bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformal Geometric Algebra–Based Geometric Modeling Method for Forward Displacement Analysis of 6-4 Stewart Platforms
Authors: Zhu Ganmin , Wei Shimin , Li Duanling , Wang Yingli , Liao Qizheng
Published: September 2023

This paper presents a novel geometric modeling method for direct displacement analysis of 6-4 Stewart platforms based on conformal geometric algebra (CGA). First, a geometric constraint relationship of four lines and a plane intersecting at a point is published. Second, a new coordinate-invariant geometric constraint equation of 6-4 Stewart platforms is deduced by CGA operation. Third, five polynomial equations are established by CGA theory. Fourth, based on the above six equations, a 5 × 5 Sylvester’s matrix is formulated by using Sylvester’s Dialytic elimination method and Gröbner bases method under the graded reverse lexicographical order. Finally, the coordinates of four points on the moving platform are revealed. Besides, a numerical example is used to prove the validity of the proposed method. The novelty of this study is that a whole geometric modeling method by geometric constraint relationship of four lines and a plane intersecting at a point is put forward under the CGA framework, which has good intuition and offers a novel idea for solving the other complex mechanisms. At the same time, Sylvester’s matrix constructed by this method is the smallest one in the known literature for forward displacement analysis of 6-4 Stewart platforms.
Methodology and Validation of Surge Modeling in a Three-Shaft Compression System
Authors: Zhao Fanzhou , Moreno Jose , Dodds John , Vahdati Mehdi
Published: September 2023

In this paper an efficient numerical strategy for computational fluid dynamics (CFD) simulation of surge events in a three-shaft engine compression system is presented. Numerical results are compared against measured data and the sources of discrepancies and uncertainties are addressed. It is discovered that the engine bleed system has a major impact in reducing the aerodynamic loading during surge in the core system. To the best knowledge of the authors, this is the first time that such a complex CFD computation is attempted and compared against real engine measured data and will provide valuable information to other CFD users as well as gas turbine manufacturers.
Thermo-Economic Assessment of Pumped Thermal Electricity Storage Systems Employing Reversible Turbomachinery
Authors: Parisi Simone , Desai Nishith Babubhai , Haglind Fredrik
Published: September 2023

The objective of this paper is to assess the thermo-economic performance of different cycle configurations for pumped thermal electricity storage (PTES), including the effects of charging electricity cost. Reversible turbomachinery is employed to reduce the capital cost. Brayton cycles with different working fluids and a subcritical Rankine cycle operating with ammonia are compared. Liquid thermal energy storage systems are used. For the Brayton cycle, also packed bed storage systems are considered as an alternative.

A new cost correlation for turbomachines, initially developed for organic Rankine cycles, is adapted for compressors and reversible machines. This correlation is based on the number of stages and physical size of the machine, which are estimated considering thermodynamic as well as mechanical limitations on the enthalpy difference that can be attained per stage.

The results indicate that for a plant size of 50 MW and a discharge duration of 8 hours, the Brayton system with liquid storage and helium as a working fluid has the lowest levelized cost of storage at 0.138 $/kWh, mainly due to the high thermal conductivity of the fluid. Packed bed systems were found to be more expensive than liquid storage systems due to the large cost of the pressure vessels, with cost parity reached at a discharge duration of 4 hours. However, at this duration lithium ion batteries are likely to be cheaper. The results suggest that the levelized cost of storage for the Rankine cycle is slightly higher, 0.151 $/kWh. In addition, the Rankine cycle has disadvantages related to the higher storage volume and less flexibility for part load operation.
Line Chilldown and Flow Boiling Heat Transfer Characteristics of Stainless Steel Tubes
Authors: Narayanan Jayachandran K. , Shingote Chinmay , Qiu Yue , Hartwig Jason W. , Mackey Jeffrey R. , Kassemi Mohammad , Kharangate Chirag R.
Published: September 2023

