bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrodynamic Forces for HVDC Cable Bundles Under Wave and Steady Current Conditions
Authors: Griffiths Terry , Pretorius Joshua , Tong Feifei , An Hongwei , Draper Scott , Riverola Calavia Javier , Ledoux Bart , Pistani Fabrizio
Published: August 2024

A collaborative study between The University of Western Australia (UWA), Southern Cross University (SCU), Aurora Offshore Engineering (AOE) and Jan de Nul (JDN) was undertaken to investigate the hydrodynamic forces experienced by a single cable and cable bundle at various angular orientations under steady and oscillatory flow conditions. Physical model testing was undertaken at the UWA Large O-Tube (LOT) Facility, which is located at UWA’s Coastal Ocean Research Laboratories (CORL). This testing was conducted at 1:1 scale, with the capacity of the O-Tube able to replicate flow conditions relevant for design. Computational Fluid Dynamics (CFD) modelling was undertaken to complement the physical testing and aid in interpretation of the results, including flow visualization and accounting for the effects of flow blockage in the water flume.

These test results represent novel contributions to the understanding of hydrodynamic forces for HVDC single pipe and bundle configurations accounting for the influence of a number of critical flow parameters, including Reynolds number (current velocity), Keulegan-Carpenter number (wave characteristics), surface roughness (pipe features), incoming turbulence intensity and bundle orientation. It is anticipated that these improvements in understanding contribute very helpfully to improving the safe workable range of metocean conditions in which these cables may be installed, lowering the risks of cable damage and improving the costs of installing the cables.
Annular Fluid Forces Generated by a Non-Newtonian Fluid With Variable Flowrate and Non-Uniform Rotational Pipe Movement
Authors: Cayeux Eric
Published: August 2024

In drilling operations, the precise estimation of annular fluid forces on a pipe is important to determine the drill-string movement in dynamic conditions. Yet, drilling fluids have a complex rheological behavior, and the inner pipe is usually eccentric and rotates. The pipe movement is usually non-uniform like for example when there are torsional stick-slips. Furthermore, the flow of liquid in the annulus is usually unsteady either because of pump acceleration or because of the axial pipe movement. With all these non-uniform movements of the inner pipe geometrical boundary and the accelerated flow of the fluid itself, it is unclear what is the hydraulic force applied by the fluid on the exterior of the pipe. A relationship that links the pipe movement to the total hydraulic force is derived. However, the total hydraulic force applies to both the wellbore and the pipe, and it is not evident in which proportion the total hydraulic force contributes to the hydraulic force on the pipe. To address this problem, computational fluid dynamic simulations are run to estimate the hydraulic force on a pipe subject to dynamic flow and pipe rotation conditions. It is found that even though the total hydraulic force varies substantially due to the dynamic boundary conditions, the proportion of the force that applies to the pipe varies in a much lesser extent. This proportion is compared to theoretical value corresponding to Newtonian fluids in steady-state conditions. It is found that the proportion is a linear function of the proportion for Newtonian fluids.
The Importance of Local Hydroelastic Effects When Calculating Structural Response From Measured Wave Slamming Pressures
Authors: Abrahamsen Bjørn Christian , Holstad Anders , Hellan Øyvind
Published: August 2024

The effect of hydroelasticity on local structural response due to measured wave impact loads are discussed. The structure considered are the vertical beams at the upper flare of a SEVAN SSP FPSO. The first method uses a modal method with uniform and constant added mass. The accuracy of this type of calculation is investigated through comparisons with a complete hydroelastic calculation. These hydroelastic calculations account for the load modifications due to the structural response in a consistent manner. This means that the added mass is time dependent and the effect of slam damping is included. As the load modifications due to the structural deformation is primarily a dynamic effect, the effect of hydroelasticity is discussed through dynamic amplification factors (DAF). The analyses show that the calculated DAFs relevant for the measured wave slamming loads are in a range where the simplified method using only uniform and constant added mass overestimates the structural response considerably in most cases. As an example, the responses from the simplified calculations are in the range of 30 to 40% higher than the response from the fully hydroelastic calculations for the two wave slams with the highest pressures.
A Calibrated Service Life Wear Model for the Pressure Armor Layer in Unbonded Flexible Pipes
Authors: Nielsen Christian Bergenstof , Christiansen Mads Peter , Gupta Abhishek , Juul Nicolai Ytterdal , Dhar Somrita , Pedersen Tommy
Published: August 2024

An important design driver of an unbonded flexible pipe is often the fatigue life of the tensile armor layers. However, in pursuit of providing the market with durable, high-spec flexible pipe structures suited for increasingly higher operating bore pressures, it has also been found that the wear of the pressure armor layer should also be understood and quantified to assess the service life of a flexible pipe.

This paper presents a novel approach to getting a direct coupling between the full-scale modeling of the flexible pipe and the wear of the pressure armor. This was done by measuring the wear of pressure armor samples extracted from an in-plane bending test portfolio. In this way, it has been possible to correlate the wear level to a large range of loads, pipe diameters, steel grades, and pressure armor geometries.

