bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Modeling, Uncertainty Analysis, and Experimental Study of a New Cable-Driven Parallel Robot With Interval Variables
Authors: Zhou Bin , Li Sipan , Wang Zhiyuan , Chen Bing , Zi Bin 
Published: January 2025

Abstract
Based on the Chebyshev polynomial method (CPM) and interval theory, this article establishes the relationship between uncertain parameters and the dynamic response of a new cable-driven parallel robot (CDPR). Meanwhile, the time-varying characteristic of uncertain parameters in the dynamic uncertainty analysis of the model is considered in this article, effectively enhancing the accuracy of the dynamic response. The mechanical design and kinematic modeling are conducted, and the dynamic model is established based on the Lagrangian method. Thus, uncertain parameters including the length of the lifting arm L, the angle of the lifting arm rotation on the support plate α, and the length of the payload l are defined as interval variables, and the dynamic equilibrium equation with interval variables is derived. Numerical examples show that the CPM has a higher accuracy than the first-order interval perturbation method (FOIPM), and a higher efficiency than the Monte Carlo method (MCM) when it comes to solve the dynamic response of the CDPR with uncertain parameters. Experimental results demonstrate the effectiveness of dynamic modeling and the CPM in achieving efficient dynamic response and show that the largest relative error between the theoretical and experimental values for the dynamic response of the CDPR with uncertain parameter L is 1.466%; the largest relative error with uncertain parameter α is 0.783%; the largest relative error with uncertain parameter l is 0.857%; and the largest relative error with multiple uncertain parameters is 1.513%.
Large Language Models for Computer-Aided Design Fine Tuned: Dataset and Experiments
Authors: Sun Yuewan , Li Xingang , Sha Zhenghui 
Published: January 2025

Abstract
Despite the power of large language models (LLMs) in various cross-modal generation tasks, their ability to generate 3D computer-aided design (CAD) models from text remains underexplored due to the scarcity of suitable datasets. Additionally, there is a lack of multimodal CAD datasets that include both reconstruction parameters and text descriptions, which are essential for the quantitative evaluation of the CAD generation capabilities of multimodal LLMs. To address these challenges, we developed a dataset of CAD models, sketches, and image data for representative mechanical components such as gears, shafts, and springs, along with natural language descriptions collected via Amazon Mechanical Turk. By using CAD programs as a bridge, we facilitate the conversion of textual output from LLMs into precise 3D CAD designs. To enhance the text-to-CAD generation capabilities of GPT models and demonstrate the utility of our dataset, we developed a pipeline to generate fine-tuning training data for GPT-3.5. We fine-tuned four GPT-3.5 models with various data sampling strategies based on the length of a CAD program. We evaluated these models using parsing rate and intersection over union (IoU) metrics, comparing their performance to that of GPT-4 without fine-tuning. The new knowledge gained from the comparative study on the four different fine-tuned models provided us with guidance on the selection of sampling strategies to build training datasets in fine-tuning practices of LLMs for text-to-CAD generation, considering the trade-off between part complexity, model performance, and cost.
Inverse Design of Three-Dimensional Variable Curvature Pneumatic Soft Actuators
Authors: Liu Tong , Wang Xiaojie 
Published: January 2025

Abstract
The inverse design of soft actuators refers to a design methodology that derives the actuator's geometric and material parameters based on the desired target shape. This approach offers an efficient solution for developing soft actuators with complex geometries, enabling the precise matching of intricate deformation targets. Furthermore, it facilitates personalized customization and design optimization for complex application scenarios. In this article, we present a novel inverse design method for three-dimensional (3D) variable curvature pneumatic soft actuators and incorporate buckling deformation to improve shape matching. By analyzing variable cross-sectional actuators, we demonstrate that cross-sectional curvature is determined solely by its shape, enabling specific curvatures to be achieved by adjusting the cross-sectional geometry. To process input 3D point coordinates and calculate curve curvatures, we introduce cubic spline interpolation and the three-point circle method. Additionally, a minimum discretization method is proposed to identify the helical axis for helical curves. Finally, based on the actuator's deformation model, we develop an inverse design program to achieve the desired actuator shape. Finite element simulations and experimental validation confirm the effectiveness of this approach, demonstrating that the fabricated actuators can precisely match complex 3D variable curvature shapes. The proposed approach has broad potential applications in situations that require specific, repetitive use, such as specific object grasping and customized medical rehabilitation devices.
Design and Performance Experiment of a Combined Cold Storage Plate Refrigerated Container Based on Phase Change Material
Authors: Chen Junwen , Kang Na , Wang Yu , Asfandyar Khan Dawar 
Published: January 2025