As part of the ongoing efforts to develop and test a two-phase flow chilldown experimental setup onboard the International Space Station (ISS), experiments are conducted to analyze the line chilldown and flow boiling heat transfer characteristics of SS-316 using a simulant fluid PF-5060 in this study. The cryogenic transfer line chilldown process is pre-dominated by the film boiling regime for most of the duration followed by transition and nucleate boiling regimes. The line chilldown tests performed in this study are designed to mimic the cryogenic transfer line chilldown by heating the tubes to around 250 °C and then allowing the PF-5060 liquid flow to cool down the tubes. The test module consists of the main heated section, and a bypass section to maintain the flow rate while the test section preheating is undergoing. The main heating section is 60 cm long with wall temperature measurements at top and bottom sides of the tubes placed at equal distances. A fibre-glass insulated Nichrome tape heater achieves the desired initial temperature conditions, and a three-way valve activates to divert flow from the bypass section to the main test section when all the wall thermocouples read 250 °C or above. The present experimental design captured the entire chilldown curve from film boiling to single phase liquid regions.
Experimental Study of Enhanced Heat Transfer in Phase Change Material Based Thermal Energy Storage in Compact Heat Exchangers
Authors: Kannan Sarath , Jog Milind A. , Manglik Raj M.
Published: September 2023

Experimental data for the performance of a novel ultracompact thermal energy storage (TES) heat exchanger, designed as a micro-channel finned-tube exchanger are presented. A salt hydrate phase change material (PCM), Lithium Nitrate Trihydrate (LiNO3·3H2O; Tsf = 30°C, hsf = 274 kJ/kg), was encased on the fin side with water as the heat-cooling fluid. The TES performance was characterized experimentally to establish: (a) average heat transfer rates and power density with 10 and 24 fins/inch heat exchanger designs, and (b) TES reliability under thermal cycling field conditions. With high average heat transfer coefficients (Upcm = 100–500 W/m2K), a substantially high power density is obtained (∼ 367 kW/m3 during freezing) primarily due to the reduction in the PCM encasement length scale (L < 3 mm). In the thermal cycling test, the TES was subjected to accelerated heating and cooling cycles under typical arid region conditions (diurnal variation between 42°C–25°C). Employing the self-seeding method to obviate subcooling, the TES was found to exhibit stable long-cycle operation with very high-power density. The results clearly establish that highly compact heat exchangers used as TES units are significantly superior and attractive alternatives to conventional ones.
Composite Phase Change Material With Metal Foam in Shell and Convergent Tube Thermal Energy Storage Systems
Authors: Buonomo Bernardo , Golia Maria Rita , Manca Oronzio , Nardini Sergio , Plomitallo Renato Elpidio
Published: September 2023

In order to decrease the negative effects on the environment and to handle the problem of a temporal and methodological mismatch between the energy required and the energy produced, energy storage systems have become highly relevant. In the proposed investigation, a simulation on a vertical shell and convergent tube geometry at different inclination angles composed of metal foam filled with a phase change material (PCM) is performed. The aluminum foam is used as porous media filled with pure paraffin wax as the PCM. The top, bottom, and external surfaces of the hollow cylinder are thought to be adiabatic, whereas the inner surface temperature is supposed to be constantly above the PCM melting point. Darcy-Forchheimer model is used to analyze the aluminum foam saturated with paraffin under the assumption of the local thermal non-equilibrium (LTNE), while the enthalpy-porosity theory is used to represent the phase change process in paraffin wax. Ansys-Fluent commercial code is used to perform the numerical solutions of the governing equations. The results of numerical simulations are shown as a function of time and are reported in terms of melting time, average temperature, and specific enthalpy. They show that the higher is the inclination angle, the faster is the system to reach the maximum energy stored. The converging system reaches the maximum energy storable faster than the diverging one.
A Bayesian Spatio-Temporal Modeling Approach to the Inverse Heat Conduction Problem
Authors: Olabiyi Ridwan , Pandey Hari , Hu Han , Iquebal Ashif
Published: September 2023

