bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph Neural Network-Based Link Prediction for Highly Imbalanced Network Data
Authors: Xiao Yinshuang , Sha Zhenghui 
Published: November 2024

Abstract
The rapid advancement of graph neural networks (GNN) has revolutionized the integration of complex network and neural network models, fostering diverse engineering applications such as the classification of assembly parts and the prediction of customer preferences. GNN-based link prediction (LP), as a representative study, has shown utility in resource allocation and system performance evaluation, as evidenced in the existing literature. However, the inherent challenge of imbalanced network data (i.e., sparse network) from engineering domains poses obstacles to accurate link predictions due to the lack of training data of positive links, leading to biases and reduced performance. In contrast to existing studies that focus on enhancing model architecture, this paper concentrates on exploring preprocessing methods, e.g., the data undersampling strategies, and two post-processing methods for accuracy calculation based on 1) probability threshold-based labeling and 2) probability rank-based labeling, and studies their impacts on the prediction results with a given GNN-based LP model architecture. Real-world network data sourced from shared mobility systems and product market systems, which exhibit various levels of imbalance, are used as test cases. This study contributes to a better understanding of effective data undersampling strategies and post-processing methods for handling imbalanced network data when applying GNN-based LP to real-world complex systems.
Designing Remote Monitoring for Smart Manufacturing Facilities: Hazard Identification and Classification
Authors: Ballestas Caseysimone , Singh Mansidak , Vu Duy , Fillingim Kenton Blane , Goucher-Lambert Kosa 
Published: November 2024

Abstract
This study investigates the process of hazard identification in complex manufacturing environments during the design phase, emphasizing the significance of the design process in developing designs that effectively mitigate hazards in contexts with numerous variables, such as a variety of machines, sensors, actuators, and agents. Through a mixed-methods approach, the objective of this work is to understand how the evolution of design outcomes across various stages might influence a designer’s ability to recognize both standard and novel hazards. To achieve this understanding, an experimental design task was conducted with six designers from a national lab specializing in manufacturing technologies. This approach combined qualitative and quantitative data analysis from a one-hour virtual session with participants. Findings suggest that the complexity of identifying hazards in a high-dimensional design space is challenging within a limited time frame and that the identification of hazards is significantly influenced by the stage of the design task and the initial design decisions, indicating the need for extended time and strategic initial planning in the design process to enhance hazard identification.
Gear Prediction System Based on Ultrasonic Radar and Machine Learning
Authors: Feng Xu , Yang Bo , Yu Liangyao , Hu Ruibo 
Published: November 2024

Abstract
With the rapid development of intelligent vehicles, the emergence of various assisted driving functions has enhanced safety during driving. However, the current mode of shifting in vehicles is mainly through the driver actively operating the gear lever. This mode of shifting not only reduces the usable space inside the vehicle due to the presence of the shifting mechanism but also, because shifting relies more heavily on the driver’s judgment of the environment, incidents of traffic accidents caused by driver’s misoperations and misjudgments occur frequently. To address this issue, this paper proposes a method for predicting the driver’s intention to move forward or backward based on ultrasonic radar. Firstly, a method for detecting obstacles around the vehicle using ultrasonic radar is proposed, which utilizes a pair of ultrasonic radars arranged in an array to locate obstacles around the vehicle based on the principle of elliptical positioning. Based on the location information of obstacles, a simplified vehicle kinematics model is used in conjunction with basic vehicle parameter information to determine the vehicle’s passability. Furthermore, a dataset for different gear shifting targets of the driver in various scenarios is established and trained, equipping the model with the capability to automatically shift gears for the vehicle in different situations. Experimental results show that this method can accurately select the appropriate gear for the vehicle in daily shifting scenarios, thereby enhancing the convenience and safety of driving for the driver in different shifting contexts.
Exploring Latent System Design Description and Requirement Similarities Using Transformer Based Contextual Embeddings
Authors: Carroll Cody L. , Yang Xiaoou , Chen Cheng , Morkos Beshoy 
Published: November 2024

