bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast strains isolated from fermented beverage produce extracellular vesicles with anti-inflammatory effects
Authors: Nenciarini Stefano , Amoriello Roberta , Bacci Giovanni , Cerasuolo Benedetta , Di Paola Monica , Nardini Patrizia , Papini Alessio , Ballerini Clara , Cavalieri Duccio 
Published: January 2024

AbstractExtracellular vesicles (EVs) are lipid-bilayered particles, containing various biomolecules, including nucleic acids, lipids, and proteins, released by cells from all the domains of life and performing multiple communication functions. Evidence suggests that the interaction between host immune cells and fungal EVs induces modulation of the immune system. Most of the studies on fungal EVs have been conducted in the context of fungal infections; therefore, there is a knowledge gap in what concerns the production of EVs by yeasts in other contexts rather than infection and that may affect human health. In this work, we characterized EVs obtained by Saccharomyces cerevisiae and Pichia fermentans strains isolated from a fermented milk product with probiotic properties. The immunomodulation abilities of EVs produced by these strains have been studied in vitro through immune assays after internalization from human monocyte-derived dendritic cells. Results showed a significant reduction in antigen presentation activity of dendritic cells treated with the fermented milk EVs. The small RNA fraction of EVs contained mainly yeast mRNA sequences, with a few molecular functions enriched in strains of two different species isolated from the fermented milk. Our results suggest that one of the mechanisms behind the anti-inflammatory properties of probiotic foods could be mediated by the interactions of human immune cells with yeast EVs.
Acute ischemic stroke prediction and predictive factors analysis using hematological indicators in elderly hypertensives post-transient ischemic attack
Authors: Shu Chang , Zheng Chenguang , Luo Da , Song Jie , Jiang Zhengyi , Ge Le 
Published: January 2024

AbstractElderly hypertensive patients diagnosed with transient ischemic attack (TIA) are at a heightened risk for developing acute ischemic stroke (AIS). This underscores the critical need for effective risk prediction and identification of predictive factors. In our study, we utilized patient data from peripheral blood tests and clinical profiles within hospital information systems. These patients were followed for a three-year period to document incident AIS. Our cohort of 11,056 individuals was randomly divided into training, validation, and testing sets in a 5:2:3 ratio. We developed an XGBoost model, developed using selected indicators, provides an effective and non-invasive method for predicting the risk of AIS in elderly hypertensive patients diagnosed with TIA. Impressively, this model achieved a balanced accuracy of 0.9022, a recall of 0.8688, and a PR-AUC of 0.9315. Notably, our model effectively encapsulates essential data variations involving mixed nonlinear interactions, providing competitive performance against more complex models that incorporate a wider range of variables. Further, we conducted an in-depth analysis of the importance and sensitivity of each selected indicator and their interactions. This research equips clinicians with the necessary tools for more precise identification of high-risk individuals, thereby paving the way for more effective stroke prevention and management strategies.
Volcanic forcing of high-latitude Northern Hemisphere eruptions
Authors: Fuglestvedt Herman F. , Zhuo Zhihong , Toohey Matthew , Krüger Kirstin 
Published: January 2024

