET and temperature to regional deforestation.
A Strengthened Teleconnection of the Quasi‐Biennial Oscillation and Tropical Easterly Jet in the Past Decades in E3SMv1
Authors: Li Yuanpu , Richter Jadwiga H. , Chen Chih‐Chieh , Tang Qi 
Published: August 2023

AbstractThe Energy Exascale Earth System Model version 1 (E3SMv1) is a new global model that can generate a weakened tropical easterly jet (TEJ) during the easterly quasi‐biennial oscillation (EQBO) and a strengthened TEJ during the westerly QBO (WQBO), which is referred to as the QBO‐TEJ teleconnection. Although the longitudinal structure of the QBO‐TEJ teleconnection is different between reanalysis and simulations, we hypothesize that simulations can still provide insights into the observed long‐term changes in the QBO‐TEJ teleconnection. The Atmospheric Model Intercomparison Project historical simulations (AMIP‐historical) generate a strengthened trend in the correlation between the QBO and TEJ indices in the period of 1950–2014 as in reanalysis. The comparison of the AMIP‐historical and the Coupled Model Intercomparison Project coupled historical simulations (coupled‐historical) shows that the warming of the Indian Ocean has played a vital role in the strengthened QBO‐TEJ teleconnection over the past six decades.
Conserved role for PCBP1 in altered RNA splicing in the hippocampus after chronic alcohol exposure
Authors: Carvalho Luana , Chen Hu , Maienschein-Cline Mark , Glover Elizabeth J. , Pandey Subhash C. , Lasek Amy W. 
Published: August 2023

AbstractWe previously discovered using transcriptomics that rats undergoing withdrawal after chronic ethanol exposure had increased expression of several genes encoding RNA splicing factors in the hippocampus. Here, we examined RNA splicing in the rat hippocampus during withdrawal from chronic ethanol exposure and in postmortem hippocampus of human subjects diagnosed with alcohol use disorder (AUD). We found that expression of the gene encoding the splicing factor, poly r(C) binding protein 1 (PCBP1), was elevated in the hippocampus of rats during withdrawal after chronic ethanol exposure and AUD subjects. We next analyzed the rat RNA-Seq data for differentially expressed (DE) exon junctions. One gene,Hapln2, had increased usage of a novel 3′ splice site in exon 4 during withdrawal. This splice site was conserved in humanHAPLN2and was used more frequently in the hippocampus of AUD compared to control subjects. To establish a functional role for PCBP1 inHAPLN2splicing, we performed RNA immunoprecipitation (RIP) with a PCBP1 antibody in rat and human hippocampus, which showed enriched PCBP1 association near theHAPLN2exon 4 3′ splice site in the hippocampus of rats during ethanol withdrawal and AUD subjects. Our results indicate a conserved role for the splicing factor PCBP1 in aberrant splicing ofHAPLN2after chronic ethanol exposure. As theHAPLN2gene encodes an extracellular matrix protein involved in nerve conduction velocity, use of this alternative splice site is predicted to result in loss of protein function that could negatively impact hippocampal function in AUD.
Mitochondria dysregulation contributes to secondary neurodegeneration progression post-contusion injury in human 3D in vitro triculture brain tissue model
Authors: Liaudanskaya Volha , Fiore Nicholas J. , Zhang Yang , Milton Yuka , Kelly Marilyn F. , Coe Marly , Barreiro Ariana , Rose Victoria K. , Shapiro Matthew R. , Mullis Adam S. , Shevzov-Zebrun Anna , Blurton-Jones Mathew , Whalen Michael J. , Symes Aviva J. , Georgakoudi Irene , Nieland Thomas J. F. , Kaplan David L. 
Published: August 2023