Abstract
Engineering design is heavily influenced by system requirements, as they span the entire design process. Generally, requirements are not utilized to convey system information outside the design process. System information is generally conveyed to stakeholders, such as end users, through generalized descriptions. While requirements and system descriptions both represent the same system to different audiences, the understanding of how each class is related is not well explored, which Large Language Models have now allowed us to do. We employ a method of using pre-trained contextual embeddings from RoBERTa and the resulting UMAP projections to draw conclusions about local and global embedding space characteristics from text-based system information. Though some systems may exhibit overlap or regionalization, results demonstrate that each class (requirements and descriptions) can be utilized to compare similarities between systems from a functional perspective but cannot be directly compared when trying to use requirements and descriptions jointly in the embedding space. The degree to which a system is novel is distinct in the description-based embedding space only by means of the underlying technological principles and not from the form. The implications of this have impacts on designers attempting to leverage LLMs in an attempt to understand how products are differentiable and novel in comparison to other existing systems when either the function of the product is unique, or the physical aspects of the product are significantly different.
Standardized Approach for Assessing Fiber Device Resiliency
Authors: Galligan Conor , Alves Daniel 
Published: November 2024

Abstract
Fiber-attached photonic devices are critical to myriad government systems, e.g. Laser Communication [1], yet most commercially available photonic devices are not tested to the harsh environments required of fielded systems. While there are well-established guidelines for electronic device component testing, such as NASA’s EEE-INST-002 [2], there is no such specification for photonics destined for ruggedized non-telecom environments. This paper presents a specification developed to guide the evaluation of fiber-attached photonic devices for use in ruggedized systems. Component-level testing is specified with the intent of evaluating the likelihood of failure prior to integration into a higher-level assembly, well before system-level environmental testing. This specification was developed leveraging MIT Lincoln Laboratory’s decades of experience successfully upscreening fiber devices for use in delivered government prototypes, as well as surveys of government and industry photonic and electronic device standards. The document a) identifies the technical risks inherent in various component types, b) provides a framework to assess the relevance of manufacturers’ testing, and c) suggests tests that could be performed to burn down the identified risks as a function of key mission parameters such as environment, cost, schedule, and risk tolerance.
Evaluation of Additively Printed Filters on High-Temperature Performance on the Aerojet Platform Using Ceramics Substrate and Laser Ablation Process
Authors: Lall Pradeep , Karakitie Daniel , Soni Ved , Miller Scott 
Published: November 2024

Abstract
Additive processes have gained prominence, employing liquid nanoparticle inks with volatile organic solvent carriers. Printed electronics, known for their advantages over conventional subtractive manufacturing, have found widespread application, particularly in mass-producing antennas for consumer electronics. Aerosol jet printing has been extensively researched for its versatility across orthogonal and traditional 2D surfaces, including compatibility with wire bonding and the development of sensor components crucial for IoT technologies. This research focuses on exploring the performance and process-property interactions of the chips-first fabrication approach with water-based inks on ceramic substrates. Using an iterative approach involving computer-aided design, laser ablation of component pockets, component attachment in pockets, additive printing on fixed components on ceramic substrates with several layers of metallization, and performance testing using frequency response analysis were undertaken. The initial phase meticulously tests the traces printing on a ceramic substrate, followed by the functionality and performance of discrete components. Subsequently, a systematic investigation assessed the circuit realization and the performance. The study aimed to identify key parameters and techniques optimizing the attachment process on ceramic substrates, ensuring the performance and functionality of realized circuits.
Targeted antimicrobial regimens for Gram-negative prosthetic joint infections: a prospective multicenter study
Authors: Hanssen Jaap L. J. , van der Wal Robert J. P. , Mahdad Rachid , Keizer Stefan , Delfos Nathalie M. , van der Lugt Joris C. T. , Veldkamp Karin Ellen , Nolte Peter A. , Leendertse Masja , Gelinck Luc B. S. , Mollema Femke P. N. , Schippers Emile F. , Wattel-Louis Hanke G. , Nelissen Rob G. H. H. , Scheper Henk , de Boer Mark G. J. 
Published: November 2024