These measurements, combined with other details of full- and small-scale tests, have made it possible to develop a calibrated model that assesses the wear in the pressure armor layer. In this manner, it is now possible to quantify the wear in service conditions and use it to establish the influence on the service life.

The originality in this work is twofold: Based on wear measurements on pressure armor wires extracted from full-scale specimens, the wear rate in the pressure armor layer is shown to scale with slip amplitude. This phenomenon is known generally but has not been reported earlier for the unbonded flexible pipe. Further, the wear data from full-scale test specimens has been used to produce a calibrated model.

Even though the failure mode in the pressure armor has shown to be rare, it is important to include the relevant phenomenon in the model as pressures increase.
Simulation-Based Analysis of Parametric Rolling in Head Sea Conditions
Authors: Agrahri Gangesh Kumar , Somayajula Abhilash
Published: August 2024

This paper focuses on a significant maritime challenge, investigating the dangerous phenomenon called parametric rolling in KRISO Container Ships (KCS) using advanced numerical methods. The publicly available data from KCS serves as a valuable benchmark for study. The study highlights the benefits of employing numerical simulations, which provide a cost-effective and controlled approach to understanding complex non-linear phenomena like parametric rolling. The research highlights how fine hull structure, pronounced bow flare and flat transom stern in Container Ships make them particularly vulnerable to this phenomenon. The study employs a time-domain nonlinear simulation tool (HydRA - Hydrodyanamics Response Amplitude) with six degrees of freedom to simulate the ship’s motion nearly accurately. The tool effectively integrates linear radiation and scattering forces from the frequency domain program while handling the non-linear aspects of incident, restoring, and inertial forces. Comprehensive testing of the simulation tool against the head sea (at zero speed) conditions contributing to parametric rolling confirms its close approximation of parametric roll behaviour. This thorough study notably advances the safety of container ships and their crews by offering a more profound comprehension of the complex dynamics associated with parametric rolling and the crucial elements that impact its occurrence. The knowledge derived from this research is vital in refining ship designs and establishing effective measures to mitigate the risks associated with parametric rolling.
Down-Scale Wave Hydrodynamic Analysis for Marine Structures - the NORA-SARAH Approach
Authors: Wang Widar Weizhi , Christakos Konstantinos , Pákozdi Csaba , Bihs Hans
Published: August 2024

In a simulation-based and data-driven engineering approach, open-access met-ocean data sets and open-source simulation tools are critical elements for marine structure designs. In this work, the authors propose a combined approach for down-scale numerical modelling from offshore met-ocean data to wave loads on structures. The large-scale hind-cast database NORA3 and NORA10 from the Norwegian Meteorology Institute (MET) are used as offshore inputs. The open-source spectral wave model SWAN is used to simulate offshore waves in combination with local wind forcing. The spectral modelling results are then used as inputs in the open-source hydrodynamics framework REEF3D. Its fully nonlinear potential flow (FNPF) module REEF3D::FNPF is used for phase-resolving coastal wave propagation and nonlinear transformation simulations. The arbitrary Eulerian-Lagrangian (ALE) method is integrated into the FNPF model for highly efficient multi-body farm-scale force calculations and extreme events identifications. The extreme events are then closely examined using the hydrodynamic coupling (HDC) approach by transferring the flow kinematics from REEF3D::FNPF to the high-fidelity computational fluid dynamics (CFD) model REEF3D::CFD for fluid-structure interaction analysis. The down-scale approach using the open-access met-ocean data NORA3 and open-source numerical tools and techniques SWAN-REEF3D-ALE-HDC (SARAH) leads to the open and efficient preliminary and detailed design procedure: the NORA-SARAH procedure. This article elaborates on the procedure and demonstrates its effectiveness with an example of a navigational signal tower assessment on the Norwegian coast.
Wave Diffraction and Radiation From a Floating Platform With a Moonpool Array
Authors: Zhou Yao , Zhao Xuanlie , Geng Jing , Guedes Soares C.
Published: August 2024

Floating platforms equipped with multiple moonpools offer tremendous potential for applications in advanced offshore aquaculture. This paper investigates the hydrodynamics of a floating platform equipped with multiple moonpools, highlighting their promising applications in advanced offshore aquaculture. Utilizing an in-house linear potential-flow solver, a thorough analysis of a floating platform integrated with an array of moonpools is conducted. The investigation includes a detailed comparative study on the hydrodynamic behaviour of platforms with and without moonpools, providing the physical explanations governing the observed distinctions. Additionally, we explore wave resonance phenomena within the moonpools and the impact of the configurations on the resonance behaviour is illustrated.
Numerical Simulation and Evaluation Analysis of Ship Tunnel Passage Schemes Under Complex Waterway Conditions
Authors: Lian Zhengchen , Wang Lizheng
Published: August 2024

