bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical Modeling Toolbox for Diffraction Problems of Common Shaped Bodies
Authors: Nguyen Nhu 
Published: August 2024

Abstract
The present study aims to develop an open-source Python-based toolbox for the theoretical modeling of diffraction problems in commonly shaped bodies. The project has dual objectives: 1) to offer a quick and efficient means for design exploration during the initial project phase and 2) to serve as a tool for code comparison and benchmarking for numerical models. While numerical solvers are commonly employed due to the complexity of obtaining exact solutions, our prior work on OSWEC modeling has demonstrated the advantages of an analytical approach, characterized by a simple setup and significantly quick computational time (typically less than a second for a hundred cases). This analytical approach is well-suited for early stages of project development, encompassing design space exploration and device geometry optimization. The current phase of the toolbox includes diffraction solutions for three fundamental cylindrical bodies: bottom-seated surface-piercing cylinder, truncated cylinder, and bottom-seated surface-piercing elliptical cylinder. The outputs encompass domain velocity potentials, excitation forces, and moments, all validated using Capytaine (a Boundary Element Method modeling program). The project is ongoing and is planned for expansion to provide solutions for other shapes. Additionally, an extension of the program to include radiation problems is also scheduled.
Procedure to Include the Dynamic Loads of Catenary Shaped Risers on FPSO Roll Motion Assessments
Authors: Chads Carlos Eduardo , de Tarso Esperança Paulo 
Published: August 2024

Abstract
This work describes a procedure to include dynamic loads of catenary shaped risers to the roll motion response calculation of a Floating Production Storage and Offloading (FPSO) unit in the frequency domain. The procedure involves the application of an asymptotic solution for the dynamic tension at the top of risers based on the work of Aranha & Pinto [1]. It is assumed, as an approximation, that the riser dynamic tensions are sinusoidal when the FPSO is under the action of regular waves (this hypothesis is related to the assumption that the quadratic hydrodynamic damping is linearized in the chosen formulation). Since the dynamic tension expression is amplitude dependent, the described procedure is iterative. This work is restricted to the heave and roll motions, but focused on the roll response analyses. The roll response was analyzed for the case study FPSO under beam regular waves coming from portside and starboard, with 60 catenary shaped flexible risers connected. The roll RAOs calculated with the described procedure have presented a good agreement with the roll motions calculated with a coupled time-domain model in OrcaFlex™. From the hull “point of view”, the effect of the riser loads can be considered as equivalent to additional inertia, damping and stiffness effects, which are quantified for the case study of this work.
Vertical Axis Autorotation Current Turbine (VAACT) Analysis With Power Take-Off System
Authors: Soares Rodrigo B. , Fernandes Antonio C. , S. Sales Junior Joel 
Published: August 2024

Abstract
This research paper examines the effectiveness of the Vertical Axis Autorotation Current Turbine (VAACT) by conducting simulations using a two-dimensional Computational Fluid Dynamics (CFD) model. The verification and validation are carried out using the recommended practices from the International Towing Tank Conference (ITTC) [1]. The verification process includes checking the domain, grid, and time-step, and the model results are compared to tests at the Laboratory of Waves and Currents (LOC-COPPE/UFRJ) using an S-shaped VAACT profile. In the CFD environment, the power take-off (PTO) system is modeled by adding an external torque due to the PTO system and the damping coefficient (Kt) into a User-Defined Function (UDF). The validation is performed at Reynolds numbers ranging from 70,000 to 135,000. The time series analysis indicates that both lift and drag forces play a crucial role in the turbine’s performance. Although the instantaneous efficiency is in phase with the drag force, the lift is responsible for driving the device at smaller drag magnitudes. Additionally, the torque coefficient is in phase with the lift force, which implies that the hydrodynamic performance can be governed by it. The analysis also reveals that the returning blade adds a resisting torque on the turbine, which may impact its performance, as represented by high-pressure points at this blade.
Validation of Local Structural Loads Computed by OpenFAST Against Measurements From the FOCAL Experimental Campaign
Authors: Carmo Lucas , Bergua Roger , Wang Lu , Robertson Amy 
Published: August 2024

