bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical analyses for the evolution of biogenic volatile organic compounds (BVOC) emission strategy
Authors: Hirose Sotaro , Satake Akiko 
Published: July 2024

AbstractPlants emit biogenic volatile organic compounds (BVOCs) as signaling molecules, playing a crucial role in inducing resistance against herbivores. Neighboring plants that eavesdrop on BVOC signals can also increase defenses against herbivores or alter growth patterns to respond to potential risks of herbivore damage. Despite the significance of BVOC emissions, the evolutionary rationales behind their release and the factors contributing to the diversity in such emissions remain poorly understood. To unravel the conditions for the evolution of BVOC emission, we developed a spatially explicit model that formalizes the evolutionary dynamics of BVOC emission and non‐emission strategies. Our model considered two effects of BVOC signaling that impact the fitness of plants: intra‐individual communication, which mitigates herbivore damage through the plant's own BVOC signaling incurring emission costs, and inter‐individual communication, which alters the influence of herbivory based on BVOC signals from other individuals without incurring emission costs. Employing two mathematical models—the lattice model and the random distribution model—we investigated how intra‐individual communication, inter‐individual communication, and spatial structure influenced the evolution of BVOC emission strategies. Our analysis revealed that the increase in intra‐individual communication promotes the evolution of the BVOC emission strategy. In contrast, the increase in inter‐individual communication effect favors cheaters who benefit from the BVOCs released from neighboring plants without bearing the costs associated with BVOC emission. Our analysis also demonstrated that the narrower the spatial scale of BVOC signaling, the higher the likelihood of BVOC evolution. This research sheds light on the intricate dynamics governing the evolution of BVOC emissions and their implications for plant–plant communication.
Patterns and controls of topographic change within the deflation basins of a trough and bowl coastal blowout
Authors: Smyth Thomas , Fox Beth , Rooney Paul , Bodenbender Brian , De Vries‐Zimmerman Suzanne , O'Keeffe Nicholas 
Published: July 2024

AbstractIn North‐West Europe and throughout the world, dune systems are increasingly stabilised by vegetation, due to both human intervention and changes in climate. Blowouts are erosional hollows produced by wind erosion in vegetated or semi‐vegetated dune systems. Where active blowouts are present in vegetated dunes, they provide a source of dynamism and sediment in an otherwise fixed environment. The transition from a fixed vegetated dune to an active blowout is poorly understood, however, and anthropogenic attempts to reactivate areas of bare sand in dunes are often unsuccessful. In this study, we measured topographic change at a monthly resolution in the deflation basins of one bowl and one trough blowout over a 23‐month period in Ainsdale Sand Dunes National Nature Reserve, North‐West England. Our results show that monthly surface change in the blowouts did not correlate strongly with the transport capacity of winds measured at a meteorological station 10 km south of the site. Precipitation was found to have a moderate negative correlation with all indices of surface change, that is, the more it rained the less the surface changed. Inter‐annual (23 months) patterns of topographic change in the bowl and trough blowouts were distinctly different. In the deflation basin of the bowl blowout erosion predominantly took place on the erosional walls facing into the prevailing winds, while minimal change occurred on the erosional walls facing away from the prevailing wind direction. This produced a moderate negative correlation between surface change and slope, that is, the steeper the slope, the more erosion occurred. In the trough blowout, erosion took place in the centre of the deflation basin and minimal change was measured on the easternmost erosional wall, which faced the prevailing winds. Patterns of monthly topographic change were highly variable and demonstrated that changes in the direction of above‐threshold winds can cause blowout walls and floors to ‘flip’ from erosional to depositional surfaces. These findings highlight the variability and complexity of surface change in blowouts and demonstrate that patterns vary because of landform morphology and climatic conditions.
Ecotoxicological Effects of Microplastics Combined With Antibiotics in the Aquatic Environment: Recent Developments and Prospects
Authors: Du Jia , Huang Wenfei , Pan Ying , Xu Shaodan , Li Huanxuan , Jin Meiqing , Liu Qinghua 
Published: July 2024