AbstractTraumatic Brain injury-induced disturbances in mitochondrial fission-and-fusion dynamics have been linked to the onset and propagation of neuroinflammation and neurodegeneration. However, cell-type-specific contributions and crosstalk between neurons, microglia, and astrocytes in mitochondria-driven neurodegeneration after brain injury remain undefined. We developed a human three-dimensional in vitro triculture tissue model of a contusion injury composed of neurons, microglia, and astrocytes and examined the contributions of mitochondrial dysregulation to neuroinflammation and progression of injury-induced neurodegeneration. Pharmacological studies presented here suggest that fragmented mitochondria released by microglia are a key contributor to secondary neuronal damage progression after contusion injury, a pathway that requires astrocyte-microglia crosstalk. Controlling mitochondrial dysfunction thus offers an exciting option for developing therapies for TBI patients.
ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana
Authors: Zubrycka Agata , Dambire Charlene , Dalle Carbonare Laura , Sharma Gunjan , Boeckx Tinne , Swarup Kamal , Sturrock Craig J. , Atkinson Brian S. , Swarup Ranjan , Corbineau Françoise , Oldham Neil J. , Holdsworth Michael J. 
Published: August 2023

AbstractOxygen is a key signalling component of plant biology, and whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana, key features of the associated PLANT CYSTEINE OXIDASE (PCO) N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain untested or unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance and are essential for root development and survival under oxygen limiting conditions in soil. We determine the combined effects of ERFVIIs in controlling gene expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine sulphonic acid oxidation level of ERFVIIs was observed, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.
A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
Authors: Faure Léon , Mollet Bastien , Liebermeister Wolfram , Faulon Jean-Loup 
Published: August 2023

AbstractConstraint-based metabolic models have been used for decades to predict the phenotype of microorganisms in different environments. However, quantitative predictions are limited unless labor-intensive measurements of media uptake fluxes are performed. We show how hybrid neural-mechanistic models can serve as an architecture for machine learning providing a way to improve phenotype predictions. We illustrate our hybrid models with growth rate predictions of Escherichia coli and Pseudomonas putida grown in different media and with phenotype predictions of gene knocked-out Escherichia coli mutants. Our neural-mechanistic models systematically outperform constraint-based models and require training set sizes orders of magnitude smaller than classical machine learning methods. Our hybrid approach opens a doorway to enhancing constraint-based modeling: instead of constraining mechanistic models with additional experimental measurements, our hybrid models grasp the power of machine learning while fulfilling mechanistic constrains, thus saving time and resources in typical systems biology or biological engineering projects.
Theoretical assessment of persistence and adaptation in weeds with complex life cycles
Authors: Lauenroth Dana , Gokhale Chaitanya S. 
Published: August 2023

AbstractHerbicide-resistant weeds pose a substantial threat to global food security. Perennial weed species are particularly troublesome. Such perennials as Sorghum halepense spread quickly and are difficult to manage due to their ability to reproduce sexually via seeds and asexually through rhizomes. Our theoretical study of S. halepense incorporates this complex life cycle with control measures of herbicide application and tillage. Rooted in the biology and experimental data of S. halepense, our population-based model predicts population dynamics and target-site resistance evolution in this perennial weed. We found that the resistance cost determines the standing genetic variation for herbicide resistance. The sexual phase of the life cycle, including self-pollination and seed bank dynamics, contributes substantially to the persistence and rapid adaptation of S. halepense. While self-pollination accelerates target-site resistance evolution, seed banks considerably increase the probability of escape from control strategies and maintain genetic variation. Combining tillage and herbicide application effectively reduces weed densities and the risk of control failure without delaying resistance adaptation. We also show how mixtures of different herbicide classes are superior to rotations and mono-treatment in controlling perennial weeds and resistance evolution. Thus, by integrating experimental data and agronomic views, our theoretical study synergistically contributes to understanding and tackling the global threat to food security from resistant weeds.
Autonomous quantum error correction and fault-tolerant quantum computation with squeezed cat qubits
Authors: Xu Qian , Zheng Guo , Wang Yu-Xin , Zoller Peter , Clerk Aashish A. , Jiang Liang 
Published: August 2023