Under the current trend of green development of ships, the technical requirements of ship types should fully reflect the level of green development of ship types. Meanwhile, the adaptability assessment between ships and complex waterways is also an important manifestation of ship operation efficiency. This article focuses on the environmental characteristics of the complex navigation channel in the Three Gorges Dam, and designs a tunnel passage mode using electric propulsion (towing) wheels. Specifically, by designing the overall plan and using STAR-CCM software for numerical simulation calculation of electric propulsion wheel passing through tunnels, and designing the power scheme of electric propulsion wheel, to ensure the safe, green, and efficient passage of ships passing through complex waterways. Furthermore, evaluation indicators are selected for this design scheme, and the AHP-VIKOR evaluation model is used to solve the evaluation problem of ship power push operation mode in the navigation tunnel of the Three Gorges New Channel under uncertain conditions. Finally, it can be concluded that, under the premise of engineering conditions and acceptable costs, for environmental considerations, the use of ship pushing method can be considered in the Three Gorges Navigation Tunnel. It is recommended that the pushing speed of the ship in the navigation tunnel should not exceed 2.5m/s, and the pushing auxiliary system should be equipped with 5–6 sets in one direction, 10–12 sets in the system, and at least one spare pushing wheel should be equipped; At the same time, it is necessary to consider adding corresponding intelligent navigation devices and strengthening security management to improve the security of the top push method.
Case Studies of BEM Solver Accuracy With the Open-Source Code Capytaine
Authors: Ancellin Matthieu , Nguyen Nhu
Published: August 2024

Capytaine is an open-source Python-based Boundary Element Method (BEM) program designed to simulate wave-structure interactions employing linear potential flow theory in frequency domain. A long term work is currently underway to improve its performance and accuracy, which is behind its commercial counterparts. The present paper focuses on two steps of the numerical resolution: the choice between the direct and indirect boundary integral equation and the accuracy of the tabulation used as surrogate model of the Green function. The results are illustrated on two test cases for which issues had been previously reported, namely the floating cylinder with a thin heave plate and the DeepCWind floating offshore wind turbine platform reference model. The inaccuracy of previous versions of Capytaine on these two test cases is explained and new results are presented in comparison with WAMIT and HAMS.
Investigation of Structural Anomaly Reported at Top Section of Flexible Riser
Authors: Pasqualino Ilson Paranhos , Duarte Ribeiro Rodrigo , de Carvalho Pinheiro Bianca
Published: August 2024

The present study aims to carry out a structural analysis of an anomaly found in a 14-inch flexible riser, used to transfer natural gas from an FSRU unit (Floating Storage Regasification Unit) to a thermoelectric plant, located close to the Brazilian coast. The work aims to carry out global and local numerical-structural analysis of the riser, using data obtained from riser design and from a riser sample taken from a similar structure. As a result of the project, we seek to understand the cause of the anomaly found during visual survey and evaluate the permissible operating conditions, avoiding the worsening of the anomaly and a possible, but unlikely, failure. The work included data collecting from available design documentation, sample dissection to gather riser layers geometry, the development of a numerical model for global analysis to verify loading conditions to be used in the detailed local model, the development of a numerical model to simulate riser layers in other to reproduce expected responses. The finite element model detailed the internal carcass, the pressure barrier, and the internal pressure armor. The paper concluded that the anomaly is a result of the operational loads and that there is no risk of failure or leakage.
A System for Continuous Assurance and Certifications of Data Quality for Digital Twins
Authors: Hansen Ove H. , Jaiswal Vivek , Stang Jørgen
Published: August 2024

A digital twin is a digital representation of a physical asset and is critically dependent on data collection and transmission. The physical and digital parts need to communicate and exchange data with each other for the digital twin to perform its function and deliver value over time. Increasingly, the data utilized for digital twin solutions may be hosted in multiple locations such as third-party cloud services, in-house servers, other digital twins, or other sources. The different sources of data enable operations at scale and multiple new business opportunities. However, it also brings with it challenges related to data quality and cyber security. The capabilities of digital twins need interoperable solutions, which means that digital twins can connect, communicate, and exchange qualified data or services without requiring extra effort or adaptation. A formal certification of data products used for digital twins will improve trust and reduce risk.

Data values and quality are changing and need to be fit for use within acceptable risk. Bad data, lack of data and security breaches can and will jeopardize business critical operations and need to be governed by strategies, and management of change processes and tools. There is a need for a system for continuous assurance and certifications of data quality and cyber security.

The described system is currently under development for quality assurance and certification of data products for the maritime and the energy industry. The result could be a game-changer when it comes to trust and reliability for digital twins.