Abstract
Both microplastics and antibiotics are commonly found contaminants in aquatic ecosystems. Microplastics have the ability to absorb antibiotic pollutants in water, but the specific adsorption behavior and mechanism are not fully understood, particularly in relation to the impact of microplastics on toxicity in aquatic environments. We review the interaction, mechanism, and transport of microplastics and antibiotics in water environments, with a focus on the main physical characteristics and environmental factors affecting adsorption behavior in water. We also analyze the effects of microplastic carriers on antibiotic transport and long-distance transport in the water environment. The toxic effects of microplastics combined with antibiotics on aquatic organisms are systematically explained, as well as the effect of the adsorption behavior of microplastics on the spread of antibiotic resistance genes. Finally, the scientific knowledge gap and future research directions related to the interactions between microplastics and antibiotics in the water environment are summarized to provide basic information for preventing and treating environmental risks. Environ Toxicol Chem 2024;43:1950–1961. © 2024 SETAC
Methodology and reporting quality of patient and public versions of guidelines in China: A systematic review
Authors: Liu Hui , Yao Yuanyuan , Yang Nan , Wang Zijun , Luo Xufei , Peng Dongrui , Zhang Huayu , Zhao Junxian , He Hongfeng , Liu Xingrong , Chen Yaolong , Estill Janne 
Published: July 2024

AbstractIntroductionThe development of patient and public versions of guidelines (PVGs) in China is still in its early stages. The aim of this article is to systematically identify the PVGs published or released in China, analyse their development methods, and assess their reporting quality.MethodsWe searched five major literature databases and conducted supplementary searches to identify all PVGs published or released by 8 January 2023 in China. After screening the literature according to the inclusion and exclusion criteria, we analysed the development methodology and evaluated the reporting quality of the included PVGs using the Reporting Items for Practice Guidelines in Healthcare‐Public or Patient Versions of Guidelines (RIGHT‐PVG). We reported this systematic review in compliance with the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) guidelines.ResultsA total of 3795 records were first identified, and 17 PVGs were included. Nine PVGs reported their development methodology: seven used de novo development (similar to developing clinical practice guidelines [CPGs]), and two rewrote the recommendations of an existing CPG. The reporting quality differed substantially between the PVGs. The PVGs adhered to between 8 and 16 (47.1%–94.1%) of the 17 RIGHT‐PVG items, with a median of 9. All PVGs specified the topic addressed in the PVGs, introduced the target condition, described the purpose, scope and target users and had precise recommendations. In contrast, none of the PVGs listed questions for patients to ask their healthcare providers.ConclusionsOnly few PVGs have so far been released in China. Most PVGs were developed de novo from the evidence, while some were instead rewritten from an existing CPG. In addition, we encourage PVGs developers to follow RIGHT‐PVG checklist when writing the guidelines in the future.
Comparing virtual reality and simulation to teach the assessment and management of acute surgical scenarios: A pilot study
Authors: Tran Mi‐Tra , Ahmad Manal , Patel Kirtan , Argyriou Orestis , Davies Alun , Shalhoub Joseph 
Published: July 2024

