bluuebunny/crossref_metadata_2025_split huggingface dataset:
Terahertz electric-field-driven dynamical multiferroicity in SrTiO3
Authors: Basini M. , Pancaldi M. , Wehinger B. , Udina M. , Unikandanunni V. , Tadano T. , Hoffmann M. C. , Balatsky A. V. , Bonetti S. 
Published: April 2024

Abstract
The emergence of collective order in matter is among the most fundamental and intriguing phenomena in physics. In recent years, the dynamical control and creation of novel ordered states of matter not accessible in thermodynamic equilibrium is receiving much attention1–6. The theoretical concept of dynamical multiferroicity has been introduced to describe the emergence of magnetization due to time-dependent electric polarization in non-ferromagnetic materials7,8. In simple terms, the coherent rotating motion of the ions in a crystal induces a magnetic moment along the axis of rotation. Here we provide experimental evidence of room-temperature magnetization in the archetypal paraelectric perovskite SrTiO3 due to this mechanism. We resonantly drive the infrared-active soft phonon mode with an intense circularly polarized terahertz electric field and detect the time-resolved magneto-optical Kerr effect. A simple model, which includes two coupled nonlinear oscillators whose forces and couplings are derived with ab initio calculations using self-consistent phonon theory at a finite temperature9, reproduces qualitatively our experimental observations. A quantitatively correct magnitude was obtained for the effect by also considering the phonon analogue of the reciprocal of the Einstein–de Haas effect, which is also called the Barnett effect, in which the total angular momentum from the phonon order is transferred to the electronic one. Our findings show a new path for the control of magnetism, for example, for ultrafast magnetic switches, by coherently controlling the lattice vibrations with light.
FSC-certified forest management benefits large mammals compared to non-FSC
Authors: Zwerts Joeri A. , Sterck E. H. M. , Verweij Pita A. , Maisels Fiona , van der Waarde Jaap , Geelen Emma A. M. , Tchoumba Georges Belmond , Donfouet Zebaze Hermann Frankie , van Kuijk Marijke 
Published: April 2024

Abstract
More than a quarter of the world’s tropical forests are exploited for timber1. Logging impacts biodiversity in these ecosystems, primarily through the creation of forest roads that facilitate hunting for wildlife over extensive areas. Forest management certification schemes such as the Forest Stewardship Council (FSC) are expected to mitigate impacts on biodiversity, but so far very little is known about the effectiveness of FSC certification because of research design challenges, predominantly limited sample sizes2,3. Here we provide this evidence by using 1.3 million camera-trap photos of 55 mammal species in 14 logging concessions in western equatorial Africa. We observed higher mammal encounter rates in FSC-certified than in non-FSC logging concessions. The effect was most pronounced for species weighing more than 10 kg and for species of high conservation priority such as the critically endangered forest elephant and western lowland gorilla. Across the whole mammal community, non-FSC concessions contained proportionally more rodents and other small species than did FSC-certified concessions. The first priority for species protection should be to maintain unlogged forests with effective law enforcement, but for logged forests our findings provide convincing data that FSC-certified forest management is less damaging to the mammal community than is non-FSC forest management. This study provides strong evidence that FSC-certified forest management or equivalently stringent requirements and controlling mechanisms should become the norm for timber extraction to avoid half-empty forests dominated by rodents and other small species.
Ligand efficacy modulates conformational dynamics of the µ-opioid receptor
Authors: Zhao Jiawei , Elgeti Matthias , O’Brien Evan S. , Sár Cecília P. , EI Daibani Amal , Heng Jie , Sun Xiaoou , White Elizabeth , Che Tao , Hubbell Wayne L. , Kobilka Brian K. , Chen Chunlai 
Published: April 2024