Abstract
The cold chain is a critical component in the transportation of food and pharmaceuticals, with refrigerated transportation equipment representing a significant sector within this domain. This article presents a design scheme aimed at achieving uniform temperature and extended cold storage duration to enhance the performance of combined cold storage plate refrigerated containers. Utilizing the principles of combined cold storage, we designed the combined cold storage plates and the refrigerated container. We compared the performance of various phase change materials (PCMs)—specifically 2-octanone, n-undecane, n-tetradecane, and water—from the perspectives of equal mass combination schemes and equal phase change latent heat value schemes. Our findings indicate that the equal mass combination scheme, which employs n-tetradecane as the inner layer and water as the outer layer, exhibits superior performance. Additionally, we evaluated the effective cold preservation time, melting time, minimum temperature, uniformity coefficient, and cold power consumption of the combined cold storage plates in different placement configurations (side placement and diagonal placement) within the refrigerated container. The results demonstrate that the refrigerated container utilizing the equal mass combination scheme with n-tetradecane and water in a diagonal placement configuration performs optimally. This experimental conclusion serves as a reference for advancing the application of combined cold storage plate refrigerated containers in ultra-low-temperature control.
Numerical Study on Unsteady Flow of a Supersonic Partial Admission Impulse Turbine
Authors: Li Tongxi , Wang Jiakang , Wang Zhiheng , Xi Guang 
Published: January 2025

Abstract
Partial admission is an essential method to ensure the effective operation of turbines in various operating conditions. The transition section of partial admission turbines is pivotal in governing the unsteadiness and nonuniformity, yet its flow dynamics remain elusive. To enhance the comprehension within supersonic partial admission impulse (SPAI) turbines, this study uses 3D unsteady simulations on a single-stage SPAI turbine with four nozzles to understand its dynamics and compares the performance of centralized and symmetrical nozzle arrangements. The findings reveal that shock waves are produced in the admission area, followed by two flow separations, while the turbulent, stagnant fluid exists in the nonadmission area. A strong shock wave is formed at the entrance of the transition section channel leaving the admission area. High- and low-energy gases mix in the subsequent channel and undergo an emptying process, resulting in significant energy loss. Furthermore, blades undergo fluctuating aerodynamic forces, and phenomena of under- and over-shoot are observed as the blades enter or exit the admission area, impeding turbine rotation or providing an additional torque. When adopting symmetrical nozzle arrangements, the mixing process is strengthened, resulting in a 0.29% decrease in the isentropic efficiency with the spacing of 40 deg and a 1.30% decrease with the spacing of 60 deg compared to the centralized arrangement. However, the lateral force and overturning moment on the rotor are mitigated. Consequently, in practical engineering, adopting a symmetrical arrangement is a feasible solution to ensure the stability and safety of SPAI turbine operation.
A novel FadL family outer membrane transporter is involved in the uptake of polycyclic aromatic hydrocarbons
Authors: Meng Qiu , Liang Yuxuan , Xu Yinming , Li Saiyue , Huang Haiyan , Xu Yuanyou , Cao Feifei , Yin Jianhua , Zhu Tingheng , Gao Haichun , Yu Zhiliang 
Published: January 2025