A wide range of science and engineering problems involve inferring the system behavior and the physical models from indirect observations. These are known as inverse problems. Unlike forward problems (predictive models), inverse problems are difficult to solve due to ill-posedness arising from one or more of non-existence, non-uniqueness (existence of many solutions), or instability (small perturbations in the measurements emerging from noise could lead to large changes in the solution). Therefore, direct inversion of the inverse problem in complex real-world systems is impractical. Several modeling approaches have been developed and adopted in the literature. However, the existing approaches do not consider spatio-temporal relationships. Meanwhile, various real systems and processes exist whose inverse problems can be comfortably modeled using spatio-temporal modeling techniques. We present a spatio-temporal inverse model considering interaction effects for modeling this type of inverse problem. We adopted a Bayesian inference framework for the subsequent parameter estimation problem and developed a Gibbs sampling algorithm to sample from the posterior distribution of the parameter of interest. Finally, we evaluate the proposed modeling technique and solution framework using several case studies of inverse problems in diverse heat conduction domains. Compared with conventional methods, the proposed framework performs better and can be adopted for solving inverse problems with spatio-temporal properties in various scientific and engineering domains.
Electron-enhanced high power impulse magnetron sputtering with a multilevel high power supply: Application to Ar/Cr plasma discharge
Authors: Zgheib J. , Berthelot L. , Tranchant J. , Ginot N. , Besland M.-P. , Caillard A. , Minea T. , Rhallabi A. , Jouan P.-Y.
Published: September 2023

A high-power impulse magnetron sputtering (HiPIMS) power supply, called e-HiPIMS, has been developed and used to deposit chromium thin films within an argon discharge. This power supply comprises three stages; each can deliver a voltage pulse up to 300 V. The advantage of this power supply is the possibility of tailoring a pulse waveform on the cathode with several voltage levels. This e-HiPIMS can operate in the standard HiPIMS mode (s-HiPIMS) and multipulse HiPIMS mode. Each voltage sequence is independently managed regarding the width, delay, and voltage level. They can all be synchronized, giving the s-HiPIMS, or shifted in time and added to each other. Hence, the idea is to favor a specific ion population compared to others, according to the process needs and the targeted application. A beneficial example used a three-pulse sequence with different voltage levels. The influence of the temporal behavior on the plasma parameters, namely, currents and electron energy, has been studied for each pulse sequence. The results show that the discharge current stays within the same order of magnitude as in the standard HiPIMS. The reference current level can be obtained quickly, adding a short over-pulse, even if its voltage level is relatively low. Furthermore, measurements by the Langmuir probe reveal that a maximum electron density is obtained at 0.2 and 0.6 Pa of argon for a configuration that adds two distinguished voltage-pulse sequences, one between 5 and 15 μs and the other between 20 and 40 μs. It comes out that this e-HiPIMS sequence significantly increases the electron density.
Examining the effect of high-frequency information on the classification of conversationally produced English fricatives
Authors: Kharlamov Viktor , Brenner Daniel , Tucker Benjamin V.
Published: September 2023

This study examines the role of frequencies above 8 kHz in the classification of conversational speech fricatives [f, v, θ, ð, s, z, ʃ, ʒ, h] in random forest modeling. Prior research has mostly focused on spectral measures for fricative categorization using frequency information below 8 kHz. The contribution of higher frequencies has received only limited attention, especially for non-laboratory speech. In the present study, we use a corpus of sociolinguistic interview recordings from Western Canadian English sampled at 44.1 and 16 kHz. For both sampling rates, we analyze spectral measures obtained using Fourier analysis and the multitaper method, and we also compare models without and with amplitudinal measures. Results show that while frequency information above 8 kHz does not improve classification accuracy in random forest analyses, inclusion of such frequencies can affect the relative importance of specific measures. This includes a decreased contribution of center of gravity and an increased contribution of spectral standard deviation for the higher sampling rate. We also find no major differences in classification accuracy between Fourier and multitaper measures. The inclusion of power measures improves model accuracy but does not change the overall importance of spectral measures.
Two-point microrheology and diffusing wave spectroscopy
Authors: Li Qi , Dennis Kimberly A. , Lee Yu-Fan , Furst Eric M.
Published: September 2023