Examples and reference cases of the independent and automated digital quality assurance and certification system for digital twins will cover management of changes, cyber security, data quality, or automated compliance assessments and statements. The use cases present technical and practical solutions and the system to meet the continuous assurance and certification requirements as well as learnings from ongoing projects.
Theoretical Analysis on Mechanically Lined Pipe Fabrication
Authors: Wei Rongzhi , Vaz Murilo Augusto , Hu Xuefeng
Published: August 2024

Mechanically Lined Pipe (MLP) is a double-walled pipe comprising a carbon steel outer pipe internally coated with a thin layer of Corrosion Resistance Alloy (CRA). This CRA layer serves to safeguard the outer pipe against corrosive substances presented in the production fluid from offshore O&G fields, while the high strength low carbon steel outer pipe bears majority of external loads. The process of hydroforming expansion represents the predominant technique employed in affixing the liner into the carrier pipe. Precise and dependable theoretical models have been consistently sought for enhancing the fabrication efficiency and serving as a benchmark for subsequent failure analysis. The Tresca criterion has been adopted in stress-strain analysis of MLP due to its mathematical simplicity. Nevertheless, it is worth noting that the Tresca criterion is widely acknowledged for its conservative approach in predicting the yielding of metallic material. Consequently, the accuracy of employing the Tresca criterion in analyzing the fabrication of MLP is arguable. To further enhance accuracy, the infinitesimal strain theory and von Mises yield criterion are applied in conducting theoretical analysis for the MLP processing. The stress state within liner after being fully-plastified and loaded with external interfacial contact pressure is derived with radial displacement compatibility. And residual contact pressure is derived analytically through the circumferential strain compatibility method. The interfacial contact pressure, residual contact pressure and hydraulic expansion pressure working range of one set MLP liner and carrier pipe is predicted using the improved model with von Mises criterion.
On the Potential Impact of Climate Change on Design of Offshore Wind Turbines
Authors: Amlashi Hadi
Published: August 2024

A reliability-based approach for offshore wind turbine design is proposed to account for climate change of metocean conditions and uncertainty related to the estimates of future extreme weather and other metocean parameters. The impact of expected wave and wind climate change on OWT design is demonstrated for monopile-supported OWTs with site-specific metocean conditions. The presented examples show consequences of climate change for the fore-aft bending failure probability of bottom-fixed support structure. To maintain the safety level in the current IEC-61400 based-design, the safety factors should be increased by 30–35 % if the fore-aft total bending moment increases by 35%, due to climate change-related extreme weather. However, it should be noted that the ability to adopt climate change adaptation strategies may imply that the current practice of designing of OWTs may require less rigorous changes in the future. The impact of this adaptation and uncertainty associated with it should be accounted for.
Causal Convolution LengthNet Model for Slender Marine Structures
Authors: Machado Vinicius , Sagrilo Luis
Published: August 2024

Finite element modeling (FEM) is the standard way to evaluate structural responses based on the physics of the application. They are often used for time-domain analysis, simulating a set of stochastic loading cases on slender marine structures, and carrying out different types of nonlinearities. While the irregular wave approach offers a closer approximation to structural responses due to environmental loadings’ stochastic nature, it is more demanding computationally. To reduce simulation time while ensuring accuracy, this study introduces strategies to design artificial neural network (ANN) frameworks using deep learning algorithms. The LengthNet class type can predict responses at multiple structural nodes simultaneously, both temporally and spatially, cutting down training time, especially when dealing with a high number of nodes. This work introduces the LengthNet model based on causal convolutional neural networks, which outperforms the state-of-the-art LengthNet based on Recurrent Neural Networks and the NodeNet model. A significant improvement in the PAC (Percentage of Accurate Cases) metric was observed for the Lazy-Wave configuration. Different fatigue regions are processed at the same time, going from the upper regions down to the touchdown zone (TDZ), passing through local analysis and fatigue quantification via the S-N curve. Predicted damage values versus the ground truth ones are also presented.
Investigation of VIV Responses of Slender Structures Under Waves and Currents
Authors: Wu Jie , Yin Decao , Lie Halvor , Grytøyr Guttorm , Hogg Brendan Francis
Published: August 2024

The slender marine structures, such as marine risers and dynamic power cables, etc. are exposed to waves and currents. Vibrations due to periodic vortex shedding around the structure can lead to fast accumulation of fatigue damage and amplified drag loads. Vortex Induced Vibrations (VIV) often represent a safety risk and a major design consideration adding notable costs to all stages of the system development. It is known that the presence of waves may disrupt organized vortex shedding and affect structures’ dynamic responses and resulting drag loads. However, the present frequency domain VIV prediction tools can only consider constant current. The fatigue damages due to VIV and waves have to be calculated independently, and then combined afterwards. In addition, the influences on the drag loads are neglected. These have been some of the major uncertainties in the present design practice, which is more pronounced for shallow water applications, e.g., power cables to floating wind turbines. There are both lack of understanding of the wave-VIV interactions and reliable prediction tools.

