bluuebunny/crossref_metadata_2025_split huggingface dataset:
Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells
Authors: Kobayashi-Ishihara Mie , Frazão Smutná Katarína , Alonso Florencia E. , Argilaguet Jordi , Esteve-Codina Anna , Geiger Kerstin , Genescà Meritxell , Grau-Expósito Judith , Duran-Castells Clara , Rogenmoser Selina , Böttcher René , Jungfleisch Jennifer , Oliva Baldomero , Martinez Javier P. , Li Manqing , David Michael , Yamagishi Makoto , Ruiz-Riol Marta , Brander Christian , Tsunetsugu-Yokota Yasuko , Buzon Maria J. , Díez Juana , Meyerhans Andreas 
Published: May 2023

AbstractLatency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 protein (SLFN12) as an HIV-1 restriction factor that establishes a post-transcriptional block in HIV-1-infected cells and thereby inhibits HIV-1 replication and virus reactivation from latently infected cells. The inhibitory activity is dependent on the HIV-1 codon usage and on the SLFN12 RNase active sites. Within HIV-1-infected individuals, SLFN12 expression in PBMCs correlated with HIV-1 plasma viral loads and proviral loads suggesting a link with the general activation of the immune system. Using an RNA FISH-Flow HIV-1 reactivation assay, we demonstrate that SLFN12 expression is enriched in infected cells positive for HIV-1 transcripts but negative for HIV-1 proteins. Thus, codon-usage dependent translation inhibition of HIV-1 proteins participates in HIV-1 latency and can restrict the amount of virus release after latency reversal.
Nitric oxide is a host cue for Salmonella Typhimurium systemic infection in mice
Authors: Jiang Lingyan , Li Wanwu , Hou Xi , Ma Shuai , Wang Xinyue , Yan Xiaolin , Yang Bin , Huang Di , Liu Bin , Feng Lu 
Published: May 2023

AbstractNitric oxide (NO) is produced as an innate immune response against microbial infections. Salmonella Typhimurium (S. Typhimurium), the major causative pathogen of human gastroenteritis, induces more severe systemic disease in mice. However, host factors contributing to the difference in species-related virulence are unknown. Here, we report that host NO production promotes S. Typhimurium replication in mouse macrophages at the early infection stage by activating Salmonella pathogenicity island-2 (SPI-2). The NO signaling-induced SPI-2 activation is mediated by Fnr and PhoP/Q two-component system. NO significantly induced fnr transcription, while Fnr directly activated phoP/Q transcription. Mouse infection assays revealed a NO-dependent increase in bacterial burden in systemic organs during the initial days of infection, indicating an early contribution of host NO to virulence. This study reveals a host signaling-mediated virulence activation pathway in S. Typhimurium that contributes significantly to its systemic infection in mice, providing further insights into Salmonella pathogenesis and host–pathogen interaction.
Introducing field evaporation energy loss spectroscopy
Authors: Rousseau Loïc , Normand Antoine , Morgado Felipe F. , Marie Scisly Søreide Hanne-Sofie , Stephenson Leigh T. , Hatzoglou Constantinos , Da Costa Gérald , Tehrani Kambiz , Freysoldt Christoph , Gault Baptiste , Vurpillot François 
Published: May 2023

AbstractRetrieving information on the chemical and bonding states of atoms in a material in three-dimensions is challenging even for the most advanced imaging techniques. Here, we demonstrate that this information is accessible via straight-flight-path atom probe tomography experimental data, however it requires additional processing. Using an activation energy model that involves linear field dependance, and complementing it with DFT simulations, we extract the ion energy loss related to the kinetics of the field evaporation process from the mass peak shape. In turn, we reconstruct how evaporated atoms were originally bound to the surface. We name our data processing approach evaporation energy loss spectroscopy (FEELS), and showcase its application by analyzing microstructural features and defects in an array of metallic materials. Finally, we discuss the general applicability of FEELS to any atom probe data set.
Observing high-k magnons with Mie-resonance-enhanced Brillouin light scattering
Authors: Wojewoda Ondřej , Ligmajer Filip , Hrtoň Martin , Klíma Jan , Dhankhar Meena , Davídková Kristýna , Staňo Michal , Holobrádek Jakub , Krčma Jakub , Zlámal Jakub , Šikola Tomáš , Urbánek Michal 
Published: May 2023