The dynamics of charged and hard-sphere silica colloidal suspensions are measured using diffusing wave spectroscopy and are interpreted by the Generalized Stokes–Einstein Relation (GSER). At high concentration, the resulting moduli are in good qualitative agreement with bulk rheology, including the frequency response, but are higher by a quantitative factor. We show that the “two-point” GSER, which derives from the correlated motion of the colloidal particles, provides a better quantitative agreement between bulk and microrheology. The two-point GSER applies generally when the average scattering vector sampled by the multiple scattering events corresponds to a length scale greater than the scatterer diameter. We discuss applications for characterizing colloid interactions by measuring the high-frequency moduli of suspensions and extend the two-point analysis to tracer particle microrheology measurements of a semiflexible biopolymer network.
Highly Trained Biathletes With a Fast-Start Pacing Pattern Improve Time-Trial Skiing Performance by Pacing More Evenly
Authors: Losnegard Thomas , Lund-Hansen Magne , Stubbe Erland Vedeler , Granrud Even Dahlen , Luchsinger Harri , Sandbakk Øyvind , Kocbach Jan
Published: September 2023

Purpose: In sprint biathlon, a J-shaped pacing pattern is commonly used. We investigated whether biathletes with a fast-start pacing pattern increase time-trial skiing and shooting performance by pacing more evenly. Methods: Thirty-eight highly trained biathletes (∼21 y, 27 men) performed an individual 7.5 (3 × 2.5 km for women) or 10-km (3 × 3.3 km for men) time trial on roller skis with a self-selected pacing strategy (day 1). Prone (after lap 1) and standing shooting (after lap 2) stages were performed using paper targets. Based on their pacing strategy in the first time trial (ratio between the initial ∼800-m segment pace on lap 1 and average ∼800-m segment pace on laps 1–3), participants were divided into an intervention group with the fastest starting pace (INT, n = 20) or a control group with a more conservative starting pace (CON, n = 18). On day 2, INT was instructed to reduce their starting pace, while CON was instructed to maintain their day 1 strategy. Results: INT increased their overall time-trial performance more than CON from day 1 to day 2  (mean ± 95% CI; 1.5% ± 0.7% vs 0.0% ± 0.9%, P = .02). From day 1 to day 2, INT reduced their starting pace (5.0% ± 1.5%, P < .01), with reduced ratings of perceived exertion during lap 1 (P < .05). For CON, no change was found for starting pace (−0.8% ± 1.2%) or ratings of perceived exertion between days. No differences were found for shooting performance for either group. Conclusion: Highly trained biathletes with a pronounced fast-start pattern improve skiing performance without any change in shooting performance by pacing more evenly.
Developing Coaches’ Knowledge of the Athlete–Coach Relationship Through Formal Coach Education: The Perceptions of Football Association Coach Developers
Authors: Newland Andrew , Cronin Colum , Cook Gillian , Whitehead Amy
Published: September 2023

Developing high-quality athlete–coach (A–C) relationships improves both athlete performance and well-being. However, content relating to the A–C relationship has been underrepresented within coach education. The study evaluates how coaches completing the English Football Association’s Union of European Football Associations A and B licenses develop knowledge of the A–C relationship. It does so by drawing on the perspectives of those who design and deliver the courses. Semistructured interviews were completed with nine experienced Football Association coach developers alongside a document analysis of seven key course documents. Data were analysed through an inductive thematic analysis and five themes were generated: (a) coach developers understand that the A–C relationship is built on trust, care, and hard and soft interpersonal approaches; (b) the triad of knowledge impacts on the A–C relationship, not just interpersonal knowledge; (c) the A–C relationship is not meaningfully addressed in the formalised course content; (d) in situ visits provide an effective medium to develop knowledge of the A–C relationship; and (e) the assessment framework does not align with the formalised course content. Findings demonstrate, despite a diversification in content, the A–C relationship is introduced in a superficial manner. Future research should clarify the knowledge coaches require to develop high-quality A–C relationships within a high-performance footballing context.
Battery metal recycling by flash Joule heating
Authors: Chen Weiyin , Chen Jinhang , Bets Ksenia V. , Salvatierra Rodrigo V. , Wyss Kevin M. , Gao Guanhui , Choi Chi Hun , Deng Bing , Wang Xin , Li John Tianci , Kittrell Carter , La Nghi , Eddy Lucas , Scotland Phelecia , Cheng Yi , Xu Shichen , Li Bowen , Tomson Mason B. , Han Yimo , Yakobson Boris I. , Tour James M.
Published: September 2023