AbstractBackground and AimsTraditional apprenticeship‐based surgical training presents with challenges, especially in acute scenarios. Simulation provides the current standard of facilitating surgical training in a low‐risk environment but is restricted by limited accessibility and high costs. Virtual reality (VR) offers immersive three‐dimensional computer‐generated training scenarios and can connect users from various locations. We aimed to compare the performance of junior doctors to manage an acute surgical scenario using VR and mannequin‐based simulation. We hypothesised that VR would be as effective as mannequin‐based simulation in performance outcomes.MethodsThis multicentre, randomised controlled pilot study was conducted with eighteen junior doctor volunteers (Foundation and Core Trainee Year 1). Ten were randomly allocated to VR and eight to mannequin‐based simulation. Participants completed questionnaires and a 15‐min pneumothorax scenario. Quantitative metrics included overall score, time‐to‐critical decisions, and academic buoyancy scores (ABS). Qualitative metrics included participants' likes and dislikes of their allocated simulation modality.ResultsVR participants scored significantly higher than mannequin‐based simulation participants in overall scores (74.30% (SD ± 5.08%) vs. 59.75% (SD ± 10.14) (p = 0.04)), and technical skills aspects (77.20% (SD ± 8.01%) vs. 65.00% (SD ± 8.21%) (p = 0.01)). Mannequin‐based simulation participants initiated critical decisions faster and demonstrated a trend towards a faster mean time‐to‐completion (p = 0.06). ABS scores increased for both study groups, though was only significant for VR participants (p ≤ 0.01). VR participants liked how VR fostered independent learning but disliked the formulaic content and impaired communication‐learning compared to mannequin‐based simulation.ConclusionBoth VR and mannequin‐based simulation training are effective in training junior doctors in acute surgical scenarios but present different educational benefits. Future research should recruit a larger sample size for a full comparative randomised controlled trial.
Effects of climate variability and change on groundwater impacts of forestry plantations
Authors: Benyon Richard G. , Doody Tanya M. , Lawson Jeff , Hay Anthony , Myers Baden 
Published: July 2024

AbstractQuantifying water use of various water consumers is an essential part of sustainable water management. Annual evapotranspiration (ET) of plantation forests often exceeds that of dryland agriculture, which in South Africa and South Australia has resulted in restrictions on plantation development. In the latter case, water licences are issued to commercial forestry plantations to account for higher ET compared to dryland pasture. Unlike irrigated crops, it is not practicable to measure water use of plantations directly and so in South Australia a set of ‘deemed’ average water use rates has been applied since 2013, based on species and depth to groundwater. Since South Australia's ‘deemed’ rates were calculated, additional plot‐scale measurements of annual ET from plantations <2 years old and post‐canopy closure have been used to quantify various components of ET. This has enabled development of two empirical ET models for plantations in South Australia's Lower Limestone Coast, and facilitated an advanced understanding of the effect of plantations on hydrological processes, particularly in relation to groundwater use. In this study, we applied these models to estimate rotation‐averaged annual ET and net groundwater impacts (net groundwater extraction plus recharge reduction compared to pasture) of plantations, driven by climate and groundwater depth, for comparison with the deemed rates. The modelling suggests that the groundwater impacts of plantations vary in space and time and that the deemed rates over‐estimate these impacts, on average. Accounting for variation in the effects of climate on the various components of ET, both spatially and temporally, may allow for more flexible rules for water resource allocation than using any simple, rule‐of‐thumb approach.
Generalised evasive subspaces
Authors: Gruica Anina , Ravagnani Alberto , Sheekey John , Zullo Ferdinando 
Published: July 2024

AbstractWe introduce and explore a new concept of evasive subspace with respect to a collection of subspaces sharing a common dimension, most notably partial spreads. We show that this concept generalises known notions of subspace scatteredness and evasiveness. We establish various upper bounds for the dimension of an evasive subspace with respect to arbitrary partial spreads, obtaining improvements for the Desarguesian ones. We also establish existence results for evasive spaces in a nonconstructive way, using a graph theory approach. The upper and lower bounds we derive have a precise interpretation as bounds for the critical exponent of certain combinatorial geometries. Finally, we investigate connections between the notion of evasive space we introduce and the theory of rank‐metric codes, obtaining new results on the covering radius and on the existence of minimal vector rank‐metric codes.
Effects of N levels on land productivity and N2O emissions in maize–soybean relay intercropping
Authors: Fu Zhidan , Chen Ping , Li Yuze , Luo Kai , Lin Ping , Li Yiling , Yang Huan , Yuan Xiaoting , Peng Xinyue , Yang Lida , Pu Tian , Wu Yushan , Wang Xiaochun , Yang Wenyu , Yong Taiwen 
Published: July 2024