AbstractThe µ-opioid receptor (µOR) is an important target for pain management1 and molecular understanding of drug action on µOR will facilitate the development of better therapeutics. Here we show, using double electron–electron resonance and single-molecule fluorescence resonance energy transfer, how ligand-specific conformational changes of µOR translate into a broad range of intrinsic efficacies at the transducer level. We identify several conformations of the cytoplasmic face of the receptor that interconvert on different timescales, including a pre-activated conformation that is capable of G-protein binding, and a fully activated conformation that markedly reduces GDP affinity within the ternary complex. Interaction of β-arrestin-1 with the μOR core binding site appears less specific and occurs with much lower affinity than binding of Gi.
Visualizing chaperone-mediated multistep assembly of the human 20S proteasome
Authors: Adolf Frank , Du Jiale , Goodall Ellen A. , Walsh Richard M. , Rawson Shaun , von Gronau Susanne , Harper J. Wade , Hanna John , Schulman Brenda A. 
Published: April 2024

AbstractDedicated assembly factors orchestrate the stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here we report cryo-electron microscopy reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, as well as how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors and reveals conceptual principles underlying human proteasome biogenesis, thus providing an explanation for many previous biochemical and genetic observations.
ForCenS-LGM: a dataset of planktonic foraminifera species assemblage composition for the Last Glacial Maximum
Authors: Jonkers Lukas , Mix Alan , Voelker Antje , Risebrobakken Bjørg , Smart Christopher W. , Ivanova Elena , Arellano-Torres Elsa , Eynaud Frédérique , Naoufel Haddam , Max Lars , Rossignol Linda , Simon Margit H. , Martins Maria Virgínia Alves , Petró Sandro , Caley Thibaut , Dokken Trond , Howard Will , Kucera Michal 
Published: April 2024

AbstractSpecies assemblage composition of marine microfossils offers the possibility to investigate ecological and climatological change on time scales inaccessible using conventional observations. Planktonic foraminifera - calcareous zooplankton - have an excellent fossil record and are used extensively in palaeoecology and palaeoceanography. During the Last Glacial Maximum (LGM; 19,000 – 23,000 years ago), the climate was in a radically different state. This period is therefore a key target to investigate climate and biodiversity under different conditions than today. Studying LGM climate and ecosystems indeed has a long history, yet the most recent global synthesis of planktonic foraminifera assemblage composition is now nearly two decades old. Here we present the ForCenS-LGM dataset with 2,365 species assemblage samples collected using standardised methods and with harmonised taxonomy. The data originate from marine sediments from 664 sites and present a more than 50% increase in coverage compared to previous work. The taxonomy is compatible with the most recent global core top dataset, enabling direct investigation of temporal changes in foraminifera biogeography and facilitating seawater temperature reconstructions.
A Lacticaseibacillus rhamnosus secretome induces immunoregulatory transcriptional, functional and immunometabolic signatures in human THP-1 monocytes
Authors: Jeffrey Michael P. , Saleem Lin , MacPherson Chad W. , Tompkins Thomas A. , Clarke Sandra T. , Green-Johnson Julia M. 
Published: April 2024

AbstractMacrophage responses to activation are fluid and dynamic in their ability to respond appropriately to challenges, a role integral to host defence. While bacteria can influence macrophage differentiation and polarization into pro-inflammatory and alternatively activated phenotypes through direct interactions, many questions surround indirect communication mechanisms mediated through secretomes derived from gut bacteria, such as lactobacilli. We examined effects of secretome-mediated conditioning on THP-1 human monocytes, focusing on the ability of the Lacticaseibacillus rhamnosus R0011 secretome (LrS) to drive macrophage differentiation and polarization and prime immune responses to subsequent challenge with lipopolysaccharide (LPS). Genome-wide transcriptional profiling revealed increased M2-associated gene transcription in response to LrS conditioning in THP-1 cells. Cytokine and chemokine profiling confirmed these results, indicating increased M2-associated chemokine and cytokine production (IL-1Ra, IL-10). These cells had increased cell-surface marker expression of CD11b, CD86, and CX3CR1, coupled with reduced expression of the M1 macrophage-associated marker CD64. Mitochondrial substrate utilization assays indicated diminished reliance on glycolytic substrates, coupled with increased utilization of citric acid cycle intermediates, characteristics of functional M2 activity. LPS challenge of LrS-conditioned THP-1s revealed heightened responsiveness, indicative of innate immune priming. Resting stage THP-1 macrophages co-conditioned with LrS and retinoic acid also displayed an immunoregulatory phenotype with expression of CD83, CD11c and CD103 and production of regulatory cytokines. Secretome-mediated conditioning of macrophages into an immunoregulatory phenotype is an uncharacterized and potentially important route through which lactic acid bacteria and the gut microbiota may train and shape innate immunity at the gut-mucosal interface.
Machine learning reveals differential effects of depression and anxiety on reward and punishment processing
Authors: Grabowska Anna , Zabielski Jakub , Senderecka Magdalena 
Published: April 2024