In present study, a model test of a steel catenary riser (SCR) subjected to wave and VIV loads carried out at SINTEF Ocean were studied. Relevant test cases were selected and analysed to understand the influences of wave loads on VIV responses. Nonlinear time domain VIV simulation using VIVANA-TD were also carried out, which showed good agreement between prediction and model test results. Other relevant studies were also examined and parameters that may affect structure responses under wave and VIV loads were discussed.
Nylon Ropes for Mooring of Floating Offshore Wind Turbines: The NYMOOR Project
Authors: Fonseca Nuno , Føre Heidi Moe , Sørum Stian Høegh , Gaarder Rune , Leira Bernt Johan , Faria Rui Pedro , Kent Michael
Published: August 2024

Effective mooring of floating offshore wind turbines (FOWTs) is challenging, and conventional mooring designs often require line components with quite large diameters. This is mainly a consequence of large mean environmental loads from wind, namely the wind thrust force, combined with a relatively stiff mooring system. Nylon ropes have the potential to reduce stresses in mooring lines due to their flexible and elastic behaviour. However, there is very little experience with use of nylon for permanent mooring of floating structures. Of particular concern is the long-term endurance and behaviour of nylon ropes in the ocean environment. Furthermore, new material models are required to simulate mechanical properties of nylon ropes, and design analysis tools must be further developed to accommodate these new models.

The paper starts by presenting state-of-the-art in the topic of nylon ropes with focus on mooring applications. It reviews and documents advantages of nylon ropes in mooring of FOWTs with results from two case studies, and identifies knowledge gaps. Then it describes the NYMOOR research project, which addresses some of the knowledge and technological gaps. We start with the project objectives. The assumed hypotheses are formulated based on the best knowledge in the topic. Then the project methodology and the research activities are described in detail.
Study on the Collision Probability of Tandem Top-Tensioned Risers Based on the Extremes Statistical Methodology
Authors: Gu Honglu , Guo Haiyan , Meng Fanshun , Li Xiaomin , Li Fuheng
Published: August 2024

This paper aims to develop an integrated model for predicting the probability of riser collisions. This model can fully utilize the limited time series samples and dramatically reduce the computational time consumption required to accumulate enough data samples. First, a global mechanical model for the dual-riser system, which considers the current, random wave, top motion, and hydrodynamic interference effects, is constructed based on the vector form intrinsic finite element. Then, an analytical geometry-based procedure is coded, and a three-stage sieving strategy is proposed to efficiently obtain a random time series sample of the minimum distance, Cmin (t). The distribution parameters of this sample for various extreme value distributions are determined by the maximum likelihood estimation. The χ2 test, histograms, and quantile plots are used together to further assess the fitting quality of each theoretical model to the sample, and determine the optimal probability distribution form. Based on this optimal extreme value distribution model, the crossing rate of the sample is extrapolated to the failure threshold to predict the collision probability. Moreover, the probability prediction results are verified by Monte Carlo simulation and compared with the Gumbel probability paper method.
A Neural Operator for the Estimation of Wave Heights From Wind Data
Authors: Mathias Marlon S. , S. Thiersch Carlos H. , R. Patitucci Luca , R. de Barros Marcel , M. Moreno Felipe , Jordão Artur , Dottori Marcelo , R. Costa Anna H. , Gomi Edson S. , Tannuri Eduardo A.
Published: August 2024

This paper presents a Neural Operator (NOp) for estimating wave height from wind data. The NOp is a machine learning model to approximate functions from one function space to another. It is trained to map wind data to wave height. Each function is represented as a graph, with vertices corresponding to physical locations and edges carrying geographical distribution information. The model uses a convolutional kernel, allowing nodes to exchange information based on relative positions. After several convolutions, the latent values are decoded into target variables. The model is agnostic to the absolute position of each node, simplifying training and enabling application to various domains. Although a precise wave height reconstruction is impossible, as it depends on multiple other variables and on past data, we demonstrate that such a model is able to approximate previously unavailable variables from available data, including the capability of inferring it in grids and resolutions different than those used during training.
Ground-truth validation of the “earbuds method” for measuring acoustic nasalance
Authors: Carignan Christopher
Published: August 2024

Among the variety of methodological tools available for quantifying the degree of nasalization, nasometry has remained a popular choice for both academic and clinical research on speech due to its relatively low cost, portability, ease of use, and interpretability. In its simplest form, nasometry involves two microphones that independently capture the acoustic radiation from the mouth and nose. Recently, a method was proposed by Stewart and Kohlberger [(2017). Lang. Doc. Conserv. 11, 49–80] of using earbuds to achieve a similar result. Although the method has been widely used since, most notably in the context of linguistic fieldwork, it has yet to be tested against ground-truth measurements of acoustic nasalance from a commercially established device; the current study attempts to provide this ground-truth comparison. A wide variety of characteristics of the relationship between nasalance measurements created using acoustic data co-registered from a commercial nasometer, silicone earbuds, and flat earbuds are thoroughly examined. The results suggest that the “earbuds method” may provide reliable estimates of nasality when assessed at a global level (i.e., overall averages, relatively high/low nasalance scores coinciding with the presence/absence of nasalization), but that the accuracy of these estimates may decline at more fine-grained levels in different ways that are outlined in the discussion.
Psychoacoustic ranking and selection using modified knockout tournaments
Authors: Meyer-Kahlen Nils , Hyvärinen Petteri
Published: August 2024