Abstract
This work presents the validation of the local structural load modeling capability in OpenFAST for floating substructures based on data from the FOCAL experimental campaign. Previously, OpenFAST could only represent the floating substructure as a rigid body, and though this approach can model the global response of the floater in most cases, it is not able to capture the structural loads within the floater’s individual members. Consideration of local substructure loads is important for some floating designs, because the pursuit of cost reduction often results in lighter and more flexible structures. To address this limitation, the HydroDyn (hydrodynamics) and SubDyn (substructure dynamics) modules of OpenFAST have been recently extended to account for the flexibility of floating substructures. To validate this new capability, we compare the results obtained by OpenFAST with data measured during the FOCAL experimental campaign, which analyzed a 1:70 scale performance-matched model of the IEA 15-MW reference turbine atop a modified University of Maine VolturnUS-S semisubmersible in a wave basin under the action of both wind and waves. For the purposes of the present work, the most important feature of the experiment is the presence of load cells at the root of each pontoon, and our objective is to assess how well those loads are reproduced by OpenFAST. To model the distributed hydrodynamic and hydrostatic loads along the floating substructure, we adopt a strip-theory approach based on the Morison equation, and we discuss the impact of different hydrodynamic modeling options (wave stretching, MacCamy-Fuchs correction, and second-order wave kinematics) on both motions and loads. For simplicity, we focus on wave-only conditions, both regular and irregular. The results demonstrate good overall agreement for the loads at the root of the pontoons for the waves analyzed in this work, especially given the assumptions and simplifications inherent to a simple strip-theory model.
Optimizing Subsea Rock Installation for Cost Savings: A Norwegian Shelf Case Study
Authors: Xie Xiyang , Vermeulen Otilia , Gao Hao , Nazari Moeen , Asklund Per Olav , Lunde Bjørn , Rasmussen Stian Laland 
Published: August 2024

Abstract
In offshore engineering, Subsea Rock Installation (SRI) is a cost-intensive process. This study focuses on a pipe-in-pipe project in the Norwegian Continental Shelf (NCS), addressing the challenges posed by a soft-clay seabed and deep iceberg scars. Traditional 2D limit equilibrium methods (LEM) often fail to capture the complex realities of these environments, particularly in terms of 3D seabed and rock geometry, and comprehensive material behavior. The rock volume based on 2D LEM design is also over conservative. Recognizing these limitations, this research advocates for the adoption of a 3D finite element method (FEM), which offers a more accurate analysis. By employing FEM, particularly for the stability of free-span infills in deep iceberg scars, it aims to optimize rock volume usage. The results suggest potential cost reductions up to 16%, underscoring the value of embracing more comprehensive design and simulation processes. These insights offer valuable guidance for future offshore engineering projects, paving the way for more efficient and confident design strategies.
Digital Twin Modelling for Full-Electric Harbour Craft: An Integrated Hydrodynamics and Systems Model
Authors: Hadi Januwar , Zhi Yung Tay , Kudupudi Ravindra , Taskar Bhushan , Tan Ching Eng , Singh Chopra Prabjot , Peng Neil , Konovessis Dimitrios 
Published: August 2024

Abstract
Marine vessels have undergone a significant transformation with the advent of digital twin technology. Digital twins, which are virtual replicas of physical vessels, have revolutionized the maritime industry by enhancing decision-making processes that manifest in operational efficiency and better ship design. This paper presents an overview of digital twins for a marine vessel, a full-electric harbour craft, highlighting their key components, creation & validation, applications, and future potential. Furthermore, the paper discusses the integration of the hydrodynamics model as a comprehensive digital twin model. The application of digital twins is beneficial, but not limited to planning, training, and safety. It is by inferring the digital twin model for simulation to predict range & speed, crew training and stress tests respectively. The digital twin model may eventually contribute to cost savings, environmental sustainability, improved overall vessel performance, and subsequent designs.
This paper also explores the challenges and limitations of digital twins in the maritime domain, such as power & operational envelopes, interoperability, and the need for skilled personnel. Addressing these challenges is crucial for the widespread adoption and success of digital twin technology in the marine industry. The adoption of digital twins offers to redefine the way marine vessels are designed & operated, leading to a more efficient, and environmentally friendly maritime industry.
A Thermal-Electromagnetic Assessment of Dynamic Umbilicals for Ultra Deep Waters
Authors: Cestari Coutinho Filipe , Morini Rafael Giovane , Camporez Danieli 
Published: August 2024