AbstractWe propose an autonomous quantum error correction scheme using squeezed cat (SC) code against excitation loss in continuous-variable systems. Through reservoir engineering, we show that a structured dissipation can stabilize a two-component SC while autonomously correcting the errors. The implementation of such dissipation only requires low-order nonlinear couplings among three bosonic modes or between a bosonic mode and a qutrit. While our proposed scheme is device independent, it is readily implementable with current experimental platforms such as superconducting circuits and trapped-ion systems. Compared to the stabilized cat, the stabilized SC has a much lower dominant error rate and a significantly enhanced noise bias. Furthermore, the bias-preserving operations for the SC have much lower error rates. In combination, the stabilized SC leads to substantially better logical performance when concatenating with an outer discrete-variable code. The surface-SC scheme achieves more than one order of magnitude increase in the threshold ratio between the loss rate κ1 and the engineered dissipation rate κ2. Under a practical noise ratio κ1/κ2 = 10−3, the repetition-SC scheme can reach a 10−15 logical error rate even with a small mean excitation number of 4, which already suffices for practically useful quantum algorithms.
An intestinal sphingolipid confers intergenerational neuroprotection
Authors: Wang Wenyue , Sherry Tessa , Cheng Xinran , Fan Qi , Cornell Rebecca , Liu Jie , Xiao Zhicheng , Pocock Roger 
Published: August 2023

AbstractIn animals, maternal diet and environment can influence the health of offspring. Whether and how maternal dietary choice impacts the nervous system across multiple generations is not well understood. Here we show that feeding Caenorhabditis elegans with ursolic acid, a natural plant product, improves axon transport and reduces adult-onset axon fragility intergenerationally. Ursolic acid provides neuroprotection by enhancing maternal provisioning of sphingosine-1-phosphate, a bioactive sphingolipid. Intestine-to-oocyte sphingosine-1-phosphate transfer is required for intergenerational neuroprotection and is dependent on the RME-2 lipoprotein yolk receptor. Sphingosine-1-phosphate acts intergenerationally by upregulating the transcription of the acid ceramidase-1 (asah-1) gene in the intestine. Spatial regulation of sphingolipid metabolism is critical, as inappropriate asah-1 expression in neurons causes developmental axon outgrowth defects. Our results show that sphingolipid homeostasis impacts the development and intergenerational health of the nervous system. The ability of specific lipid metabolites to act as messengers between generations may have broad implications for dietary choice during reproduction.
Systematic benchmarking of single-cell ATAC-sequencing protocols
Authors: De Rop Florian V. , Hulselmans Gert , Flerin Chris , Soler-Vila Paula , Rafels Albert , Christiaens Valerie , González-Blas Carmen Bravo , Marchese Domenica , Caratù Ginevra , Poovathingal Suresh , Rozenblatt-Rosen Orit , Slyper Michael , Luo Wendy , Muus Christoph , Duarte Fabiana , Shrestha Rojesh , Bagdatli S. Tansu , Corces M. Ryan , Mamanova Lira , Knights Andrew , Meyer Kerstin B. , Mulqueen Ryan , Taherinasab Akram , Maschmeyer Patrick , Pezoldt Jörn , Lambert Camille Lucie Germaine , Iglesias Marta , Najle Sebastián R. , Dossani Zain Y. , Martelotto Luciano G. , Burkett Zach , Lebofsky Ronald , Martin-Subero José Ignacio , Pillai Satish , Sebé-Pedrós Arnau , Deplancke Bart , Teichmann Sarah A. , Ludwig Leif S. , Braun Theodore P. , Adey Andrew C. , Greenleaf William J. , Buenrostro Jason D. , Regev Aviv , Aerts Stein , Heyn Holger 
Published: August 2023

AbstractSingle-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.
Unique functional responses differentially map onto genetic subtypes of dopamine neurons
Authors: Azcorra Maite , Gaertner Zachary , Davidson Connor , He Qianzi , Kim Hailey , Nagappan Shivathmihai , Hayes Cooper K. , Ramakrishnan Charu , Fenno Lief , Kim Yoon Seok , Deisseroth Karl , Longnecker Richard , Awatramani Rajeshwar , Dombeck Daniel A. 
Published: August 2023