AbstractRecent studies suggest that depression and anxiety are associated with unique aspects of EEG responses to reward and punishment, respectively; also, abnormal responses to punishment in depressed individuals are related to anxiety, the symptoms of which are comorbid with depression. In a non-clinical sample, we aimed to investigate the relationships between reward processing and anxiety, between punishment processing and anxiety, between reward processing and depression, and between punishment processing and depression. Towards this aim, we separated feedback-related brain activity into delta and theta bands to isolate activity that indexes functionally distinct processes. Based on the delta/theta frequency and feedback valence, we then used machine learning (ML) to classify individuals with high severity of depressive symptoms and individuals with high severity of anxiety symptoms versus controls. The significant difference between the depression and control groups was driven mainly by delta activity; there were no differences between reward- and punishment-theta activities. The high severity of anxiety symptoms was marginally more strongly associated with the punishment- than the reward-theta feedback processing. The findings provide new insights into the differences in the impacts of anxiety and depression on reward and punishment processing; our study shows the utility of ML in testing brain-behavior hypotheses and emphasizes the joint effect of theta-RewP/FRN and delta frequency on feedback-related brain activity.
Comparative efficacy of seven nonpharmacological interventions on global cognition in older adults with and without mild cognitive impairment: a network meta-analysis of randomized controlled trials
Authors: Seok Ji-Woo , Kim Gahye , Kim Jaeuk U. 
Published: April 2024

AbstractTo maintain current cognitive function and access greater cognitive reserves, nonpharmacological interventions may be a viable alternative for older adults with or without cognitive impairment. This study aimed to compare different nonpharmacological interventions for enhancing global cognition, including mind–body exercise, physical exercise, non-invasive brain stimulation, cognitive training intervention (CTI), acutherapy (ACU), meditation, and music therapy, by applying a network meta-analysis (NMA). Sixty-one randomized controlled trials evaluating the efficacy of interventions on global cognition in older adults with or without mild cognitive decline were selected. An NMA was conducted to compare the efficacy of different nonpharmacological interventions. The NMA revealed that mind–body exercise (standardized mean difference, 1.384; 95% confidence interval, 0.777–1.992); ACU (1.283; 0.478–2.088); meditation (0.910; 0.097–1.724); non-invasive brain stimulation (1.242; 0.254–2.230); CTI (1.269; 0.736–1.802); and physical exercise (0.977; 0.212–1.742), showed positive effects compared to passive controls. There were no significant differences between the efficacies of other interventions. Nonpharmacological interventions may potentially enhance and maintain global cognition through various pathways, such as memorizing movements and enhancing brain plasticity by reducing stress in the older adult population. Additional studies are needed to clarify the impact of other variables, including intervention methods or psychological variables.
Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules
Authors: Shiroudi Abolfazl , Śmiechowski Maciej , Czub Jacek , Abdel-Rahman Mohamed A. 
Published: April 2024