The staggering accumulation of end-of-life lithium-ion batteries (LIBs) and the growing scarcity of battery metal sources have triggered an urgent call for an effective recycling strategy. However, it is challenging to reclaim these metals with both high efficiency and low environmental footprint. We use here a pulsed dc flash Joule heating (FJH) strategy that heats the black mass, the combined anode and cathode, to >2100 kelvin within seconds, leading to ~1000-fold increase in subsequent leaching kinetics. There are high recovery yields of all the battery metals, regardless of their chemistries, using even diluted acids like 0.01 M HCl, thereby lessening the secondary waste stream. The ultrafast high temperature achieves thermal decomposition of the passivated solid electrolyte interphase and valence state reduction of the hard-to-dissolve metal compounds while mitigating diffusional loss of volatile metals. Life cycle analysis versus present recycling methods shows that FJH significantly reduces the environmental footprint of spent LIB processing while turning it into an economically attractive process.
Inversely engineered biomimetic flexible network scaffolds for soft tissue regeneration
Authors: Cao Shunze , Wei Yu , Bo Renheng , Yun Xing , Xu Shiwei , Guan Yanjun , Zhao Jianzhong , Lan Yu , Zhang Bin , Xiong Yingjie , Jin Tianqi , Lai Yuchen , Chang Jiahui , Zhao Qing , Wei Min , Shao Yue , Quan Qi , Zhang Yihui
Published: September 2023

Graft-host mechanical mismatch has been a longstanding issue in clinical applications of synthetic scaffolds for soft tissue regeneration. Although numerous efforts have been devoted to resolve this grand challenge, the regenerative performance of existing synthetic scaffolds remains limited by slow tissue growth (comparing to autograft) and mechanical failures. We demonstrate a class of rationally designed flexible network scaffolds that can precisely replicate nonlinear mechanical responses of soft tissues and enhance tissue regeneration via reduced graft-host mechanical mismatch. Such flexible network scaffold includes a tubular network frame containing inversely engineered curved microstructures to produce desired mechanical properties, with an electrospun ultrathin film wrapped around the network to offer a proper microenvironment for cell growth. Using rat models with sciatic nerve defects or Achilles tendon injuries, our network scaffolds show regenerative performances evidently superior to that of clinically approved electrospun conduit scaffolds and achieve similar outcomes to autologous nerve transplantation in prevention of target organ atrophy and recovery of static sciatic index.
A wireless, solar-powered, optoelectronic system for spatial restriction-free long-term optogenetic neuromodulations
Authors: Park Jaejin , Kim Kyubeen , Kim Yujin , Kim Tae Soo , Min In Sik , Li Bowen , Cho Young Uk , Lee Chanwoo , Lee Ju Young , Gao Yuyan , Kang Kyowon , Kim Do Hyeon , Choi Won Jun , Shin Hyun-Beom , Kang Ho Kwan , Song Young Min , Cheng Huanyu , Cho Il-Joo , Yu Ki Jun
Published: September 2023

