bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular allergen sensitization drives phenotypes of severe asthma in children: Evidence from a megacity cohort (SAMP)
Authors: Bourgoin‐Heck Mélisande , Wolff‐Goldnadel Victoria , Chantran Yannick , Saf Sarah , Guiddir Tamazoust , Amat Flore , Rancière Fanny , Momas Isabelle , Wanin Stéphanie , Rose Thierry , Saint‐Pierre Philippe , Just Jocelyne 
Published: December 2024

AbstractBackgroundSeveral major sensitization profiles have been described in children with asthma, but it remains unclear how these profiles relate to asthma phenotypes. The aim of this study was to determine allergenic sensitization profiles in a megacity cohort (SAMP).MethodsThis was a cross‐sectional analysis performed from 2011 to 2015 including preschool and school‐age children with severe and moderate asthma from the SAMP cohort. We performed ALEX multiplex array and carried out cluster analysis.ResultsData from 367 children were analyzed: 224 of preschool age and 143 of school age, respectively 84 (38%) and 114 (80%) presented at least one allergic sensitization. At preschool age, three clusters were identified: Cluster 1, Few sensitizations to inhaled allergen molecular families and non‐type 2 (T2) inflammation (n = 61); Cluster 2, Predominant sensitization to HDM molecular families (n = 16); Cluster 3, Severe asthma with multiple sensitizations to inhaled and food allergen molecular families (n = 7). At school age, five clusters were identified: Cluster 1, Few sensitizations to inhaled allergen molecular families and non‐T2 inflammation (n = 43); Cluster 2, Predominant sensitization to HDM molecular families (n = 31); Cluster 3, Predominant sensitization to PR‐10 protein family (n = 25); Cluster 4, Severe asthma with predominant sensitization to tropomyosin family (n = 11); Cluster 5, Severe asthma with multiple sensitizations to inhaled and food allergen molecular families (n = 4).ConclusionThese results underline the heterogeneity of sensitization profiles in severe allergic childhood asthma. The most severe asthma phenotypes were associated with multiple sensitizations to both inhaled and food allergen molecular families as expected, and to the tropomyosin molecular family, a novel finding.
Plant Architecture Optimizes the Trait‐Based Description and Classification of Vegetation
Authors: Liu Biying , Yuan Sihao , Chen Zhihui , Zhao Panpan , Wang Yi , Chu Wei , Zhang Shuo , Zhao Wensheng , Tan Shiqin , Zhou Ting , Peng Shaolin 
Published: December 2024

ABSTRACTTrait‐based approaches offer valuable perspectives for vegetation classification, but functional traits struggle to capture resource allocation among competing plants, showing limitations across scales. This study aimed to introduce plant architecture to enhance trait‐based vegetation classification. Based on a forest transect survey along China's eastern coast from 2021 to 2023, data from 32 plots of coastal dwarf forests (CDF), characterized primarily by reduced plant height, and normal noncoastal dwarf forests (NCDF) were obtained. Their community characteristics were quantified, and classification and clustering models assessed the advantages of plant architecture in distinguishing these communities. The results indicated plant architecture traits are more critical for distinguishing different community types than leaf‐based functional traits. Additionally, plant architecture traits are effective in clustering plant associations within the same community type. Because plant architectural traits are closely linked to habitat, phylogeny and community structure, providing a comprehensive description of vegetation. In contrast, traditional plant functional traits primarily reflect habitat information related to soil nutrients. Our findings underscore the importance of plant architecture in optimizing trait‐based vegetation classification and suggest that variations in the plasticity of plant architecture traits may support the classification of CDF as a distinct vegetation unit.
Microplastics and Nanoplastics Alter the Physicochemical Properties of Willow Trees and Lead to Mortality in Leaf Beetle Larvae
Authors: Zhu Peipei , Zhang Yanping , Deng Mengqi , Zhang Yuxin , Luo Jing , Han Runhua , Xu Letian 
Published: December 2024