AbstractLocal probing of dynamic excitations such as magnons and phonons in materials and nanostructures can bring new insights into their properties and functionalities. For example, in magnonics, many concepts and devices recently demonstrated at the macro- and microscale now need to be realized at the nanoscale. Brillouin light scattering (BLS) spectroscopy and microscopy has become a standard technique for spin wave characterization, and enabled many pioneering magnonic experiments. However, the conventional BLS cannot detect nanoscale waves due to its fundamental limit in maximum detectable quasiparticle momentum. Here we show that optically induced Mie resonances in nanoparticles can be used to extend the range of accessible quasiparticle’s wavevectors beyond the BLS fundamental limit. These experiments involve the measurement of thermally excited as well as coherently excited high momentum magnons. Our findings demonstrate the capability of Mie-enhanced BLS and significantly extend the usability of BLS microscopy for magnonic and phononic research.
Investigating the electronic states of UTe2 using X-ray spectroscopy
Authors: Wilhelm Fabrice , Sanchez Jean-Pierre , Braithwaite Daniel , Knebel Georg , Lapertot Gérard , Rogalev Andrei 
Published: May 2023

AbstractThe recent discovery of superconductivity in paramagnetic UTe2 turns spotlight on a serious candidate for spin-triplet state. To draw a complete picture of the superconducting state in UTe2 precise knowledge of the electronic properties of the 5 f states of Uranium is missing. We report on x-ray absorption and magnetic circular dichroism experiments performed at the U M4,5 edges at 2.7 K. At ambient pressure the 5 f electron count is found to be in-between 2.6 and 2.8. Partial delocalization of the 5 f electrons is further confirmed by the reduced value of the U orbital to spin magnetic moment ratio. The 5 f count is reduced by as large as 7 percent at the transition to a magnetically ordered state at Pc ≈ 1.5 GPa. At pressures above 4 GPa, the 5 f count increases back towards U3+ in the tetragonal phase. The observed “valence instabilities” and their interplay with magnetism seem to be important ingredients to understand the electronic structure in UTe2 in different phases.
Landslide susceptibility modeling by interpretable neural network
Authors: Youssef K. , Shao K. , Moon S. , Bouchard L.-S. 
Published: May 2023

AbstractLandslides are notoriously difficult to predict because numerous spatially and temporally varying factors contribute to slope stability. Artificial neural networks (ANN) have been shown to improve prediction accuracy but are largely uninterpretable. Here we introduce an additive ANN optimization framework to assess landslide susceptibility, as well as dataset division and outcome interpretation techniques. We refer to our approach, which features full interpretability, high accuracy, high generalizability and low model complexity, as superposable neural network (SNN) optimization. We validate our approach by training models on landslide inventories from three different easternmost Himalaya regions. Our SNN outperformed physically-based and statistical models and achieved similar performance to state-of-the-art deep neural networks. The SNN models found the product of slope and precipitation and hillslope aspect to be important primary contributors to high landslide susceptibility, which highlights the importance of strong slope-climate couplings, along with microclimates, on landslide occurrences.
Half of the greenhouse gas emissions from China’s food system occur during food production
Authors: Liu Gang , Zhang Fan , Deng Xiangzheng 
Published: May 2023

AbstractFood systems are responsible for a third of global anthropogenic greenhouse gas emissions and there has been an increasing research focus on food-system greenhouse gases. However, limited attention has been paid to emissions from the regional trade network associated with food systems. Here we developed a multi-regional input-output-based hybrid life cycle assessment model and traced China’s food-system greenhouse gas emissions from farm to fork. China’s food system emitted 2.4 (95%; confidence interval range: 1.6–3.2) gigatons CO2-equivalent in 2019, and half were emitted at the production stage. There were substantial differences in the emission structure and sources among the provinces. Further analysis indicated that the differences among provinces were caused by the separation of food production and consumption. People living in wealthier coastal and central regions consumed food from western and northeastern regions. Therefore, the government should consider interregional synergies when developing strategies to reduce food-system greenhouse gas emissions.
Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes
Authors: McCully Alexandra L , Loop Yao McKenna , Brower Kara K , Fordyce Polly M , Spormann Alfred M 
Published: May 2023