AbstractHigh-latitude explosive volcanic eruptions can cause substantial hemispheric cooling. Here, we use a whole-atmosphere chemistry-climate model to simulate Northern Hemisphere (NH) high-latitude volcanic eruptions of magnitude similar to the 1991 Mt. Pinatubo eruption. Our simulations reveal that the initial stability of the polar vortex strongly influences sulphur dioxide lifetime and aerosol growth by controlling the dispersion of injected gases after such eruptions in winter. Consequently, atmospheric variability introduces a spread in the cumulative aerosol radiative forcing of more than 20%. We test the aerosol evolution’s sensitivity to co-injection of sulphur and halogens, injection season, and altitude, and show how aerosol processes impact radiative forcing. Several of these sensitivities are of similar magnitude to the variability stemming from initial conditions, highlighting the significant influence of atmospheric variability. We compare the modelled volcanic sulphate deposition over the Greenland ice sheet with the relationship assumed in reconstructions of past NH eruptions. Our analysis yields an estimate of the Greenland transfer function for NH extratropical eruptions that, when applied to ice core data, produces volcanic stratospheric sulphur injections from NH extratropical eruptions 23% smaller than in currently used volcanic forcing reconstructions. Furthermore, the transfer function’s uncertainty, which propagates into the estimate of sulphur release, needs to be at least doubled to account for atmospheric variability and unknown eruption parameters. Our results offer insights into the processes shaping the climatic impacts of NH high-latitude eruptions and highlight the need for more accurate representation of these events in volcanic forcing reconstructions.
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information
Authors: Giulini Marco , Honorato Rodrigo V. , Rivera Jesús L. , Bonvin Alexandre M. J. J. 
Published: January 2024

AbstractThe formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data. We demonstrate its use by various examples ranging from showing the increased interaction complexity of eukaryotic proteins, 20% of which on average have more than 3 different interfaces compared to only 10% for prokaryotes, to associating different functions to different interfaces. In the context of modelling biomolecular assemblies, we introduce the concept of “recognition entropy”, related to the number of possible interfaces of the components of a protein-protein complex, which we demonstrate to correlate with the modelling difficulty in classical docking approaches. The identified interface clusters can also be used to generate various combinations of interface-specific restraints for integrative modelling. The ARCTIC-3D software is freely available at github.com/haddocking/arctic3d and can be accessed as a web-service at wenmr.science.uu.nl/arctic3d.
Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling
Authors: Raybould Matthew I. J. , Turnbull Oliver M. , Suter Annabel , Guloglu Bora , Deane Charlotte M. 
Published: January 2024

AbstractAntibodies with lambda light chains (λ-antibodies) are generally considered to be less developable than those with kappa light chains (κ-antibodies). Though this hypothesis has not been formally established, it has led to substantial systematic biases in drug discovery pipelines and thus contributed to kappa dominance amongst clinical-stage therapeutics. However, the identification of increasing numbers of epitopes preferentially engaged by λ-antibodies shows there is a functional cost to neglecting to consider them as potential lead candidates. Here, we update our Therapeutic Antibody Profiler (TAP) tool to use the latest data and machine learning-based structure prediction, and apply it to evaluate developability risk profiles for κ-antibodies and λ-antibodies based on their surface physicochemical properties. We find that while human λ-antibodies on average have a higher risk of developability issues than κ-antibodies, a sizeable proportion are assigned lower-risk profiles by TAP and should represent more tractable candidates for therapeutic development. Through a comparative analysis of the low- and high-risk populations, we highlight opportunities for strategic design that TAP suggests would enrich for more developable λ-antibodies. Overall, we provide context to the differing developability of κ- and λ-antibodies, enabling a rational approach to incorporate more diversity into the initial pool of immunotherapeutic candidates.
Carbapenem-resistant Escherichia coli exhibit diverse spatiotemporal epidemiological characteristics across the globe
Authors: Huang Jiewen , Lv Chao , Li Min , Rahman Tanvir , Chang Yung-Fu , Guo Xiaokui , Song Zhen , Zhao Yanan , Li Qingtian , Ni Peihua , Zhu Yongzhang 
Published: January 2024