AbstractDopamine neurons are characterized by their response to unexpected rewards, but they also fire during movement and aversive stimuli. Dopamine neuron diversity has been observed based on molecular expression profiles; however, whether different functions map onto such genetic subtypes remains unclear. In this study, we established that three genetic dopamine neuron subtypes within the substantia nigra pars compacta, characterized by the expression of Slc17a6 (Vglut2), Calb1 and Anxa1, each have a unique set of responses to rewards, aversive stimuli and accelerations and decelerations, and these signaling patterns are highly correlated between somas and axons within subtypes. Remarkably, reward responses were almost entirely absent in the Anxa1+ subtype, which instead displayed acceleration-correlated signaling. Our findings establish a connection between functional and genetic dopamine neuron subtypes and demonstrate that molecular expression patterns can serve as a common framework to dissect dopaminergic functions.
Sialic acids Neu5Ac and KDN in adipose tissue samples from individuals following habitual vegetarian or non-vegetarian dietary patterns
Authors: Guerrero-Flores Gerardo N. , Pacheco Fabio J. , Boskovic Danilo S. , Pacheco Sandaly O. S. , Zhang Guangyu , Fraser Gary E. , Miles Fayth L. 
Published: August 2023

AbstractSialic acids (Sias) are a class of sugar molecules with a parent nine-carbon neuraminic acid, generally present at the ends of carbohydrate chains, either attached to cellular surfaces or as secreted glycoconjugates. Given their position and structural diversity, Sias modulate a wide variety of biological processes. However, little is known about the role of Sias in human adipose tissue, or their implications for health and disease, particularly among individuals following different dietary patterns. The goal of this study was to measure N-Acetylneuraminic acid (Neu5Ac), N-Glycolylneuraminic acid (Neu5Gc), and 2-keto-3-deoxy-d-glycero-d-galacto-nononic acid (KDN) concentrations in adipose tissue samples from participants in the Adventist Health Study-2 (AHS-2) and to compare the abundance of these Sias in individuals following habitual, long-term vegetarian or non-vegetarian dietary patterns. A method was successfully developed for the extraction and detection of Sias in adipose tissue. Sias levels were quantified in 52 vegans, 56 lacto-vegetarians, and 48 non-vegetarians using LC–MS/MS with Neu5Ac-D-1,2,3-13C3 as an internal standard. Dietary groups were compared using linear regression. Vegans and lacto-ovo-vegetarians had significantly higher concentrations of Neu5Ac relative to non-vegetarians. While KDN levels tended to be higher in vegans and lacto-ovo-vegetarians, these differences were not statistically significant. However, KDN levels were significantly inversely associated with body mass index. In contrast, Neu5Gc was not detected in human adipose samples. It is plausible that different Neu5Ac concentrations in adipose tissues of vegetarians, compared to those of non-vegetarians, reflect a difference in the baseline inflammatory status between the two groups. Epidemiologic studies examining levels of Sias in human adipose tissue and other biospecimens will help to further explore their roles in development and progression of inflammatory conditions and chronic diseases.
Search-and-rescue in the Central Mediterranean Route does not induce migration: Predictive modeling to answer causal queries in migration research
Authors: Rodríguez Sánchez Alejandra , Wucherpfennig Julian , Rischke Ramona , Iacus Stefano Maria 
Published: August 2023

AbstractState- and private-led search-and-rescue are hypothesized to foster irregular migration (and thereby migrant fatalities) by altering the decision calculus associated with the journey. We here investigate this ‘pull factor’ claim by focusing on the Central Mediterranean route, the most frequented and deadly irregular migration route towards Europe during the past decade. Based on three intervention periods—(1) state-led Mare Nostrum, (2) private-led search-and-rescue, and (3) coordinated pushbacks by the Libyan Coast Guard—which correspond to substantial changes in laws, policies, and practices of search-and-rescue in the Mediterranean, we are able to test the ‘pull factor’ claim by employing an innovative machine learning method in combination with causal inference. We employ a Bayesian structural time-series model to estimate the effects of these three intervention periods on the migration flow as measured by crossing attempts (i.e., time-series aggregate counts of arrivals, pushbacks, and deaths), adjusting for various known drivers of irregular migration. We combine multiple sources of traditional and non-traditional data to build a synthetic, predicted counterfactual flow. Results show that our predictive modeling approach accurately captures the behavior of the target time-series during the various pre-intervention periods of interest. A comparison of the observed and predicted counterfactual time-series in the post-intervention periods suggest that pushback policies did affect the migration flow, but that the search-and-rescue periods did not yield a discernible difference between the observed and the predicted counterfactual number of crossing attempts. Hence we do not find support for search-and-rescue as a driver of irregular migration. In general, this modeling approach lends itself to forecasting migration flows with the goal of answering causal queries in migration research.