ABSTRACTPolystyrene micro‐ and nanoplastics (MNPs) are increasingly found in terrestrial environments, posing risks across the food web. However, the potential impacts of MNPs transfer on plant‐insect interactions remains largely unknown. In this study, consumption of willow plants (Salix maizhokunggarensis) exposed to 10.0 mg/L MNPs for 21 days inhibited survival and reduced body weight in Plagiodera versicolora larvae unlike those exposed to lower concentrations or shorter durations (0.1, 1.0 and 10.0 mg/L MNPs for 7 or 14 days). MNPs exposure increased lignin content and leaf thickness in willows, leading to decreased leaf consumption and increased mouthpart wear in P. versicolora larvae. Transcriptome and gut microbiota analyses revealed significant downregulation of genes related to digestion, intestinal homoeostasis, immunity, and growth/development along with profound alterations in gut microbiota composition. Notably, the abundance of the pathogenic bacterium Pseudomonas increased significantly. The gut barrier was disrupted, allowing gut bacteria to translocate into the haemolymph, accelerating larval mortality. Overall, MNPs altered plant physiology, making willow plants unsuitable for herbivore consumption and indirectly influenced herbivore survival by modulating gut bacteria. These findings offer novel insights into the cascading ecological effects and risks of MNPs, highlighting potential impacts on plant‐herbivore interactions, biodiversity, and ecosystem health in terrestrial ecosystems.
Speckled Laser Pump–Thermoreflectance Microscopy Probe to Measure and Study Micro/Nanoscale Thermal Transport: Numerical Simulation
Authors: Zhang Yifan , Luo Zuni , Xie Zhikun , Wang Jingwen , Cao Kun , Chen Ke 
Published: December 2024

Abstract
Nondiffusive thermal transport in solids and their micro/nanostructures is a key subject in the research of micro/nanoscale heat conduction. A number of laser and optical techniques to measure or capture the nondiffusive behaviors of heat carriers have been developed, such as transient thermoreflectance, time-domain thermoreflectance (TDTR), transient thermal grating (TTG), and so on. Here, we propose a novel method to study micro/nanoscale heat transport, namely, speckled laser pump–thermoreflectance microscopy probe. In this technique, micrometer to few hundred nanometer size random heat spots are generated by a speckled laser pump pulse, and the time–space evolution of heat spots are recorded by thermoreflectance microscopy images of the probe pulses arriving at different delay times. Fourier transform is applied to analyze the thermoreflectance images and extract the thermal decaying time for different spatial frequencies and along different in-plane directions. Thermal conductivity at different spatial frequencies, which includes the nondiffusive transport information, is obtained in this way. By numerically performing simulation of anisotropic Brownian motion and solving phonon Boltzmann transport equations under the initial condition of random heat spots, we retrieve the preset anisotropic thermal conductivity and the nondiffusive behavior of reduced thermal conductivity with increasing spatial frequencies, proving the validity of this technique. The innovative method can also be applied to study electron and spin transports, and holds the potential to facilitate the experimental research and understanding of nanoscale energy transport.
Computational Analysis of Flow and Transport Suggests Reduced Oxygen Levels Within Intracranial Aneurysms, Especially in Individuals With Sickle-Cell Disease
Authors: Bazzi Marisa S. , Wiputra Hadi , Wood David K. , Barocas Victor H. 
Published: December 2024

Abstract
Sickle cell disease (SCD) is a genetic condition characterized by an abundance of sickle hemoglobin in red blood cells. SCD patients are more prone to intracranial aneurysms (ICA) compared to the general population, with distinctive features such as multiple intracranial aneurysms: 66% of SCD patients with ICAs have multiples ICAs, compared to 20% in nonsickle patients. The exact mechanism behind these associations is not fully understood, but there is a hypothesized link between hypoxic conditions in blood vessels and impaired synthesis of extracellular matrix, which may weaken the vessel walls, favoring aneurysm formation and rupture. SCD patients experience reduced oxygen levels in their blood, potentially exacerbating hypoxia in intracranial aneurysms, and potentially creating a feedback loop that could contribute to aneurysm development and early onset in these patients. In this work, we performed a series of computational studies (Fluent) using idealized geometries to investigate the key differences in the oxygen transport and blood flow dynamics inside an aneurysm formation for sickle and nonsickle cases. We found that using sickle cell disease parameters resulted in a 14% to 68% reduction in blood flow and a 37% to 70% reduction in oxygen availability within the aneurysm, depending on the vessel curvature and the aneurysm throat diameter, due to factors including oxygen-dependent viscosity and alteration in the oxygen transport. The results indicate that depending on geometry and flow characteristics, some degree of hypoxia maybe present in aneurysm bulb and would be more severe in sickle-cell disease patients. This study hopes to bring into attention the potential presence of hypoxic environment in the aneurysm bulb.
A Generalized Machining Process Damping Model for Orthogonal Cutting
Authors: Theraroz Jonathan , Tuysuz Oguzhan 
Published: December 2024