AbstractCarbapenem-resistant Escherichia coli (CREC) poses a severe global public health risk. This study reveals the worldwide geographic spreading patterns and spatiotemporal distribution characteristics of resistance genes in 7918 CREC isolates belonging to 497 sequence types (ST) and originating from 75 countries. In the last decade, there has been a transition in the prevailing STs from highly virulent ST131 and ST38 to higher antibiotic-resistant ST410 and ST167. The rise of multi-drug resistant strains of CREC carrying plasmids with extended-spectrum beta-lactamase (ESBL) resistance genes could be attributed to three important instances of host-switching events. The spread of CREC was associated with the changing trends in blaNDM-5, blaKPC-2, and blaOXA-48, as well as the plasmids IncFI, IncFII, and IncI. There were intercontinental geographic transfers of major CREC strains. Various crucial transmission hubs and patterns have been identified for ST131 in the United Kingdom, Italy, the United States, and China, ST167 in India, France, Egypt, and the United States, and ST410 in Thailand, Israel, the United Kingdom, France, and the United States. This work is valuable in managing CREC infections and preventing CREC occurrence and transmission inside healthcare settings and among diverse hosts.
High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species
Authors: Fleck Steven J. , Tomlin Crystal , da Silva Coelho Flavio Augusto , Richter Michaela , Danielson Erik S. , Backenstose Nathan , Krabbenhoft Trevor , Lindqvist Charlotte , Albert Victor A. 
Published: January 2024

AbstractWith populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.
Absence of the Great Whirl giant ocean vortex abates productivity in the Somali upwelling region
Authors: Jebri Fatma , Srokosz Meric , Raitsos Dionysios E. , Jacobs Zoe L. , Sanchez-Franks Alejandra , Popova Ekaterina 
Published: January 2024

AbstractSomali upwelling is the fifth largest upwelling globally with high productivity, attracting tuna migratory species. A key control on the upwelling productivity is its interaction with one of the world’s largest oceanic eddies, the Great Whirl inducing a strong downwelling signal. Here, we use satellite-derived observations to determine the Great Whirl impact on the extent of the upwelling-driven phytoplankton bloom. We find that following decreases in upwelling intensity, productivity has declined by about 10% over the past two decades. The bloom extent has also been diminishing with an abrupt decrease around 2006–2007, coinciding with an abrupt increase in the downwelling effect. Absent or weak Great Whirl leads to the occurrence of smaller anticyclonic eddies with a resulting downwelling stronger than when the Great Whirl is present. We suggest that 2006–2007 abrupt changes in the bloom and downwelling extents’ regimes, are likely driven by Indian Ocean Dipole abrupt shift in 2006.
Modeling the scattering polarization in the solar Ca I 4227Å line with angle-dependent PRD effects and bulk velocities
Authors: Guerreiro N. , Janett G. , Riva S. , Benedusi P. , Belluzzi L. 
Published: January 2024

Context. Modeling the scattering polarization signals of strong chromospheric lines requires solving the radiative transfer problem for polarized radiation, out of local thermodynamic equilibrium, taking partial frequency redistribution (PRD) effects into account. This problem is extremely challenging from a computational standpoint and, so far, most studies have been carried out by either modeling PRD effects under the angle-average approximation or by considering academic models of the solar atmosphere. Thanks to a new solution strategy, applicable to atomic systems that allow for a linearization of the problem, accurate solutions can now be routinely obtained in realistic 1D models, taking angle-dependent (AD) PRD effects into account.
Aims. This work is aimed at assessing the suitability and performance of this new approach to handling dynamic scenarios. At the same time, it aims to explore the joint impact of magnetic fields and bulk velocities on the scattering polarization profiles of strong resonance lines, accounting for AD PRD effects and considering more realistic atmospheric models than in previous investigations.
Methods. By using a two-level atomic model for neutral calcium, we synthesized the intensity and polarization profiles of the Ca I 4227 Å line. Our calculations were performed in 1D atmospheric models, both semi-empirical and extracted from 3D magnetohydrodynamic simulations, including vertical bulk velocities and magnetic fields of arbitrary strength and orientation, both constant and varying with height.
Results. We obtained accurate solutions after only a few iterations across all considered scenarios. Even when formulating the problem in the observer’s reference frame, the frequency and angular grids required for accurate results were easily manageable. The calculated profiles showed the expected signatures of bulk velocities: wavelength shifts, enhancement of the line-core polarization amplitude, and prominent asymmetries in the wing signals. The results obtained in atmospheric models with complex thermal, dynamic, and magnetic structures unveiled the broad diversity of features in the emergent radiation that can be expected from realistic scenarios.
Conclusions. The presented results assess the suitability of the proposed solution strategy and its parallel implementation, thus supporting its generalization to the 3D case. Our applications in increasingly realistic atmospheric models showed the difficulty related to precisely establishing the individual weight of bulk velocities and magnetic fields in the shape of the emergent profiles. This highlights the need to account for both these physical ingredients to perform reliable inversions of observed scattering polarization profiles.
The orbit of HD 142527 B is too compact to explain many of the disc features
Authors: Nowak M. , Rowther S. , Lacour S. , Meru F. , Nealon R. , Price D. J. 
Published: January 2024