ABSTRACT

Fluoroquinolones (FQs) are considered the most effective antimicrobial treatment for Gram-negative prosthetic joint infection (GN-PJI). Alternatives are needed due to increasing FQ resistance and side effects. We aimed to compare different targeted antimicrobial strategies for GN-PJI managed by debridement, antibiotics, and implant retention (DAIR) or one-stage revision surgery (1SR) and to review the literature of oral treatment options for GN-PJI. In this prospective, multicenter, registry-based study, all consecutive patients with a PJI caused by a Gram-negative microorganism (including mixed infections with Gram-positive microorganisms), managed with DAIR or 1SR from 2015 to 2020, were included. Minimum follow-up was 1 year. Patients underwent targeted therapy with oral FQ, oral cotrimoxazole, or intravenous or oral β-lactams. Survival analysis was performed with use of Kaplan-Meier and Cox proportional hazards models to identify factors potentially associated with treatment failure. Seventy-four patients who received either FQ (
n
= 47, 64%), cotrimoxazole (
n
= 13, 18%), or β-lactams (
n
= 14, 18%) were included. Surgical strategy consisted of DAIR (
n
= 72) or 1SR (
n
= 2). Median follow-up was 449 days (interquartile range 89–738 days). Failure free survival did not differ between the FQ (72%) and cotrimoxazole (92%) groups (log rank,
P
= 0.13). This outcome did not change when excluding all pseudomonal PJI in the FQ group. Cotrimoxazole is a potential effective targeted antimicrobial therapy for patients with GN-PJI. A randomized controlled trial is needed to confirm the findings of this study.
A conserved interaction between the effector Sca4 and host clathrin suggests additional contributions for Sca4 during rickettsial infection
Authors: Vondrak Cassandra J. , Sit Brandon , Suwanbongkot Chanakan , Macaluso Kevin R. , Lamason Rebecca L. 
Published: November 2024

ABSTRACT

Intracellular bacterial pathogens deploy secreted effector proteins that manipulate diverse host machinery and pathways to promote infection. Although many effectors carry out a single function or interaction, there are a growing number of secreted effectors capable of interacting with multiple host factors. However, few effectors secreted by arthropod-borne obligate intracellular
Rickettsia
species have been linked to multiple host targets. Here, we investigated the conserved rickettsial secreted effector Sca4, which was previously shown to interact with host vinculin in donor cells to promote cell-to-cell spread in the model
Rickettsia
species
R. parkeri
. We discovered that Sca4 also binds the host cell protein clathrin heavy chain (CHC,
CLTC
) via a conserved segment in the Sca4 N-terminus. In mammalian host cells, ablation of
CLTC
expression or chemical inhibition of endocytosis reduced
R. parkeri
cell-to-cell spread
,
indicating that clathrin promotes efficient spread. Unexpectedly, the contribution of CHC to spread was independent of Sca4 and appeared restricted to the recipient host cell, suggesting that the Sca4–clathrin interaction regulates another aspect of the infectious lifecycle. Indeed,
R. parkeri
lacking Sca4 or expressing a Sca4 truncation unable to bind clathrin had markedly reduced burdens in tick cells, hinting at a cell type-specific function for the Sca4–clathrin interaction. Sca4 homologs from diverse
Rickettsia
species also bound clathrin, suggesting that the function of this novel effector–host interaction may be broadly important for rickettsial infection. We conclude that Sca4 has multiple targets during infection and that rickettsiae may manipulate host endocytic machinery to facilitate several stages of their life cycles.
A global lipid map of severe fever with thrombocytopenia syndrome virus infection reveals glycerophospholipids as novel prognosis biomarkers
Authors: Tian Panpan , Zhao Liwei , Zhang Guiting , Chen Shixing , Zhang Wanying , Ou Mingrong , Sun Yidan , Chen Yuxin 
Published: November 2024