ABSTRACT

Gram-negative bacteria play a pivotal role in the bioremediation of persistent organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs). Because the outer membrane (OM) of these bacteria hinders the direct permeation of hydrophobic substances into the cells, trans-OM proteins are required for the uptake of PAHs. However, neither the characteristics of PAH transporters nor the specific transport mechanism has been well interpreted. In this study, we revealed the participation of a novel FadL family transporter, PadL, in the biodegradation of the representative PAH phenanthrene in
Novosphingobium pentaromativorans
US6-1, an efficient PAH-degrading bacterium. PadL facilitates the cross-OM transport of phenanthrene, thus upregulating the expression of the gene
ahdA1e
that is critical to the PAH catabolism. We then showed that hydrophobic amino acid residues in the substrate binding pockets of PadL are essential for the binding of PAHs, such as phenanthrene and benzo[
a
]pyrene. PadL homologs commonly exist in most of the PAH-degrading species from
Sphingomonas
and
Novosphingobium
. The characterization of PadL provided in this study holds significant potential for improving the PAH biodegradation efficiency.

IMPORTANCE
Persistent organic pollutants, including polycyclic aromatic hydrocarbons (PAHs), pose serious threats to human health, and biodegradation has been applied as an efficient strategy for PAH removal. However, due to the high hydrophobicity of PAHs, their uptake is hindered by the bacterial outer membrane, restraining degradation efficiency. The present study reveals the critical roles of a novel FadL family protein (PadL) in the biodegradation of PAHs. PadL specifically transports PAHs such as phenanthrene and benzo[a]pyrene and PadL homologs generally exist in PAH-degrading bacteria of Sphingomonas and Novosphingobium. Our findings fill the knowledge gap in the bacterial trans-membrane uptake process of PAHs and provide a future direction for enhancing the bacterial PAH bioremediation capacity.
Development of a conditional plasmid for gene deletion in non-model
Fusobacterium nucleatum
strains
Authors: Zhou Peng , G C Bibek , Wu Chenggang 
Published: January 2025

ABSTRACT

Fusobacterium nucleatum
is an opportunistic pathogen with four subspecies:
nucleatum
(FNN),
vincentii
(FNV),
polymorphum
(FNP), and
animalis
(FNA), each with distinct disease potentials. Research on fusobacterial pathogenesis has mainly focused on the model strain ATCC 23726 from FNN. However, this narrow focus may overlook significant behaviors of other FNN strains and those from other subspecies, given the genetic and phenotypic diversity within
F. nucleatum
. While ATCC 23726 is highly transformable, most other
Fusobacterium
strains exhibit low transformation efficiency, complicating traditional gene deletion methods that rely on non-replicating plasmids. To address this, we developed a conditional plasmid system in which the RepA protein, essential for replication of a pCWU6-based shuttle plasmid, is controlled by an inducible system combining an
fdx
promoter with a theophylline-responsive riboswitch. This system allows plasmid replication in host cells upon induction and plasmid loss when the inducer is removed, forcing chromosomal integration via homologous recombination in the presence of the antibiotic thiamphenicol. We validated this approach by targeting the
galK
gene, successfully generating mutants in FNN (ATCC 23726, CTI-2), FNP (ATCC 10953), FNA (21_1A), and the closely related species
Fusobacterium periodonticum
. Incorporating a
sacB
counterselection marker in this conditional plasmid enabled the deletion of the
radD
gene in non-model strains. Interestingly, while
radD
deletion in 23726, 10953, and 21_1A abolished coaggregation with
Actinomyces oris
, the CTI-2 mutant retained this ability, suggesting the involvement of other unknown adhesins. This work significantly advances gene deletion in genetically recalcitrant
F. nucleatum
strains, enhancing our understanding of this pathogen.