This paper introduces a ranking and selection approach to psychoacoustic and psychophysical experimentation, with the aim of identifying top-ranking samples in listening experiments with minimal pairwise comparisons. We draw inspiration from sports tournament designs and propose to adopt modified knockout (KO) tournaments. Two variants of modified KO tournaments are described, which adapt the tree selection sorting algorithm and the replacement selection algorithm known from computer science. To validate the proposed method, a listening experiment is conducted, where binaural renderings of seven chamber music halls are compared regarding loudness and reverberance. The rankings obtained by the modified KO tournament method are compared to those obtained from a traditional round-robin (RR) design, where all possible pairs are compared. Moreover, the paper presents simulations to illustrate the method's robustness when choosing different parameters and assuming different underlying data distributions. The study's findings demonstrate that modified KO tournaments are more efficient than full RR designs in terms of the number of comparisons required for identifying the top ranking samples. Thus, they provide a promising alternative for this task. We offer an open-source implementation so that researchers can easily integrate KO designs into their studies.
An impedance tube technique for estimating the insertion loss of earplugs
Authors: Carillo K. , Doutres O. , Sgard F.
Published: August 2024

This paper proposes a quick and straightforward technique for estimating the insertion loss (IL) of earplugs measured on an acoustical test fixture (ATF) using a commercial impedance tube. In this method, the earplug's acoustic properties (i.e., its transmission loss and the reflection coefficient of its medial surface) are determined from its transfer matrix measured using the three-microphones impedance tube method modified here for the current application. The IL is then estimated using a one-dimensional analytical model of open and occluded earcanals based on the wavefield decomposition theory. The method is evaluated numerically and experimentally from 50 Hz to 6.5 kHz. The numerical study allows for verifying the accuracy of the proposed approach in comparison to a simplified model of an ATF earcanal excited by normal incidence plane wave and diffuse field excitation. The experimental evaluation, which involves six earplugs (including five commercially available ones) representing various earplug families, demonstrates the accuracy of the estimation method, yielding results with a maximum difference of 3 dB compared to ATF measurements, on average, among the tested earplugs.
Evaluating the Impact of Seated Pilates on Functional Outcomes Among Those With Mild, Moderate, and Severe Multiple Sclerosis Impairment: A Pilot Feasibility Trial
Authors: Adamson Brynn , Lindsay Keston G. , Almasri Layla , Koppele Duffy Meghann , Kirkpatrick Stacy , Hernandez Manuel E.
Published: August 2024

This pilot study assessed the feasibility and functional benefits of a twice-weekly, 12-week, virtual, seated, group-based Pilates program in persons with mild to severe multiple sclerosis (MS). Participants were randomized into either a Pilates-only group or a Pilates group, which also incorporated hip and shoulder-cuff activation exercises. Process, management, and scientific-feasibility metrics were analyzed descriptively. Functional outcomes, physical activity, and MS-related outcomes (impact, fatigue, and quality of life) were measured pre- and postintervention and analyzed using mixed-effects models, analysis of variance, and cluster analysis. Twenty-two participants completed baseline testing. Sixteen completed the intervention and postintervention testing. Collapsed across groups, analyses demonstrated improvements in the Timed 25-Foot Walk (36%), Timed Up-and-Go (13%), and the Berg Balance Scale (10%, statistically significant). Neither between-groups differences nor physical activity or MS outcome changes were significant. Participants reported high satisfaction. Findings suggest that virtual, seated Pilates is feasible and may confer balance benefits to individuals with MS.
Compensating atmospheric adjustments reduce the volcanic forcing from Hunga stratospheric water vapor enhancement
Authors: Wang Yuwei , Huang Yi
Published: August 2024

The 2022 eruption of the Hunga submarine volcano injected an unprecedented volume of water vapor into the stratosphere, presenting a unique, natural experiment for ascertaining the influence of stratospheric water vapor within the global radiation budget. This study examines the radiative forcings of the Hunga stratospheric water vapor enhancement, comparing stratosphere-adjusted radiative forcing derived from offline methods to an effective radiative forcing derived from Earth System Model simulations. Assuming a uniform 2 parts per million mass mixing ratio increase of water vapor in the Southern Hemisphere stratosphere, we estimated the instantaneous, stratosphere-adjusted, and overall effective radiative forcing to be −0.04, 0.08, and 0.05 W m
−2
, respectively. The lower magnitude of the positive volcanic stratospheric water vapor effective radiative forcing is due to compensating effects from atmospheric adjustments. Ensemble simulations of a coupled atmosphere-ocean model suggest a surface warming of 0.05 K, affirming a limited influence on global mean surface temperature from the volcanic stratospheric water vapor injection.
A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates
Authors: Mukhopadhyay Urbi , Levantovsky Sophie , Carusone Teresa Maria , Gharbi Sarah , Stein Frank , Behrends Christian , Bhogaraju Sagar
Published: August 2024