Abstract
Chatter vibrations in machining degrade the surface quality, cause premature tool and machine failures, and reduce the productivity. The dynamic interference between the cutting tool and the wavy part surface damps the machining process in the presence of vibrations. Machining process damping improves the chatter stability especially for difficult-to-cut materials and is even more pronounced via optimized cutting edge geometries. However, there is not any analytical model that can consider arbitrary edge profiles in modeling the process damping. This study introduces a new generalized analytical model to predict the process damping forces for any two-dimensional cutting edge geometries by taking the vibration parameters, work material properties, cutting conditions, and cutting edge geometry into account. That is achieved by discretizing the tool–workpiece contact using a series of springs with a nonlinear Winkler foundation and by employing a material constitutive model to describe the behavior of the deformed springs beyond elasticity. The process damping force is calculated from the contact pressure between the edge and the work material and linearized with an equivalent viscous damper dissipating the same energy. The proposed model has been verified experimentally and numerically for different tool geometries. It is demonstrated that the model can eliminate the time-intensive experimental and numerical identification of process damping coefficients and can digitalize the design phase of cutting tools by rapidly evaluating their machining dynamics performance in place of physical tests.
Computational Model for Hot Deformation Behavior of AA2024/SiC Composites Emphasizing the Effect of Volume Fraction and Particle Size
Authors: Hashmi Anisah Farooq , Li Fuguo , Zhao Qian , Li Qinghua , Zhu E. , Tanveer Muhammad , Gopi K. R. 
Published: December 2024

Abstract
The hot deformation behavior of AA2024/SiC composite was investigated by experimental and finite element simulation (FEM) methods. The influence of different particle volume fractions (VFs) and sizes on the mechanical behavior of AA2024/SiC composites was studied. An integrated numerical model was developed using a modified Johnson–Cook model for the AA2024 matrix implemented via VUHARD subroutine and the Johnson–Holmquist model 2 for the SiC particles. Simulations were performed at higher temperatures (673–753 K) and varying strain rates (0.01–1 s−1) within a random microstructure-based FEM framework using abaqus. The FEM results are in close agreement with the experimental data, particularly in the true stress–strain curves, indicating that the developed FEM model effectively captures the hot workability of AA2024/SiC composites under varying temperature conditions, SiC volume fractions, and particle sizes (PSs). The results showed that the reinforcement of SiC particles into the AA2024 matrix significantly improved its hot workability by reducing dislocation mobility. The flow stress of composites increased with SiC content and decreased with the reinforcement particle size. The composites reinforced with 5 µm SiC particles had a higher peak flow stress of 145.945 MPa than the others at 673 K and a strain rate of 1 s−1. Similarly, at constant temperature and strain rate, the peak flow stress of the composite material increased from 87 MPa to 145.945 MPa (PS = 5 µm at 673 K and strain rate 1 s−1) as the VF increased from 1% to 20%.
Simulation Study of the Upper-Limb Isometric Wrench Feasible Set With Glenohumeral Joint Constraints
Authors: Rezzoug Nasser , Skuric Antun , Padois Vincent , Daney David 
Published: December 2024

Abstract
The aim of this work is to improve musculoskeletal-based models of the upper-limb wrench feasible set (WFS), i.e., the set of achievable maximal wrenches at the hand for applications in collaborative robotics and computer aided ergonomics. In particular, a recent method performing wrench capacity evaluation called the iterative convex hull method (ICHM) is upgraded in order to integrate nondislocation and compression limitation constraints at the glenohumeral (GH) joint not taken into account in the available models. Their effects on the amplitude of the force capacities at the hand, glenohumeral joint reaction forces and upper-limb muscles coordination in comparison to the original iterative convex hull method are investigated in silico. The results highlight the glenohumeral potential dislocation for the majority of elements of the wrench feasible set with the original iterative convex hull method and the fact that the modifications satisfy correctly stability constraints at the glenohumeral joint. Also, the induced muscles coordination pattern favors the action of stabilizing muscles, in particular the rotator-cuff muscles, and lowers that of known potential destabilizing ones according to the literature.
The fourth-stage autoinfective larva of
Strongyloides stercoralis
: redescription and diagnostic implications
Authors: Zhao Huan , Koehler Anson V. , Truarn Cameron , Bradford Damien , New David W. , Speare Rick , Gasser Robin B. , Sheorey Harsha , Bradbury Richard S. 
Published: December 2024