Numerous wireless optogenetic systems have been reported for practical tether-free optogenetics in freely moving animals. However, most devices rely on battery-powered or coil-powered systems requiring periodic battery replacement or bulky, high-cost charging equipment with delicate antenna design. This leads to spatiotemporal constraints, such as limited experimental duration due to battery life or animals’ restricted movement within specific areas to maintain wireless power transmission. In this study, we present a wireless, solar-powered, flexible optoelectronic device for neuromodulation of the complete freely behaving subject. This device provides chronic operation without battery replacement or other external settings including impedance matching technique and radio frequency generators. Our device uses high-efficiency, thin InGaP/GaAs tandem flexible photovoltaics to harvest energy from various light sources, which powers Bluetooth system to facilitate long-term, on-demand use. Observation of sustained locomotion behaviors for a month in mice via secondary motor cortex area stimulation demonstrates the notable capabilities of our device, highlighting its potential for space-free neuromodulating applications.
Neuromorphic sequence learning with an event camera on routes through vegetation
Authors: Zhu Le , Mangan Michael , Webb Barbara
Published: September 2023

For many robotics applications, it is desirable to have relatively low-power and efficient onboard solutions. We took inspiration from insects, such as ants, that are capable of learning and following routes in complex natural environments using relatively constrained sensory and neural systems. Such capabilities are particularly relevant to applications such as agricultural robotics, where visual navigation through dense vegetation remains a challenging task. In this scenario, a route is likely to have high self-similarity and be subject to changing lighting conditions and motion over uneven terrain, and the effects of wind on leaves increase the variability of the input. We used a bioinspired event camera on a terrestrial robot to collect visual sequences along routes in natural outdoor environments and applied a neural algorithm for spatiotemporal memory that is closely based on a known neural circuit in the insect brain. We show that this method is plausible to support route recognition for visual navigation and more robust than SeqSLAM when evaluated on repeated runs on the same route or routes with small lateral offsets. By encoding memory in a spiking neural network running on a neuromorphic computer, our model can evaluate visual familiarity in real time from event camera footage.
Novel non-HAP class A HBV capsid assembly modulators have distinct
in vitro
and
in vivo
profiles
Authors: Vanrusselt Hannah , Kum Dieudonné Buh , Taverniti Valerio , Liu Cheng , Acosta Sanchez Abel , Corthout Nikky , Munck Sebastian , Baumert Thomas F. , Beigelman Leonid , Blatt Lawrence M. , Symons Julian A. , Deval Jerome , Raboisson Pierre , Verrier Eloi R. , Jekle Andreas , Vendeville Sandrine , Debing Yannick
Published: September 2023

Capsid assembly modulators (CAMs) are a novel class of therapeutic small molecules with the potential to address the continued global challenge posed by chronic hepatitis B (CHB). Class A CAMs (CAM-As) are particularly attractive because they induce loss of hepatitis B virus (HBV)-infected hepatocytes in animal models. All CAM-As described to date are heteroaryldihydropyrimidines (HAPs) which come with several drawbacks. Here, we report on the first non-HAP CAM-As ALG-005398 and ALG-005863 and provide a detailed
in vitro
intracellular characterization. These non-HAP CAM-As are potent inhibitors of HBV DNA production and also block the establishment of cccDNA. Non-HAP CAM-As can be classified into two distinct profiles: CAM-A
i
and CAM-A
t
, which are in turn differentiated from the HAP CAM-A
h
profile. CAM-A
i
molecules induce larger and more irregular capsids in electron microscopy and cellular HBV core protein (HBc) staining, whereas CAM-A
t
-induced capsids and aggregates are smaller but more numerous. CAM-A
i
and CAM-A
t
also induce a different subnuclear localization (no co-localization with promyelocytic leukemia bodies) and show a lower propensity to CAM-A-induced HBc-dependent cell death compared to CAM-A
h
. CAM-A
t
s ALG-005398 and ALG-006162 showed steady reductions of circulating HBsAg and HBeAg with minimal alanine aminotransferase (ALT) elevation in the adeno-associated virus (AAV)-HBV mouse model, accompanied by loss of the AAV-HBV episome and infected hepatocytes. Moreover, these effects were sustained for at least 13 weeks after end of treatment. The differentiated mechanism of action and sustained
in vivo
response make non-HAP CAM-As a promising potential component of future functional cure regimens for CHB patients.