Over 600 E3 ligases in humans execute ubiquitination of specific target proteins in a spatiotemporal manner to elicit desired signaling effects. Here, we developed a ubiquitin-specific proximity-based labeling method to selectively biotinylate substrates of a given ubiquitin ligase. By fusing the biotin ligase BirA and an Avi-tag variant to the candidate E3 ligase and ubiquitin, respectively, we were able to specifically enrich bona fide substrates of a ligase using a one-step streptavidin pulldown under denaturing conditions. We applied our method, which we named Ub-POD, to the really interesting new gene (RING) E3 ligase RAD18 and identified proliferating cell nuclear antigen and several other critical players in the DNA damage repair pathway. Furthermore, we successfully applied Ub-POD to the RING ubiquitin ligase tumor necrosis factor receptor–associated factor 6 and a U-box–type E3 ubiquitin ligase carboxyl terminus of Hsc70-interacting protein. We anticipate that our method could be widely adapted to all classes of ubiquitin ligases to identify substrates.
Photoreception and signaling in bacterial phytochrome revealed by single-particle cryo-EM
Authors: Malla Tek Narsingh , Hernandez Carolina , Muniyappan Srinivasan , Menendez David , Bizhga Dorina , Mendez Joshua H. , Schwander Peter , Stojković Emina A. , Schmidt Marius
Published: August 2024

Phytochromes are red-light photoreceptors discovered in plants with homologs in bacteria and fungi that regulate a variety of physiological responses. They display a reversible photocycle between two distinct states: a red-light–absorbing Pr state and a far-red light–absorbing Pfr state. The photoconversion regulates the activity of an enzymatic domain, usually a histidine kinase (HK). The molecular mechanism that explains how light controls the HK activity is not understood because structures of unmodified bacterial phytochromes with HK activity are missing. Here, we report three cryo–electron microscopy structures of a wild-type bacterial phytochrome with HK activity determined as Pr and Pfr homodimers and as a Pr/Pfr heterodimer with individual subunits in distinct states. We propose that the Pr/Pfr heterodimer is a physiologically relevant signal transduction intermediate. Our results offer insight into the molecular mechanism that controls the enzymatic activity of the HK as part of a bacterial two-component system that perceives and transduces light signals.
Response of
Staphylococcus aureus
physiology and Agr quorum sensing to low-shear modeled microgravity
Authors: Hauserman Matthew R. , Sullivan Leia E. , James Kimberly L. , Ferraro Mariola J. , Rice Kelly C.
Published: August 2024

Staphylococcus aureus
is commonly isolated from astronauts returning from spaceflight. Previous analysis of omics data from
S. aureus
low Earth orbit cultures indicated significantly increased expression of the Agr quorum sensing system and its downstream targets in spaceflight samples compared to ground controls. In this current study, the rotary cell culture system (RCCS) was used to investigate the effect of low-shear modeled microgravity (LSMMG) on
S. aureus
physiology and Agr activity. When cultured in the same growth medium and temperature as the previous spaceflight experiment,
S. aureus
LSMMG cultures exhibited decreased
agr
expression and altered growth compared to normal gravity control cultures, which are typically oriented with oxygenation membrane on the bottom of the high aspect rotating vessel (HARV). When
S. aureus
was grown in an inverted gravity control orientation (oxygenation membrane on top of the HARV), reduced Agr activity was observed relative to both traditional control and LSMMG cultures, signifying that oxygen availability may affect the observed differences in Agr activity. Metabolite assays revealed increased lactate and decreased acetate excretion in both LSMMG and inverted control cultures. Secretomics analysis of LSMMG, control, and inverted control HARV culture supernatants corroborated these results, with inverted and LSMMG cultures exhibiting a decreased abundance of Agr-regulated virulence factors and an increased abundance of proteins expressed in low-oxygen conditions. Collectively, these studies suggest that the orientation of the HARV oxygenation membrane can affect
S. aureus
physiology and Agr quorum sensing in the RCCS, a variable that should be considered when interpreting data using this ground-based microgravity model.