ABSTRACT

Human strongyloidiasis is often underdiagnosed or misdiagnosed, which can relate to a lack of knowledge or recognition of the importance of particular developmental/larval stages of
Strongyloides stercoralis
in making an accurate diagnosis using parasitological methods (a morphological approach or morphological features/characters). Here, we report the identification of
S. stercoralis
autoinfective fourth-stage larvae (L4a) in naturally infected humans, encountered in two clinical cases in Australia. These larvae were identified in sputum (Case 1) and bronchoalveolar lavage (Case 2) specimens by direct wet-mount microscopy. The L4a of
S. stercoralis
can be morphologically differentiated from autoinfective third-stage larvae by its conical and pointed tail and a relatively mature genital primordium with an enlarged genital rudiment and the formation of a vulva within cuticle layers. This study emphasizes the need to consider these morphological features of the L4a stage for an accurate diagnosis of
S. stercoralis
infection. A detailed morphological description of this stage is given to guide laboratory practitioners and researchers in the identification and differentiation of this unique but neglected life-cycle stage of
S. stercoralis
.
Analysis of the ubiquitin-modified proteome identifies novel host factors in Kaposi’s sarcoma herpesvirus lytic reactivation
Authors: Causey Amerria , Constantine Mathew , Oswald Jessica , Dellomo Anna , Masters Bronwyn , Omorogbe Esosa , Admon Arie , Garzino-Demo Alfredo , Ehrlich Elana 
Published: December 2024

ABSTRACT

Kaposi’s sarcoma herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma and is associated with primary effusion lymphoma (PEL), multicentric Castleman’s disease, and two inflammatory diseases. KSHV-associated cancers are primarily associated with genes expressed during latency, while other pathologies are associated with lytic gene expression. The major lytic switch of the virus, Replication and Transcription Activator (RTA), interacts with cellular machinery to co-opt the host ubiquitin proteasome system to evade the immune response as well as activate the program of lytic replication. Through stable isotope labeling using amino acids in cell culture (SILAC) labeling, ubiquitin remnant enrichment, and mass spectrometry, we have analyzed the RTA-dependent ubiquitin-modified proteome. We identified RTA-dependent changes in the populations of polyubiquitin chains, as well as changes in ubiquitinated proteins in both cells expressing RTA and naturally infected cells following lytic reactivation. We observed an enrichment of proteins that are also reported to be SUMOylated, suggesting that RTA, a small ubiquitin-like modifier (SUMO) targeting ubiquitin ligase, may function to alleviate a SUMO-dependent block to lytic reactivation. RTA targeted substrates directly through a ubiquitin ligase domain-dependent mechanism as well as indirectly through cellular ubiquitin ligase RAUL. Our ubiquitome analysis revealed an RTA-dependent mechanism of immune evasion. We provide evidence of inhibition of transporter associated with antigen processing (TAP)-dependent peptide transport, resulting in decreased human leukocyte antigen (HLA) complex stability. The results of this analysis increase our understanding of mechanisms governing the latent to lytic transition in addition to the identification of a novel RTA-dependent mechanism of immune evasion.

IMPORTANCE
Kaposi’s sarcoma herpesvirus, an AIDS-associated pathogen, is associated with multiple cancers and inflammatory syndromes. This virus has a latent and lytic lifecycle, each associated with pathogenesis and oncogenesis. Here, we identify proteins that display differential abundance in different phases of the lifecycle. We provide evidence supporting a new model of viral immune evasion. These findings increase our understanding of how the virus manipulates the host cell and provides new targets for intervention.
A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes
Authors: Ngan Wing Y. , Parab Lavisha , Bertels Frederic , Gallie Jenna 
Published: December 2024

ABSTRACT

Insertion sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element and a short duplication at the target site. It has been noted that, for some extant IS copies, no target site duplications (TSDs) are readily identifiable. TSD absence has been attributed to degeneration of the TSD after the insertion event, recombination between identical ISs, or adjacent deletions. Indeed, the latter two—recombination between ISs and adjacent deletions—are frequent causes for the absence of TSDs, which we demonstrate here in an analysis of genome sequence data from the Lenski long-term evolution experiment. Furthermore, we propose that some IS movements—namely, those that occur in association with large-scale genomic rearrangements—do not generate TSDs, and occur without evidence for recombination between ISs or adjacent deletions. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS
5
movement plus a large deletion in
Escherichia coli
C, and an IS
481
movement occurring with a large duplication in
Pseudomonas fluorescens
SBW25. Although unlikely, it is possible that the observed deletion and associated IS movement occurred in two successive events in one overnight culture. However, an IS at the center of a large-scale duplication is not readily explained, suggesting that IS element activity may promote both large-scale deletions and duplications.

IMPORTANCE

Insertion sequences are the most common mobile genetic elements found in bacterial genomes, and hence they significantly impact bacterial evolution. We observe insertion sequence movement at the center of large-scale deletions and duplications that occurred during laboratory evolution experiments with
Escherichia coli
and
Pseudomonas fluorescens
, involving three distinct types of transposase. We raise the possibility that the transposase does not mediate DNA cleavage but instead inserts into existing DNA breaks. Our research highlights the importance of insertion sequences for the generation of large-scale genomic rearrangements and raises questions concerning the mechanistic basis of these mutations.