IMPORTANCE

Fusobacterium nucleatum
is implicated in various human diseases, including periodontal disease, preterm birth, and colorectal cancer, often linked to specific strains and reflecting the species’ genetic and phenotypic diversity. Despite this diversity, most genetic research has centered on the model strain ATCC 23726, potentially missing key aspects of other strains’ pathogenic potential. This study addresses a critical gap by developing a novel conditional plasmid system that enables gene deletion in genetically recalcitrant strains of
F. nucleatum
. We successfully deleted genes in the FNN clinical strain CTI-2, the FNA strain 21_1A, and
F. periodonticum
for the first time. Our findings, particularly the varying behavior of the
radD
gene production in coaggregation across strains, underscore the complexity of
F. nucleatum
and the need for broader genetic studies. This work advances our understanding of
F. nucleatum
virulence at the strain level and provides a valuable tool for future bacterial genetics research.
The GacS/GacA two-component system strongly regulates antimicrobial competition mechanisms of
Pseudomonas fluorescens
MFE01 strain
Authors: Dupont Charly A. , Bourigault Yvann , Biziere-Maco Héloïse , Boukerb Amine M. , Latour Xavier , Barbey Corinne , Verdon Julien , Merieau Annabelle 
Published: January 2025

ABSTRACT

Pseudomonas fluorescens
MFE01 is an environmental bacterium characterized by an hyperactive type 6 secretion system (T6SS) and a strong emission of volatile organic compounds (VOCs). In a previous study, a transposition mutant, 3H5, exhibited an inactive T6SS and altered VOC emission. In 3H5, the interruption of
trpE
gene by the transposon was insufficient to explain these phenotypes. To determine the actual impact of this insertion, a comparative transcriptomic analysis was performed on the two-component system GacS/GacA, known to influence numerous phenotypes in
Pseudomonas
. The results demonstrated that the
gacS
gene is less expressed in 3H5 than in MFE01. Phenotypic analysis of a
gacS
deletion mutant, Δ
gacS
, confirmed many similarities between Δ
gacS
and 3H5. Indeed, Δ
gacS
exhibited an inactive T6SS and an altered VOC emission profile. In-depth analysis of volatilomes and phenotypes correlated with the decrease in
gacS
transcription, highlighting that the emission of 1-undecene is under the strict control of GacS/GacA. This study confirms that 1-undecene is not the sole volatile molecule responsible for MFE01’s inhibition of
Legionella
. Moreover, MFE01 has antimicrobial activity against the phytopathogenic oomycetes
Phytophthora infestans
via hydrogen cyanide (HCN) emission, which is also controlled by GacS. In MFE01, GacS/GacA is also a partial positive regulator of other VOC emission, whose reduced emission in 3H5 coincides with the decrease in
gacS
transcription.

IMPORTANCE

Our model strain
Pseudomonas fluorescens
MFE01 uses an active type VI secretion system (T6SS) and volatile compounds (VCs) to outcompete other microorganisms in the natural environment. By investigating the cellular mechanism regulating the production of these weapons, we identified the two-component system GacS/GacA. Indeed, GacS cellular membrane sensor plays a crucial role in regulating T6SS activity and VC emission. Among the latter, 1-undecene and hydrogen cyanide are strong aerial inhibitors of the
Legionella
human pathogen and the
Phytophtora infestans
major plant pest, respectively. The aim is to improve the understanding of the regulation of these volatile molecule emission and the critical role of a global regulator in both plant and human health.
Immunological findings of West Caucasian bat virus in an accidental host
Authors: Castellan Martina , Zamperin Gianpiero , Foiani Greta , Zorzan Maira , Priore Maria Francesca , Drzewnioková Petra , Melchiotti Erica , Vascellari Marta , Monne Isabella , Crovella Sergio , Leopardi Stefania , De Benedictis Paola 
Published: January 2025