ABSTRACT

Severe fever with thrombocytopenia syndrome (SFTS) is a rapidly progressing infectious disease caused by a novel bunyavirus characterized by high fever, thrombocytopenia, and multiple organ damage. While lipids play an important role in viral infections, the specific alterations in lipid metabolism during SFTSV infection remain unclear. This study aimed to elucidate the global lipid metabolic profiles of SFTS patients with mild, severe, and fatal outcomes. A total of 60 SFTS patients, consisting of 30 mild, 15 severe and 15 fatal patients, and 30 healthy controls, were enrolled for the investigation of global lipidomics in serum using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our findings revealed global alterations in the lipid signature induced by SFTSV infection and further confirmed that the glycerophospholipid metabolism pathway was profoundly affected during the progression of mild, severe, and fatal outcomes in SFTS patients. Importantly, LysoPC (20:0) and LysoPC (P-16:0) are strongly correlated with the clinical parameters of SFTSV infection. Furthermore, we demonstrated the substantial prognostic value of LysoPC (20:0) and LysoPC (P-16:0) by receiver operating characteristic (ROC) curve analysis, providing evidence for their remarkable value as prognostic biomarkers for predicting SFTS clinical outcomes. In particular, LysoPC (20:0) and LysoPC (P-16:0), along with APTT, yielded superior prognostic performance for fatal SFTS [area under the curve (AUC) = 98.4%], outperforming routine clinical parameters. Collectively, our findings revealed the lipidomic landscape after SFTSV infection, which offers new insights into the mechanisms of SFTS disease progression and suggests that targeting lipid metabolism may serve as a potential therapeutic strategy.

IMPORTANCE
This study systematically investigated the lipid landscape profile of SFTS-infected patients with different clinical outcomes. Our results revealed a global alteration in the lipid signature, particularly the glycerophospholipid metabolic pathway, induced by SFTSV infection. Notably, LysoPC (20:0) and LysoPC (P-16:0) presented remarkable prognostic value as novel biomarkers for SFTSV infection and may contribute to the prognosis of SFTS progression and appropriate interventions.
When more sugar is better—a GPI side chain modification results in a less virulent phenotype during a protozoan infection
Authors: Seeber Frank 
Published: November 2024

ABSTRACT

The assembly and function of side chain modifications of glycosylphosphatidylinositol (GPI) units (anchors or free forms) are poorly defined. In a recent study, two enzymes, PIGJ and PIGE, of the protozoan parasite
Toxoplasma gondii
were identified and shown to be involved in the assembly of such GPI side chains (J. A. Alvarez, E. Gas-Pascual, S. Malhi, J. C. Sánchez-Arcila, et al., mBio 15:e00527–24, 2024,
https://doi.org/10.1128/mbio.00527-24
). PIGJ adds N-acetylgalactosamine to the GPI core structure, while PIGE subsequently adds a terminal glucose. Deletion of PIGJ resulted in the loss of the side chain and, strikingly, increased mortality in infected mice, in contrast to PIGE knockouts. Absence of the side chain led to increased binding of the scavenger receptor CD36 to mutant parasites. In galectin-3 knockout mice, the virulent phenotype of side-chain-deficient parasites was largely lost. While the exact mechanisms remain to be elucidated by more experiments, these findings provide the first evidence for the importance of GPI side chains in parasite-host interactions
in vivo
.
Complete genome sequence of
Marinomonas
sp. strain THO17 isolated from the leaf surface of the seagrass (
Thalassia hemrichii
)
Authors: Tsuchiya Yuki , Yokoyama Ushio , Takahashi Reiji , Nakagawa Tatsunori 
Published: November 2024