Abstract
Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.
Functionally distinct mutations within AcrB underpin antibiotic resistance in different lifestyles
Authors: Trampari Eleftheria , Prischi Filippo , Vargiu Attilio V. , Abi-Assaf Justin , Bavro Vassiliy N. , Webber Mark A. 
Published: May 2023

AbstractAntibiotic resistance is a pressing healthcare challenge and is mediated by various mechanisms, including the active export of drugs via multidrug efflux systems, which prevent drug accumulation within the cell. Here, we studied how Salmonella evolved resistance to two key antibiotics, cefotaxime and azithromycin, when grown planktonically or as a biofilm. Resistance to both drugs emerged in both conditions and was associated with different substitutions within the efflux-associated transporter, AcrB. Azithromycin exposure selected for an R717L substitution, while cefotaxime for Q176K. Additional mutations in ramR or envZ accumulated concurrently with the R717L or Q176K substitutions respectively, resulting in clinical resistance to the selective antibiotics and cross-resistance to other drugs. Structural, genetic, and phenotypic analysis showed the two AcrB substitutions confer their benefits in profoundly different ways. R717L reduces steric barriers associated with transit through the substrate channel 2 of AcrB. Q176K increases binding energy for cefotaxime, improving recognition in the distal binding pocket, resulting in increased efflux efficiency. Finally, we show the R717 substitution is present in isolates recovered around the world.
Matching LOFAR sources across radio bands
Authors: Böhme L. , Schwarz D. J. , de Gasperin F. , Röttgering H. J. A. , Williams W. L. 
Published: May 2023

Aims. The recent preliminary release of the LOFAR LBA Sky Survey (LoLSS) is the first wide-area, ultra-low frequency observation published from the Low Frequency Array (LOFAR). Our aim is to combine this data set with other surveys at higher frequencies to study the spectral properties of a large sample of radio sources.
Methods. We present a new cross-matching algorithm that takes into account the sizes of the radio sources. We applied it to the LoLSS-PR, LoTSS-DR1, LoTSS-DR2 (all LOFAR), TGSS-ADR1 (GMRT), WENSS (WSRT), and NVSS (VLA) catalogues. We then studied the number of matched counterparts for LoLSS radio sources and their spectral properties.
Results. We found counterparts for 22 607 (89.5%) LoLSS sources. The remaining 2640 sources (10.5%) were identified either as an artefact in the LoLSS survey (3.6%) or flagged due to their closeness to bright sources (6.9%). We found an average spectral index of α = −0.77 ± 0.18 between LoLSS and NVSS. Between LoLSS and LoTSS-DR2, we found α = −0.71 ± 0.31. The average spectral index is independent of the flux density above S54 = 181 mJy. A comparison of the spectral slopes from LoLSS-LoTSS-DR2 with LoTSS-DR2–NVSS indicates that the probed population of radio sources shows evidence of a negative spectral curvature.
Persistent and occasional: Searching for the variable population of the ZTF/4MOST sky using ZTF Data Release 11
Authors: Sánchez-Sáez P. , Arredondo J. , Bayo A. , Arévalo P. , Bauer F. E. , Cabrera-Vives G. , Catelan M. , Coppi P. , Estévez P. A. , Förster F. , Hernández-García L. , Huijse P. , Kurtev R. , Lira P. , Muñoz Arancibia A. M. , Pignata G. 
Published: May 2023