AbstractBACKGROUNDRelay intercropping of maize and soybean can improve land productivity. However, the mechanism behind N2O emissions in this practice remains unclear. A two‐factor randomized block field trial was conducted to reveal the mechanism of N2O emissions in a full additive maize–soybean relay intercropping. Factor A was three cropping systems – that is, monoculture maize (Zea mays L.), monoculture soybean (Glycine max L. Merr.) and maize–soybean relay intercropping. Factor B was different N supply, containing no N, reduced N and conventional N. Differences in N2O emissions, soil properties, rhizosphere bacterial communities and yield advantage were evaluated.RESULTSThe land equivalent ratio was 1.55–2.44, and the cumulative N2O emission () was notably lower by 60.2% in intercropping than in monoculture, respectively. Reduced N declined without penalty on the yield advantages. The relay intercropping shifted soil properties – for example, soil organic matter, total N, and protease activity – and improved the soil microorganism community – for example, Proteobacteria and Acidobacteria. Intercropping reduced by directly suppressing nirS‐ and amoA‐regulated N2O generation during soil N cycling, or nirS‐ and amoA‐mediated soil properties shifted to reduce indirectly. Reduced N directly reduced by decreasing soil N content and reducing soil microorganism activities to alleviate N2O produced in soil N cycling.CONCLUSIONConducting a full additive maize–soybean relay intercropping with reduced nitrogen supply provides a way to alleviate N2O emissions without the penalty on the yield advantage by changing rhizosphere bacterial communities and soil N cycling. © 2024 Society of Chemical Industry.
Navigating pharmacophore space to identify activity discontinuities: A case study with BCR‐ABL
Authors: Lejmi Maroua , Geslin Damien , Bureau Ronan , Cuissart Bertrand , Ben Slima Ilef , Meddouri Nida , Borgi Amel , Lamotte Jean‐Luc , Lepailleur Alban 
Published: July 2024

AbstractThe exploration of chemical space is a fundamental aspect of chemoinformatics, particularly when one explores a large compound data set to relate chemical structures with molecular properties. In this study, we extend our previous work on chemical space visualization at the pharmacophoric level. Instead of using conventional binary classification of affinity (active vs inactive), we introduce a refined approach that categorizes compounds into four distinct classes based on their activity levels: super active, very active, active, and inactive. This classification enriches the color scheme applied to pharmacophore space, where the color representation of a pharmacophore hypothesis is driven by the associated compounds. Using the BCR‐ABL tyrosine kinase as a case study, we identified intriguing regions corresponding to pharmacophore activity discontinuities, providing valuable insights for structure‐activity relationships analysis.
Emodin suppresses mast cell migration via modulating the JAK2/STAT3/JMJD3/CXCR3 signaling to prevent cystitis
Authors: Xin Ke , Ge Manqing , Li Xukun , Su Hongwei , Ke Jingwei , Chen Kaifa , Tang Yiquan , Wang Yinghong , Lai Junyu 
Published: July 2024

AbstractAimsThis study aimed to determine the preventive effects of emodin on cyclophosphamide (CYP)‐induced cystitis and to explore the molecular mechanism.MethodsIn vivo, mice were modeled by CYP. Before a half hour of CYP treatment, Jumonji domain‐containing protein‐3 (JMJD3) inhibitors (GSK‐J4) and emodin were used to treat CYP model mice. Bladder samples were stained for hematoxylin‐eosin and toluidine blue. Next, JMJD3 was quantified by immunofluorescence staining, RT‐PCR, and Western blot. CXCR3 was quantified by Western blot and ELISA. In vitro, before stimulated by lipopolysaccharide (LPS), human bladder smooth muscle cells (hBSMCs) were transfected with pcDNA3.1‐JMJD3 plasmids, shRNA‐JMJD3 plasmids or pretreated with emodin. Collected cells to detect JMJD3 and CXCR3 ligands again; collected supernatant of culture for Transwell assay. Finally, as the JAK2 inhibitor, AG490 was used to pretreat LPS‐induced hBSMCs. Western blot was performed to quantify proteins.ResultsEmodin inhibited mast cell migration and suppressed the expression of JMJD3, CXCR3, and CXCR3 ligands, not only in vivo but also in vitro. The pharmacological effects of emodin were similar to GSK‐J4 or JMJD3 inhibition. In addition, emodin significantly downregulated the phosphorylation of JAK2 and STAT3, and inhibited JMJD3/CXCR3 axis transduction like AG490.ConclusionEmodin has a preventive effect on cystitis by inhibiting mast cell migration through inhibition of the JAK2/STAT3/JMJD3/CXCR3 signaling pathway.
Specific inhibition of α‐synuclein oligomer generation and toxicity by the chaperone domain Bri2 BRICHOS
Authors: Adam Laurène , Kumar Rakesh , Arroyo‐Garcia Luis Enrique , Molenkamp Willem Hendrik , Nowak Jan Stanislaw , Klute Hannah , Farzadfard Azad , Alkenayeh Rami , Nielsen Janni , Biverstål Henrik , Otzen Daniel E. , Johansson Jan , Abelein Axel 
Published: July 2024