AbstractThe study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives is mainly influenced by LP(e) → σ∗ electronic delocalization effects, with the highest stabilization observed on the oxygen atom of the nitroxide moiety. This work also considers electron density, atomic charges, and energetic and thermodynamic properties of the studied NO radicals, and their relative stability. The proton affinity and gas-phase basicity of the studied compounds were computed at T = 298 K for O-protonation and N-protonation, respectively. The studied DFT method calculations show that O-protonation is more stable than N-protonation, with an energy difference of 16.64–20.77 kcal/mol (22.80–25.68 kcal/mol) at the B3LYP (M06-2X) method. The AIM analysis reveals that the N–O…H interaction in H2O complexes has the most favorable hydrogen bond energy computed at bond critical points (3, − 1), and the planar configurations of TEMPO derivatives exhibit the highest EHB values. This indicates stronger hydrogen bonding interactions between the N–O group and water molecules.
Comprehensive antifungal investigation of natural plant extracts against Neosartorya spp. (Aspergillus spp.) of agriculturally significant microbiological contaminants and shaping their metabolic profile
Authors: Maj Wiktoria , Pertile Giorgia , Różalska Sylwia , Skic Kamil , Frąc Magdalena 
Published: April 2024

AbstractFungi belonging to the genus Neosartorya (teleomorph of Aspergillus spp.) are of great concern in the production and storage of berries and fruit-based products, mainly due to the production of thermoresistant ascospores that cause food spoilage and possible secretion of mycotoxins. We initially tested the antifungal effect of six natural extracts against 20 isolates of Neosartorya spp. using a traditional inhibition test on Petri dishes. Tested isolates did not respond uniformly, creating 5 groups of descending sensitivity. Ten isolates best representing of the established sensitivity clusters were chosen for further investigation using a Biolog™ MT2 microplate assay with the same 6 natural extracts. Additionally, to test for metabolic profile changes, we used a Biolog™ FF microplate assay after pre-incubation with marigold extract. All natural extracts had an inhibitory effect on Neosartorya spp. growth and impacted its metabolism. Lavender and tea tree oil extracts at a concentration of 1000 µg mL−1 presented the strongest antifungal effect during the inhibition test, however all extracts exhibited inhibitory properties at even the lowest dose (5 µg mL−1). The fungal stress response in the presence of marigold extract was characterized by a decrease of amino acids and carbohydrates consumption and an uptake of carboxylic acids on the FF microplates, where the 10 studied isolates also presented differences in their innate resilience, creating 3 distinctive sensitivity groups of high, average and low sensitivity. The results confirm that natural plant extracts and essential oils inhibit and alter the growth and metabolism of Neosartorya spp. suggesting a possible future use in sustainable agriculture as an alternative to chemical fungicides used in traditional crop protection.
Transcriptomic alterations in cortical astrocytes following the development of post-traumatic epilepsy
Authors: Leonard John , Wei Xiaoran , Browning Jack , Gudenschwager-Basso Erwin Kristobal , Li Jiangtao , Harris Elizabeth A. , Olsen Michelle L. , Theus Michelle H. 
Published: April 2024

AbstractPost-traumatic epilepsy (PTE) stands as one of the numerous debilitating consequences that follow traumatic brain injury (TBI). Despite its impact on many individuals, the current landscape offers only a limited array of reliable treatment options, and our understanding of the underlying mechanisms and susceptibility factors remains incomplete. Among the potential contributors to epileptogenesis, astrocytes, a type of glial cell, have garnered substantial attention as they are believed to promote hyperexcitability and the development of seizures in the brain following TBI. The current study evaluated the transcriptomic changes in cortical astrocytes derived from animals that developed seizures as a result of severe focal TBI. Using RNA-Seq and ingenuity pathway analysis (IPA), we unveil a distinct gene expression profile in astrocytes, including alterations in genes supporting inflammation, early response modifiers, and neuropeptide-amidating enzymes. The findings underscore the complex molecular dynamics in astrocytes during PTE development, offering insights into therapeutic targets and avenues for further exploration.
Genetic correlation and Mendelian randomization analyses support causal relationships between dietary habits and age at menarche
Authors: Guo Ruilong , Feng Ruoyang , Yang Jiong , Xiao Yanfeng , Yin Chunyan 
Published: April 2024