IMPORTANCE

S. aureus
is commonly isolated from astronauts returning from spaceflight and from surfaces within human-inhabited closed environments such as spacecraft. Astronaut health and immune function are significantly altered in spaceflight. Therefore, elucidating the effects of microgravity on
S. aureus
physiology is critical for assessing its pathogenic potential during long-term human space habitation. These results also highlight the necessity of eliminating potential confounding factors when comparing simulated microgravity model data with actual spaceflight experiments.
SARS-CoV-2 papain-like protease inhibits ISGylation of the viral nucleocapsid protein to evade host anti-viral immunity
Authors: Rhamadianti Aulia Fitri , Abe Takayuki , Tanaka Tomohisa , Ono Chikako , Katayama Hisashi , Makino Yoshiteru , Deng Lin , Matsui Chieko , Moriishi Kohji , Shima Fumi , Matsuura Yoshiharu , Shoji Ikuo
Published: August 2024

A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes mild-to-severe respiratory symptoms, including acute respiratory distress. Despite remarkable efforts to investigate the virological and pathological impacts of SARS-CoV-2, many of the characteristics of SARS-CoV-2 infection still remain unknown. The interferon-inducible ubiquitin-like protein ISG15 is covalently conjugated to several viral proteins to suppress their functions. It was reported that SARS-CoV-2 utilizes its papain-like protease (PLpro) to impede ISG15 conjugation, ISGylation. However, the role of ISGylation in SARS-CoV-2 infection remains unclear. We aimed to elucidate the role of ISGylation in SARS-CoV-2 replication. We observed that the SARS-CoV-2 nucleocapsid protein is a target protein for the HERC5 E3 ligase-mediated ISGylation in cultured cells. Site-directed mutagenesis reveals that the residue K374 within the C-terminal spacer B-N3 (SB/N3) domain is required for nucleocapsid-ISGylation, alongside conserved lysine residue in MERS-CoV (K372) and SARS-CoV (K375). We also observed that the nucleocapsid-ISGylation results in the disruption of nucleocapsid oligomerization, thereby inhibiting viral replication. Knockdown of ISG15 mRNA enhanced SARS-CoV-2 replication in the SARS-CoV-2 reporter replicon cells, while exogenous expression of ISGylation components partially hampered SARS-CoV-2 replication. Taken together, these results suggest that SARS-CoV-2 PLpro inhibits ISGylation of the nucleocapsid protein to promote viral replication by evading ISGylation-mediated disruption of the nucleocapsid oligomerization.

IMPORTANCE

ISG15 is an interferon-inducible ubiquitin-like protein that is covalently conjugated to the viral protein via specific Lys residues and suppresses viral functions and viral propagation in many viruses. However, the role of ISGylation in SARS-CoV-2 infection remains largely unclear. Here, we demonstrated that the SARS-CoV-2 nucleocapsid protein is a target protein for the HERC5 E3 ligase-mediated ISGylation. We also found that the residue K374 within the C-terminal spacer B-N3 (SB/N3) domain is required for nucleocapsid-ISGylation. We obtained evidence suggesting that nucleocapsid-ISGylation results in the disruption of nucleocapsid-oligomerization, thereby suppressing SARS-CoV-2 replication. We discovered that SARS-CoV-2 papain-like protease inhibits ISG15 conjugation of nucleocapsid protein via its de-conjugating enzyme activity. The present study may contribute to gaining new insight into the roles of ISGylation-mediated anti-viral function in SARS-CoV-2 infection and may lead to the development of more potent and selective inhibitors targeted to SARS-CoV-2 nucleocapsid protein.
High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen
Authors: Day Leslie A. , Carlson Hans K. , Fonseca Dallas R. , Arkin Adam P. , Price Morgan N. , Deutschbauer Adam M. , Costa Kyle C.
Published: August 2024

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly barcoded transposon libraries in the model methanogenic archaeon
Methanococcus maripaludis
and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in
M. maripaludis
including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that
M. maripaludi
s can utilize additional nitrogen sources including ʟ-glutamine, ᴅ-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize that it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP; group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale data set that can be used as a resource to further understand gene function and metabolism in the archaeal domain.

IMPORTANCE

Archaea are widespread in the environment, yet basic aspects of their biology remain underexplored. To address this, we apply randomly barcoded transposon libraries (RB-TnSeq) to the model archaeon
Methanococcus maripaludis
. RB-TnSeq coupled with high-throughput growth assays across over 100 unique conditions identified roles for previously uncharacterized genes, including several encoding proteins with domains of unknown function (DUFs). We also expand on our understanding of carbon and nitrogen metabolism and characterize a group IIId dissimilatory sulfite reductase-like protein as a functional sulfite reductase. This data set encompasses a wide range of additional conditions including stress, nitrogen fixation, amino acid supplementation, and autotrophy, thus providing an extensive data set for the archaeal community to mine for characterizing additional genes of unknown function.
The complete genomic sequencing of a
Klebsiella pneumoniae
isolate derived from the blood of a patient suffering from severe neurological problems in Zhengzhou, China
Authors: Yang Huishuang , Zhang Jun , Salman Sayyed , Zhu Weidong
Published: August 2024

This study presents the comprehensive analysis of the genomic sequence of
Klebsiella pneumoniae
strain FAHZZU7042hy, having a 5,690,191 bp chromosome size. This strain was obtained from a blood sample of a patient suffering from severe neurological problems in Zhengzhou, China, 2023.