Context. HD 142527 A is a young and massive Herbig Ae/Be star surrounded by a highly structured disc. The disc shows numerous morphological structures, such as spiral arms, a horseshoe region of dust emission, a set of shadows cast by an inner disc on the outer disc, and a large cavity extending from ≃30 au to ≃130 au. HD 142527 A also has a lower mass companion, HD 142527 B (M = 0.13 ± 0.03 M⊙), which is thought to be responsible for most of the structures observed in the surrounding disc.
Aims. We aim to fully constrain the orbit of HD 142527 B and determine whether the binary alone is truly responsible for the observed morphology of the HD 142527 disc.
Methods. We gathered VLTI/GRAVITY observations of HD 142527, either from our own programmes or from the ESO archive. We used this inhomogeneous set of data to extract a total of seven high-precision measurements of the relative astrometry between HD 142527 A and B, spread from mid-2017 to early 2021. Combined with what is available in the literature, these new measurements offer a total of 9 yr of astrometric monitoring on HD 142527. We used orbit fitting tools to determine the orbital parameters of HD 142527 B, and used them as inputs for a 3D hydrodynamical model of the disc to determine whether or not the binary is able to create the structures observed in the disc.
Results. Our VLTI/GRAVITY astrometry gives excellent constraints on the orbit of HD 142527 B. We show that the secondary is following an orbit of semi-major axis a = 10.80 ± 0.22 au, with moderate eccentricity (e = 0.47 ± 0.01), and has recently passed its periapsis (τ = 2020.42). With such a compact orbit, we show that HD 142527 B can only generate a gap and spiral arms of ~30 au in the disc, which is much smaller than what is revealed by observations.
Conclusions. Even from a theoretical standpoint, the observed cavity size of ~ 100 au far exceeds even the most generous predictions for a companion like HD 142527 B on such a compact orbit. Thus, we conclude that the low-mass companion cannot be solely responsible for the observed morphology of the disc surrounding the system.
Measuring precise radial velocities on individual spectral lines
Authors: Al Moulla K. , Dumusque X. , Cretignier M. 
Published: January 2024

Context. Radial velocities (RVs) of stars contain both the Doppler reflex motion of potential planetary companions and the drowning and sometimes imitating effect of stellar activity. To separate the two, previous efforts have sought proxies that only trace the activity signals, yet the sub-meter-per-second floor required for the detection of Earth-like planets remains difficult to break.
Aims. In this work, we analyze a sample of 12 G- to early M-type stars in order to investigate the feasibility of detecting a differential effect of stellar activity with photospheric depth, as traced by the spectral line-forming temperature, for observations with different sampling and noise levels.
Methods. We computed the average line formation temperature for each point in the observed wavelength grids using the spectral synthesis code PySME. The final line selection was curated to exclude blended and poorly synthesized lines. We thereafter computed the convective blueshift (CB) of the line cores of our master spectra (composed of the stacked individual spectra of each star). Finally, we extracted RV time series for certain intervals of formation temperature using a template-matching approach.
Results. We find the CB to follow a linear relation with the formation temperature of the line cores, and the CB slope to be steeper with increasing effective temperature. For the RV time series derived for different intervals of formation temperature, we find the RVs of line parts formed at higher temperatures, close to the spectral continuum, to be generally correlated with the S index, and the RVs of line parts formed at cooler temperatures, close to the spectral line cores, to be generally anti-correlated, especially for stars with low noise levels and significant variations over their magnetic cycles.
Conclusions. RVs of line parts formed in the coolest 25% of the line-forming temperature range appear to be a strong tracer of stellar activity over the magnetic cycle for several stars. By detrending the total RV time series with a multi-linear combination of residuals of RVs measured at different temperature ranges and the S index, the RV scatter can be decreased to a greater extent than with the S index alone.
FlopPITy: Enabling self-consistent exoplanet atmospheric retrievals with machine learning
Authors: Ardévol Martínez F. , Min M. , Huppenkothen D. , Kamp I. , Palmer P. I. 
Published: January 2024