Abstract
Subsea Umbilicals are design to supply different functions, according to the needs of subsea production systems. These needs can include power distribution, monitoring, hydraulic and electric control.
Ultra deep waters already present a challenge to the mechanical design of the product, demanding a high-performance structural behavior but keeping important properties such as its weight and bending stiffness.
Besides the mechanical aspects to the design of subsea umbilical, when the umbilical functions include in same cross section power function, electrical control and optical monitoring, a care shall be taken to the thermal and electromagnetic aspects.
Prysmian performed a study to assess the behavior of a dynamic umbilical applied to ultra deep water scenarios, considering the mechanical, thermal and electromagnetic aspects of design.
The study presented results that shown that the positioning of the components has a significant influence on the efficiency of the subsea umbilical under application, both in thermal and electromagnetic aspects.
Mental Fatigue in Sport—From Impaired Performance to Increased Injury Risk
Authors: Schampheleer Emilie , Roelands Bart 
Published: August 2024

The literature describing the effects of mental fatigue (MF) has grown tremendously. This is accompanied by identification of a host of performance-determining parameters affected by MF. MF results from prolonged cognitive effort and predominantly affects physical, technical, tactical, and perceptual–cognitive dimensions of sport, while physiological parameters (eg, heart rate, lactate) and physical aspects of maximal and supramaximal efforts are predominantly unaffected. The aim of this paper was to provide an overview of the parameters described in the literature as influenced by MF. By identifying the different parameters, we not only see how they affect the performance of athletes but also raise concerns about the potentially increased injury risk due to MF. Preliminary evidence suggests that subsequent disturbances in balance, motor skills, and decision-making processes could potentially increase the vulnerability to injury. An abundance of lab-based studies looked into the effects of MF on performance; however, many questions remain about the mechanisms of origin and neurophysiological causes of MF, and only small steps have been taken to translate this knowledge into practice. Thus, there is a need for more research into the underlying mechanisms of MF and the role of the brain, as well as more applied research with a high ecological validity that also takes into account the potential increased risk of injury due to MF.
Three separate pathways in
Rhizobium leguminosarum
maintain phosphatidylcholine biosynthesis, which is required for symbiotic nitrogen fixation with clover
Authors: Kleetz Julia , Mizza Ann-Sophie , Shevyreva Irina , Welter Leon , Brocks Claudia , Hemschemeier Anja , Aktas Meriyem , Narberhaus Franz 
Published: August 2024

ABSTRACT

Phosphatidylcholine (PC) is critical for the nitrogen-fixing symbiosis between rhizobia and legumes. We characterized three PC biosynthesis pathways in
Rhizobium leguminosarum
and evaluated their impact on nitrogen fixation in clover nodules. In the presence of choline, a PC synthase catalyzes the condensation of cytidine diphosphate-diacylglycerol with choline to produce PC. In the presence of lyso-PC, acyltransferases acylate this mono-acylated phospholipid to PC. The third pathway relies on phospholipid
N
-methyltransferases (Pmts), which sequentially methylate phosphatidylethanolamine (PE) through three rounds of methylation, yielding PC via the intermediates monomethyl-PE and dimethyl-PE. In
R. leguminosarum
, at least three Pmts participate in this methylation cascade. To elucidate the functions of these enzymes, we recombinantly produced and biochemically characterized them. We moved on to determine the phospholipid profiles of
R. leguminosarum
mutant strains harboring single and combinatorial deletions of PC biosynthesis genes. The cumulative results show that PC production occurs through the combined action of multiple enzymes, each with distinct substrate and product specificities. The methylation pathway emerges as the dominant PC biosynthesis route, and we pinpoint PmtS2, which catalyzes all three methylation steps, as the enzyme responsible for providing adequate PC amounts for a functional nitrogen-fixing symbiosis with clover.