ABSTRACT

Here, we report the genome sequence of the
Marinomonas
sp. strain THO17. The assembled genome consisted of a single circular chromosome of 3,920,899 bp, with a 43.6% G+C content. Genome analysis revealed that strain THO17 potentially interacts with marine plants.
Dynamics and biodiversity of microbial community among seasons in Shanxi mature vinegar fermentation by semisolid-solid process
Authors: Li Chen , Kou Rong , Jia Yingying , Fan Xiaojun , Shi Ying , Chen Qihe 
Published: November 2024

ABSTRACT

The dynamic succession and seasonal characteristics of microbiota throughout the Shanxi mature vinegar (SMV) fermentation by the semisolid-solid process were explored using high-throughput sequencing techniques. The results showed that the richness and diversity of fungi were higher than those of bacteria in a complete seasonal SMV fermentation cycle, and the microbial community was dominated by 11 taxa of bacteria and 16 taxa of fungi. In all four seasons, lactic acid bacteria and acetic acid bacteria were the dominant bacteria, while the dominant fungi varied.
Saccharomyces
and
Pichia
played an important role in spring.
Aspergillus
and
Issatchenkia
were enriched in the summer.
Kazachstania
was the dominant microorganism in autumn. While
Mesenteroides
and
Meyerozyma
were enriched in winter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis demonstrated that seasonality had a more decisive impact on microbiota composition than the fermentation stage within a season, and the microbiota structure in summer was significantly different from that in the other three seasons. Combined with the highest operational taxonomic units (OTUs) percentage (37%) of summer fungi in the Venn diagrams, it is speculated that the specific fungi may be the root cause for the relatively low SMV quality in summer. This work provided critical insights into the dynamic succession of the microbial community in SMV fermentation from a seasonality view, and the results could enrich our understanding of the microbiota involved in SMV fermentation and guide process control.

IMPORTANCE

Understanding the changes in microbial communities across different seasons is crucial for ensuring the quality of Shanxi mature vinegar (SMV) by the semisolid-solid process. In a complete seasonal cycle, the richness and diversity of fungi were higher than those of bacteria. The microbial community in summer fermentation was significantly different compared to the other three seasons. For example, the dominant microorganisms such as
Acetobacter
and
Lactobacillus
decreased in summer. Screening or modifying this group of bacteria to enhance their tolerance to high fermentation temperature is an approach to improve industrial SMV fermentation. Through co-occurrence network analysis, eight highly connected genera were identified, which may play important roles in ecosystem stability. These results also lay a theoretical foundation for the further development of multi-microbial co-fermentation. This work provides an understanding of SMV fermentation from a seasonal perspective and offers new guidance for the process control of grain vinegar brewing.
A chlorine isotope transect across Sudbury Basin (Canada) impact deposits reveals systematic isotope fractionation
Authors: Barrett T.J. , Nagashima K. , Huss G.R. , Boyce J.W. , Robinson K.L. , Kring D.A. 
Published: November 2024

Abstract
Large-scale impacts are known to have a significant effect on volatile systematics (e.g., hydrogen and chlorine) owing to syn- and post-shock pressures and temperatures allowing for ready volatile loss and isotopic fractionation. We determined the Cl isotopic composition and [Cl] and [H2O] for apatite from 10 samples of the Sudbury impact structure in Canada. The high [Cl] and invariant δ37Cl values in the lower norite are attributed to footwall assimilation in agreement with recent Zn and Pb data. The granophyre, the top of the Sudbury Igneous Complex, displays loss and fractionation of Cl (up to +6.26‰) indicative of degassing under a high gas pressure regime with high [H2O] further buffering isotope fractionation. Similar impacts on dry, airless bodies such as the Moon may have permitted greater amounts of isotopic fractionation, supporting extremely fractionated lunar materials as evidence for the large-scale impact-derived degassing hypothesis. The modest fractionation (up to +8.15‰) and morphologically distinct apatite of the Onaping Formation can be explained by post-impact hydrothermal alteration.