Aims.We present a variability-, color-, and morphology-based classifier designed to identify multiple classes of transients and persistently variable and non-variable sources from the Zwicky Transient Facility (ZTF) Data Release 11 (DR11) light curves of extended and point sources. The main motivation to develop this model was to identify active galactic nuclei (AGN) at different redshift ranges to be observed by the 4MOST Chilean AGN/Galaxy Evolution Survey (ChANGES). That being said, it also serves as a more general time-domain astronomy study.Methods.The model uses nine colors computed from CatWISE and Pan-STARRS1 (PS1), a morphology score from PS1, and 61 single-band variability features computed from the ZTF DR11gandrlight curves. We trained two versions of the model, one for each ZTF band, since ZTF DR11 treats the light curves observed in a particular combination of field, filter, and charge-coupled device (CCD) quadrant independently. We used a hierarchical local classifier per parent node approach-where each node is composed of a balanced random forest model. We adopted a taxonomy with 17 classes: non-variable stars, non-variable galaxies, three transients (SNIa, SN-other, and CV/Nova), five classes of stochastic variables (lowz-AGN, midz-AGN, highz-AGN, Blazar, and YSO), and seven classes of periodic variables (LPV, EA, EB/EW, DSCT, RRL, CEP, and Periodic-other).Results.The macro-averaged precision, recall, and F1-score are 0.61, 0.75, and 0.62 for theg-band model, and 0.60, 0.74, and 0.61, for ther-band model. When grouping the four AGN classes (lowz-AGN, midz-AGN, highz-AGN, and Blazar) into one single class, its precision-recall, and F1-score are 1.00, 0.95, and 0.97, respectively, for both thegandrbands. This demonstrates the good performance of the model in classifying AGN candidates. We applied the model to all the sources in the ZTF/4MOST overlapping sky (−28 ≤ Dec ≤ 8.5), avoiding ZTF fields that cover the Galactic bulge (|gal_b| ≤ 9 andgal_l≤ 50). This area includes 86 576 577 light curves in thegband and 140 409 824 in therband with 20 or more observations and with an average magnitude in the corresponding band lower than 20.5. Only 0.73% of theg-band light curves and 2.62% of ther-band light curves were classified as stochastic, periodic, or transient with high probability (Pinit≥ 0.9). Even though the metrics obtained for the two models are similar, we find that, in general, more reliable results are obtained when using theg-band model. With it, we identified 384 242 AGN candidates (including low-, mid-, and high-redshift AGN and Blazars), 287 156 of which havePinit≥ 0.9.
Stellar pulsations interfering with the transit light curve: Configurations with false positive misalignment
Authors: Bókon A. , Kálmán Sz. , Bíró I. B. , Szabó M. Gy. 
Published: May 2023

Aims. Asymmetric features in exoplanet transit light curves are often interpreted as an effect of gravity darkening, especially if there is spectroscopic evidence of a spin-orbit misalignment. Since other processes can also lead to light-curve asymmetries, this may lead to inaccurate gravity darkening parameters. Here, we investigate the case of non-radial pulsations as possible sources of asymmetry and likely source of misinterpreted parameters through simulations.
Methods. We obtained a series of simulated transit light curves of a hypothetical exoplanet-star system constructed to study the phenomenon: a host star with no gravity darkening exhibiting small amplitude pulsations and a typical hot Jupiter in a circular, edge-on orbit. Multiple scenarios of single- or multi-periodic, radial-, or non-radial pulsations of various amplitudes have been considered, and a proper account of the obscuring effect of transits on all the surface intensity components was carried out. The magnitude of amplitude and phase modulations of non-radial pulsations during transits was also also investigated. We then fit both a non-gravity-darkened and a gravity-darkened free spin-orbit axis model on the data. The Akaike and Bayesian information criteria were used for an objective selection of the most plausible model. We then explored the dependence of the parameter deviations on the pulsation properties to identify the specific configurations that may lead to falsely misaligned solutions.
Results. The modulation of amplitudes of non-radial pulsations during transits have extremely low levels, so that the non-radial nature of pulsations can be safely ignored. Low-amplitude pulsations generally do not affect the determination of the system parameters beyond their noise properties. However, frequencies close to multiples of the orbital frequency (n * forb) are found to cause distortions, leading to solutions that involve a side tilted stellar rotational axis; therefore, it is preferable to clean them beforehand for the sake of a improved accuracy. Additionally, in cases with higher amplitude pulsations, a preprocessing and cleaning of the pulsations before the analysis is recommended.
New thermosphere neutral mass density and crosswind datasets from CHAMP, GRACE, and GRACE-FO
Authors: Siemes Christian , Borries Claudia , Bruinsma Sean , Fernandez-Gomez Isabel , Hładczuk Natalia , den IJssel Josevan , Kodikara Timothy , Vielberg Kristin , Visser Pieter 
Published: May 2023