IMPORTANCE

Understanding the molecular mechanisms of symbiotic nitrogen fixation has important implications for sustainable agriculture. The presence of the phospholipid phosphatidylcholine (PC) in the membrane of rhizobia is critical for the establishment of productive nitrogen-fixing root nodules on legume plants. The reasons for the PC requirement are unknown. Here, we employed
Rhizobium leguminosarum
and clover as model system for a beneficial plant-microbe interaction. We found that
R. leguminosarum
produces PC by three distinct pathways. The relative contribution of these pathways to PC formation was determined in an array of single, double, and triple mutant strains. Several of the PC biosynthesis enzymes were purified and biochemically characterized. Most importantly, we demonstrated the essential role of PC formation by
R. leguminosarum
in nitrogen fixation and pinpointed a specific enzyme indispensable for plant-microbe interaction. Our study offers profound insights into bacterial PC biosynthesis and its pivotal role in biological nitrogen fixation.
Holistic understanding of trimethoprim resistance in
Streptococcus pneumoniae
using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning
Authors: Pham Nguyen-Phuong , Gingras Hélène , Godin Chantal , Feng Jie , Groppi Alexis , Nikolski Macha , Leprohon Philippe , Ouellette Marc 
Published: August 2024

ABSTRACT

Antimicrobial resistance (AMR) is a public health threat worldwide. Next-generation sequencing (NGS) has opened unprecedented opportunities to accelerate AMR mechanism discovery and diagnostics. Here, we present an integrative approach to investigate trimethoprim (TMP) resistance in the key pathogen
Streptococcus pneumoniae
. We explored a collection of 662
S
.
pneumoniae
genomes by conducting a genome-wide association study (GWAS), followed by functional validation using resistance reconstruction experiments, combined with machine learning (ML) approaches to predict TMP minimum inhibitory concentration (MIC). Our study showed that multiple additive mutations in the
folA
and
sulA
loci are responsible for TMP non-susceptibility in
S. pneumoniae
and can be used as key features to build ML models for digital MIC prediction, reaching an average accuracy within ±1 twofold dilution factor of 86.3%. Our roadmap of
in silico
analysis—wet-lab validation—diagnostic tool building could be adapted to explore AMR in other combinations of bacteria–antibiotic.

IMPORTANCE

In the age of next-generation sequencing (NGS), while data-driven methods such as genome-wide association study (GWAS) and machine learning (ML) excel at finding patterns, functional validation can be challenging due to the high numbers of candidate variants. We designed an integrative approach combining a GWAS on
S. pneumoniae
clinical isolates, followed by whole-genome transformation coupled with NGS to functionally characterize a large set of GWAS candidates. Our study validated several phenotypic
folA
mutations beyond the standard Ile100Leu mutation, and showed that the overexpression of the
sulA
locus produces trimethoprim (TMP) resistance in
Streptococcus pneumoniae
. These validated loci, when used to build ML models, were found to be the best inputs for predicting TMP minimal inhibitory concentrations. Integrative approaches can bridge the genotype-phenotype gap by biological insights that can be incorporated in ML models for accurate prediction of drug susceptibility.
Demographic and zoological drivers of infectome diversity in companion cats with ascites
Authors: Sun Yankuo , Xing Jiabao , Xu Sijia , Li Yue , Zhong Jianhao , Gao Han , Cheng Song , Dong Jun , Zhang Tianyou , Lu Gang , Baele Guy , Zhang Guihong 
Published: August 2024

ABSTRACT

Cats (
Felidae
) have become an integral part of many households. However, our understanding of the full spectrum of pathogens affecting cats (referred to as the infectome) is limited, mainly due to the inadequacy of commonly used diagnostic tools in capturing the complete diversity of potential pathogens and the prevalence of pathogen co-infections. In this study, we employed a meta-transcriptomic approach to simultaneously characterize the infectome contributing to different disease syndromes and to investigate spatial, demographic, and ecological factors influencing pathogen diversity and community composition in a cohort of 27 hospitalized cats and seven stray cats. We identified 15 species of pathogens, with
Candidatus Rickettsia tarasevichiae
and
Tritrichomonas foetus
representing potential spillover risks. Importantly, although most cases of ascites hyperplasia were explained by coinfection with multiple pathogens, we identified the potential novel clinical outcomes of
M. aubagnense
infection among cats. We demonstrated that the increase in infectome diversity can be explained by a variety of predictors including age growth, temperature increase, and a higher proportion of females, with age growth presenting the strongest effect. Fine-scale analysis indicated that a higher diversity of infectomes were harbored in young cats rather than adult ones. Our results demonstrated that most feline diseases are better explained by the presence of virus–bacteria or virus–virus coinfection. This study serves as a timely endorsement for clinical diagnosis by vets to consider the cause of a disease based on a panel of cryptical co-infecting pathogens rather than on individual infectious agents.