AbstractDietary habits are essential in the mean age at menarche (AAM). However, the causal relationship between these factors remains unclear. Therefore, this study aimed to elucidate the genetic relationship between dietary habits and AAM. Genetic summary statistics for dietary habits were obtained from the UK Biobank. GWAS summary data for AAM was obtained from the ReproGen Consortium. Linkage disequilibrium score regression was used to test genetic correlations between dietary habits and AAM. The Mendelian randomization (MR) analyses used the inverse-variance weighted method. Genetic correlations with AAM were identified for 29 candi-date dietary habits, such as milk type (skimmed, semi-skimmed, full cream; coefficient = 0.2704, Pldsc = 1.13 × 10−14). MR evaluations revealed that 19 dietary habits were associated with AAM, including bread type (white vs. any other; OR 1.71, 95% CI 1.28–2.29, Pmr = 3.20 × 10−4), tablespoons of cooked vegetables (OR 0.437, 95% CI 0.29–0.67; Pmr = 1.30 × 10−4), and cups of coffee per day (OR 0.72, 95% CI 0.57–0.92, Pmr = 8.31 × 10−3). These results were observed to be stable under the sensitivity analysis. Our study provides potential insights into the genetic mechanisms underlying AAM and evidence that dietary habits are associated with AAM.
New simplified design methods for engineering barriers around contaminated sites with Cauchy boundaries
Authors: Zhang Liyilan , Qi Yiwen , Yuan Yuxin , Tan Yaokai , Chen Guannian , Wang Yan , Wu Tao 
Published: April 2024

AbstractSince the 1980s, low-permeability slurry trench cutoff walls have been widely constructed as barriers to retard the migration of contaminants. The thickness of the cutoff walls is a key determinant of the wall service life. Through a series of theoretical derivations, simplified methods for determining the flux limit and concentration limit were proposed to determine the thickness of cutoff walls for contaminated sites with constant pollutant flux. The relative errors of both the flux-based and concentration-based methods increase as the breakthrough criterion of the ratio between the specified limit concentration of the contaminant to the source concentration (C*) and the ratio of the limited value of contaminant flux to the constant source flux (F*) increases, with a given Peclet number PL. The maximum relative error reaches 4% and 6% when C* and F* are both 0.1, which covers most practical situations in cutoff wall design. Good agreements of wall thickness were obtained between the proposed simplified methods and analytical solutions via a clear example. The proposed method can efficiently simplify the design process of cutoff walls with high accuracy, providing a basis for containing contaminated sites.
Stability analysis of rainfall-induced landslide considering air resistance delay effect and lateral seepage
Authors: Li Li , Lin Hanjie , Qiang Yue , Zhang Yi , Liang Siyu , Hu Shengchao , Xu Xinlong , Ni Bo 
Published: April 2024

AbstractAccumulation landslides are prone to occur during the continuous infiltration of heavy rainfall, which seriously threatens the lives and property safety of local residents. In this paper, based on the Green-Ampt (GA) infiltration model, a new slope rainfall infiltration function is derived by combining the effect of air resistance and lateral seepage of saturated zone. Considering that when the soil layer continues to infiltrate after the saturation zone is formed, the air involvement cannot be discharged in time, which delays the infiltration process. Therefore, the influence of air resistance factor in soil pores is added. According to the infiltration characteristics of finite long slope, the lateral seepage of saturated zone is introduced, which makes up for the deficiency that GA model is only applicable to infinite long slope. Finally, based on the seepage characteristics of the previous analysis, the overall shear strength criterion is used to evaluate the stability of the slope. The results show that the safety factor decreases slowly with the increase of size and is inversely correlated with the slope angle and initial moisture content. The time of infiltration at the same depth increases with the increase of size and slope angle, and is inversely correlated with the initial moisture content, but is less affected by rainfall intensity. By comparing with the results of experimental data and other methods, the results of the proposed method are more consistent with the experimental results than other methods.