ABSTRACT

The
Lyssavirus
genus includes seventeen viral species able to cause rabies, an acute and almost invariably fatal encephalomyelitis of mammals. Rabies virus (RABV), which represents the type species of the genus, is a multi-host pathogen that over the years has undergone multiple events of host-switching, thus occupying several geographical and ecological niches. In contrast, non-RABV lyssaviruses are mainly confined within a single natural host with rare spillover events. In this scenario, unveiling the mechanisms underlying the host immune response against a virus is crucial to understand the dynamics of infection and to predict the probability of colonization/adaptation to a new target species. Presently, the host response to lyssaviruses has only been partially explored, with the majority of data extrapolated from RABV infection. West Caucasian bat virus (WCBV), a divergent lyssavirus, has recently been associated with a spillover event to a domestic cat, raising concern about the risks to public health due to the circulation of the virus in its natural host. Through this study we have investigated the immune response determined by the WCBV versus two widely known lyssaviruses. We selected the Syrian hamster as representative of an accidental host, and chose the intramuscular route in order to mimic the natural infection. In hamsters, WCBV was highly pathogenic, determining 100% lethality and mild encephalitis. In comparison with Duvenhage virus (DUVV) and RABV, we found that WCBV displayed an intermediate ability to promote cellular antiviral response, produce pro-inflammatory cytokines, and recruit and activate lymphocytes in the hamsters’ central nervous system.

IMPORTANCE
Although all lyssaviruses cause fatal encephalomyelitis in mammals, they display a different host tropism and pathogenicity, with the ecology of Rabies virus (RABV) continually evolving and adapting to new host species. In 2020, West Caucasian bat virus (WCBV) was identified as the causative agent of rabies in a domestic cat in Italy. This event raised concerns about its public health consequences, due to the absence of biologicals against the infection. Our study investigates the host immune response triggered by WCBV in comparison with a pathogenic strain of RABV and the low pathogenic Duvenhage lyssavirus (DUVV), as a proxy to understand the mechanisms leading to lyssavirus spillover and pathogenicity. We overall confirm that previous evidence indicating an inverse relationship between lyssavirus pathogenicity and immune response is applicable for WCBV as well. Importantly, this work represents the first transcriptomic analysis of the WCBV interaction in the central nervous system with an accidental host.
Kalamari: a representative set of genomes of public health concern
Authors: Katz Lee S. , Griswold Taylor , Lindsey Rebecca L. , Lauer A. C. , Im Monica S. , Williams Grant , Halpin Jessica L. , Gómez Gerardo A. , Kucerova Zuzana , Morrison Shatavia , Page Andrew , Den Bakker Henk C. , Carleton Heather A. 
Published: January 2025

ABSTRACT

Kalamari is a resource that supports genomic epidemiology and pathogen surveillance. It consists of representative genomes and common contaminants. Kalamari also contains a custom taxonomy and software for downloading and formatting the data.
Predictive signatures of immune response to vaccination and implications of the immune setpoint remodeling
Authors: Ramos Irene 
Published: January 2025

ABSTRACT

In 2020, I featured two articles in the “mSphere of Influence” commentary series that had profound implications for the field of immunology and helped shape my research perspective. These articles were “Global Analyses of Human Immune Variation Reveal Baseline Predictors of Postvaccination Responses” by Tsang et al. (Cell 157:499–513, 2014,
https://doi.org/10.1016/j.cell.2014.03.031
) and “A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection” by Fourati et al. (Nat Commun 9:4418, 2018,
https://doi.org/10.1038/s41467-018-06735-8
). From these topics, the identification of signatures predictive of immune responses to vaccination has greatly advanced and pivoted our understanding of how the immune state at the time of vaccination predicts (and potentially determines) vaccination outcomes. While most of this work has been done using influenza vaccination as a model, pan-vaccine signatures have been also identified. The key implications are their potential use to predict who will respond to vaccinations and to inform strategies for fine-tuning the immune setpoint to enhance immune responses. In addition, investigations in this area led us to understand that immune perturbations, such as acute infections and vaccinations, can remodel the baseline immune state and alter immune responses to future exposures, expanding this exciting field of research. These processes are likely epigenetically encoded, and some examples have already been identified and are discussed in this minireview. Therefore, further research is essential to gain a deeper understanding of how immune exposures modify the epigenome and transcriptome, influence the immune setpoint in response to vaccination, and define its exposure-specific characteristics.