AbstractProtein misfolding and aggregation are involved in several neurodegenerative disorders, such as α‐synuclein (αSyn) implicated in Parkinson's disease, where new therapeutic approaches remain essential to combat these devastating diseases. Elucidating the microscopic nucleation mechanisms has opened new opportunities to develop therapeutics against toxic mechanisms and species. Here, we show that naturally occurring molecular chaperones, represented by the anti‐amyloid Bri2 BRICHOS domain, can be used to target αSyn‐associated nucleation processes and structural species related to neurotoxicity. Our findings revealed that BRICHOS predominantly suppresses the formation of new nucleation units on the fibrils surface (secondary nucleation), decreasing the oligomer generation rate. Further, BRICHOS directly binds to oligomeric αSyn species and effectively diminishes αSyn fibril‐related toxicity. Hence, our studies show that molecular chaperones can be utilized as tools to target molecular processes and structural species related to αSyn neurotoxicity and have the potential as protein‐based treatments against neurodegenerative disorders.
Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants
Authors: Hou Shurong , Liu Huan , Hu Yihui , Zhang Jie , Deng Xingyu , Li Zhenzhen , Zhang Yun , Li Xiaoxuan , Li Yishuang , Ma Lei , Yao Jianzhuang , Chen Xiabin 
Published: July 2024

AbstractHomocysteine thiolactone (HTL), a toxic metabolite of homocysteine (Hcy) in hyperhomocysteinemia (HHcy), is known to modify protein structure and function, leading to protein damage through formation of N‐Hcy‐protein. HTL has been highly linked to HHcy‐associated cardiovascular and neurodegenerative diseases. The protective role of HTL hydrolases against HTL‐associated vascular toxicity and neurotoxicity have been reported. Although several endogeneous enzymes capable of hydrolyzing HTL have been identified, the primary enzyme responsible for its metabolism remains unclear. In this study, three human carboxylesterases were screened to explore new HTL hydrolase and human carboxylesterase 1 (hCES1) demonstrates the highest catalytic activity against HTL. Given the abundance of hCES1 in the liver and the clinical significance of its single‐nucleotide polymorphisms (SNPs), six common hCES1 nonsynonymous coding SNP (nsSNPs) variants were examined and characterized for their kinetic parameters. Variants E220G and G143E displayed 7.3‐fold and 13.2‐fold lower catalytic activities than its wild‐type counterpart. In addition, the detailed catalytic mechanism of hCES1 for HTL hydrolysis was computational investigated and elucidated by Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) method. The function of residues E220 and G143 in sustaining its hydrolytic activity of hCES1 was analyzed, and the calculated energy difference aligns well with experimental‐derived results, supporting the validity of our computational insights. These findings provide insights into the potential protective role of hCES1 against HTL‐associated toxicity, and warrant future studies on the possible association between specific genetic variants of hCES1 with impaired catalytic function and clinical susceptibility of HTL‐associated cardiovascular and neurodegenerative diseases.