Context. Interpreting the observations of exoplanet atmospheres to constrain physical and chemical properties is typically done using Bayesian retrieval techniques. Since these methods require many model computations, a compromise must be made between the model’s complexity and its run time. Achieving this compromise leads to a simplification of many physical and chemical processes (e.g. parameterised temperature structure).
Aims. Here, we implement and test sequential neural posterior estimation (SNPE), a machine learning inference algorithm for atmospheric retrievals for exoplanets. The goal is to speed up retrievals so they can be run with more computationally expensive atmospheric models, such as those computing the temperature structure using radiative transfer.
Methods. We generated 100 synthetic observations using ARtful Modeling Code for exoplanet Science (ARCiS), which is an atmospheric modelling code with the flexibility to compute models across varying degrees of complexity and to perform retrievals on them to test the faithfulness of the SNPE posteriors. The faithfulness quantifies whether the posteriors contain the ground truth as often as we expect. We also generated a synthetic observation of a cool brown dwarf using the self-consistent capabilities of ARCiS and ran a retrieval with self-consistent models to showcase the possibilities opened up by SNPE.
Results. We find that SNPE provides faithful posteriors and is therefore a reliable tool for exoplanet atmospheric retrievals. We are able to run a self-consistent retrieval of a synthetic brown dwarf spectrum using only 50 000 forward model evaluations. We find that SNPE can speed up retrievals between ∼2× and ≥10× depending on the computational load of the forward model, the dimensionality of the observation, and its signal-to-noise ratio (S/N). We have made the code publicly available for the community on Github.
Synthesis of a New Heterocyclic System: Pyrimidine Structural Analogues of Natural Integrastatins A, B
Authors: Kulakov Ivan V. , Chikunov Semyon Y. , Pustolaikina Irina A. , Gatilov Yuriy V. 
Published: January 2024

AbstractIn this paper for the first time, we report a simple one-step synthesis of 5-methyl-11,12-dihydro-5H-5,11-epoxybenzo[7,8]oxocino[4,3-d]pyrimidine derivatives by acid-catalyzed cyclization reaction of various 4-methyl-5-acetyl pyrimidine derivatives with salicylic aldehyde. It was shown that 2-substituted 4-methyl-5-acetylpyrimidines successfully react to form a cyclization product. At the same time, 4-methyl-5-acetylpyrimidines with a substituent in the 6th position do not enter into the cyclization reaction. This may be caused by the negative effect of substituents in the 6th position, which hinder the free rotation of the acetyl group and prevent the formation of a stable pre-reaction complex. The structures of the obtained 5-methyl-11,12-dihydro-5H-5,11-epoxybenzo[7,8]oxocino[4,3-d]pyrimidine derivatives were confirmed using 1H NMR and 13C NMR spectroscopy, mass spectrometry, and X-ray diffraction analysis.
Retraction Note: The Role of Religious Coping in Neonatal Intensive Care Unit
Authors: Çaksen Hüseyin 
Published: January 2024

RetractionThe above article published in Journal of Child Science in Volume 13, Number 01, e54–e57, on May 4, 2023 (DOI: 10.1055/s-0043-1768637), has been retracted as it is lacking scientific base.