IMPORTANCE

Frequent studies reported the risks of cats as an intermediate host of zoonotic pathogens (e.g., SARS-CoV-2). Cats have a physically close interaction with their owners through activities like petting, kissing, and being licked on the cheek and hands. However, there are still limited studies that systematically investigate the infectome structure of cats. In this study, we employed a meta-transcriptomics approach to characterize 15 species of pathogens in cats, with
Candidatus Rickettsia tarasevichiae
first characterizing infection in diseased cats. Most feline diseases were better explained by the presence of virus–bacteria or virus–virus coinfection. The increase in infectome diversity could be influenced by a variety of predictors including age growth, temperature increase, and a higher proportion of females. A higher diversity of pathogens was harbored in young cats rather than adults. Importantly, we showed the value of linking the modern influx of meta-transcriptomics with comparative ecology and demography and of utilizing it to affirm that ecological and demographic variations impact the total infectome.
Evolution and uranium mineralization of the northern Ordos Basin revealed by detrital zircons of the Jurassic strata
Authors: Liu Yuan , Liu Hang , Jiao Yang-Quan , Zhao Jun-Hong 
Published: August 2024

Abstract
Stable sedimentary basins with complex evolutionary histories generally develop various epigenetic resources, such as sandstone-type uranium deposits. However, the genetic linkage between basin evolution and subsequent uranium mineralization remains unclear. Detrital zircon is a robust mineral, and its U-Pb ages and Lu-Hf isotopes are essential for tracing the evolution of sedimentary basins. The Ordos Basin is the largest intracontinental basin and uranium deposit region in the North China Craton. It consists of Cambrian to Ordovician marine deposits and Carboniferous to Jurassic terrestrial successions, and the origins of the terrigenous clastic sequences are dominantly influenced by the neighboring orogenic belts. This study presents new whole-rock elemental data, detrital zircon U-Pb ages, and Lu-Hf isotopes for the sandstones from the Jurassic Zhiluo Formation of the northern Ordos Basin. With data from the Paleozoic sedimentary rocks of the basin and the southern Central Asian Orogenic Belt, this study aimed to determine sediment provenances, the evolution of the northern Ordos Basin, and the potential implications for uranium mineralization. Detrital zircons from the Zhiluo Formation are generally rounded and preserve magmatic zoning structures. Their ages display four populations, 330–245 Ma, 470–350 Ma, 2100–1650 Ma, and 2750–2200 Ma, which are consistent with the tectono-thermal events of the Central Asian Orogenic Belt and the Yinshan Belt to the north, and the Alxa Block to the northwest. Both their detrital zircon ages and εHf(t) values are similar to those of the underlying sedimentary rocks. In addition, the formation has recycled carbonaceous debris, diverse clastic fragments, and Triassic fossils, and its sandstones show low index of compositional variability values (0.79–0.97) and high SiO2/Al2O3 (5.33–7.25) and Th/Sc (0.71–1.97) ratios. These lines of evidence suggest that the detritus of the Zhiluo Formation was partially derived from the underlying sedimentary strata. It should be noted that the Paleozoic to Mesozoic strata of the northern Ordos Basin also have detrital zircon age patterns and εHf(t) values similar to those of the southern Central Asian Orogenic Belt, and the secular evolution of the Ordos Basin is therefore considered to have been controlled by subduction of the Paleo-Asian Ocean and collision between the Central Asian Orogenic Belt and the North China Craton, as well as the post-collisional crustal extension that ensued. The carbonaceous debris in the Zhiluo Formation provided a reductive environment for the subsequent crystallization of reducing minerals and uranium mineralization.