We present new neutral mass density and crosswind observations for the CHAMP, GRACE, and GRACE-FO missions, filling the last gaps in our database of accelerometer-derived thermosphere observations. For consistency, we processed the data over the entire lifetime of these missions, noting that the results for GRACE in 2011–2017 and GRACE-FO are entirely new. All accelerometer data are newly calibrated. We modeled the temperature-induced bias variations for the GRACE accelerometer data to counter the detrimental effects of the accelerometer thermal control deactivation in April 2011. Further, we developed a new radiation pressure model, which uses ray tracing to account for shadowing and multiple reflections and calculates the satellite’s thermal emissions based on the illumination history. The advances in calibration and radiation pressure modeling are essential when the radiation pressure acceleration is significant compared to the aerodynamic one above 450 km altitude during low solar activity, where the GRACE and GRACE-FO satellites spent a considerable fraction of their mission lifetime. The mean of the new density observations changes only marginally, but their standard deviation shows a substantial reduction compared to thermosphere models, up to 15% for GRACE in 2009. The mean and standard deviation of the new GRACE-FO density observations are in good agreement with the GRACE observations. The GRACE and CHAMP crosswind observations agree well with the physics-based TIE-GCM winds, particularly the polar wind patterns. The mean observed crosswind is a few tens of m·s−1larger than the model one, which we attribute primarily to the crosswind errors being positive by the definition of the retrieval algorithm. The correlation between observed and model crosswind is about 60%, except for GRACE in 2004–2011 when the signal was too small to retrieve crosswinds reliably.
Artificial intelligence in radiology – beyond the black box
Authors: Gallée Luisa , Kniesel Hannah , Ropinski Timo , Götz Michael 
Published: May 2023

Background Artificial intelligence is playing an increasingly important role in radiology. However, more and more often it is no longer possible to reconstruct decisions, especially in the case of new and powerful methods from the field of deep learning. The resulting models fulfill their function without the users being able to understand the internal processes and are used as so-called black boxes. Especially in sensitive areas such as medicine, the explainability of decisions is of paramount importance in order to verify their correctness and to be able to evaluate alternatives. For this reason, there is active research going on to elucidate these black boxes.
Method This review paper presents different approaches for explainable artificial intelligence with their advantages and disadvantages. Examples are used to illustrate the introduced methods. This study is intended to enable the reader to better assess the limitations of the corresponding explanations when meeting them in practice and strengthen the integration of such solutions in new research projects.
Results and Conclusion Besides methods to analyze black-box models for explainability, interpretable models offer an interesting alternative. Here, explainability is part of the process and the learned model knowledge can be verified with expert knowledge.
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Recent Advances in the Synthesis of 5-(Hetero)aryl Uracil Derivatives
Authors: Cheng Liang , Wang Zhao-Li , Liu An-Di , Liu Li 
Published: May 2023

AbstractC5-Aryl/heteroaryl uracil-based compounds have attracted continuous interest because of their wide biological potential. In this review, we outline the primary synthetic methods used to prepare designated uracils, various combinations of which have been used to synthesize target compounds with potential biological activities. The significance of each approach and its limitations are also summarized.1	Introduction2	Coupling of Prefunctionalized Uracils with (Hetero)aryl Reagents2.1	Negishi Coupling2.2	Suzuki–Miyaura Coupling2.3	Stille Coupling3	Coupling of Functionalized Uracils with Nonactivated Aromatic (Hetero)cycles3.1	Photochemically Induced Coupling3.2	Palladium-Catalyzed Coupling4	Coupling of Nonactivated Uracil/Uridine with Functionalized Aromatic (Hetero)cycles4.1	Electrochemical Reduction4.2	Transition-Metal-Catalyzed Coupling4.3	Light-Promoted Coupling of Uracils with Diazonium Salts5	Direct Coupling of Nonactivated Uracils with Nonactivated Aromatic (Hetero)cycles6	Summary and Prospects