IMPORTANCE

Chronic hepatitis B is the most important cause of liver cancer worldwide and affects more than 290 million people. Current treatments are mostly suppressive and rarely lead to a cure. Therefore, there is a need for novel and curative drugs that target the host or the causative agent, hepatitis B virus itself. Capsid assembly modulators are an interesting class of antiviral molecules that may one day become part of curative treatment regimens for chronic hepatitis B. Here we explore the characteristics of a particularly interesting subclass of capsid assembly modulators. These so-called non-HAP CAM-As have intriguing properties in cell culture but also clear virus-infected cells from the mouse liver in a gradual and sustained way. We believe they represent a considerable improvement over previously reported molecules and may one day be part of curative treatment combinations for chronic hepatitis B.
Conditional replication and secretion of hepatitis B virus genome uncover the truncated 3′ terminus of encapsidated viral pregenomic RNA
Authors: Shen Sheng , Liu Wendong , Zeng Ge , Liang Hongyan , Yu Xiaoyang , Zhang Hu , Sun Jian , Guo Haitao
Published: September 2023

Hepatitis B virus (HBV) pregenomic RNA (pgRNA) is packaged into capsid where reverse transcription takes place to synthesize viral DNA genome, and the encapsidated pgRNA is the predominant species of serum HBV RNA in patients as a serological biomarker. In this study, by utilizing various conditional HBV replication and secretion systems, we analyzed the intracellular and extracellular capsid pgRNA and revealed that the 3′ terminus of capsid pgRNA is scatteredly distributed between DR2 and poly(A) tail, except that the viral polymerase priming-defective mutant Y63D retained the sequence upstream of 3′ DR1. Mechanistically, the heterogeneity of capsid RNA 3′ terminus is due to the endogenous viral RNaseH activity during reverse transcription and exogenous MNase digestion during capsid RNA isolation; cellular ribonucleases may also participate in this process as the Y63D pgRNA 3′ terminus in the immunoprecipitated capsid without prior MNase treatment remains truncated into 3′ DR1. The major pgRNA splicing variant 1 of 2.1 kb and the artificial 3′ DR1 and ε deletion mutants also possess a truncated 3′ end of capsid RNA, indicating that the underrepresentation of the 3′ end of encapsidated pgRNA is independent of pgRNA length or 3′ terminal sequences. Altogether, our study suggests that the 3′ region of HBV capsid pgRNA downstream of 3′ DR1 is likely positioned outside of the capsid or loosely encapsulated, and thus is ribonuclease accessible. Furthermore, the detailed features of capsid pgRNA 3′ terminus will shed light on HBV pgRNA encapsidation and reverse transcription and aid the development of better diagnostics of serum HBV RNA.

IMPORTANCE

The biogenesis and clinical application of serum HBV pgRNA have been a research hotspot in recent years. This study further characterized the heterogeneity of the 3′ terminus of capsid RNA by utilizing a variety of experimental systems conditionally supporting HBV genome replication and secretion, and reveal that the 3′ truncation of capsid pgRNA is catalyzed by cellular ribonuclease(s) and viral RNaseH at positions after and before 3′ DR1, respectively, indicating the 3′ DR1 as a boundary between the encapsidated portion of pgRNA for reverse transcription and the 3′ unprotected terminus, which is independent of pgRNA length and the 3′ terminal sequence. Thus, our study provides new insights into the mechanism of pgRNA encapsidation and reverse transcription, as well as the optimization of serum HBV RNA diagnostics.
Complete genome sequence of soybean geminivirus A in soybean in Korea
Authors: Bak Sangmin , Kwon Mina , Baek Seungbin , Min Jean Geung , Kang Dong Hyun , Kim Minseok , Lee Hong-Kyu , Lee Su-Heon
Published: September 2023

Soybean geminivirus A (SGVA), a member of the family Geminiviridae, was detected in a survey of early-stage soybean. The complete genome sequence of SGVA isolate Habin was determined, revealing its characteristics and similarity to Korean and Chinese isolates. This study contributes to understanding the impact of SGVA on soybean production.
Constraining flow and sediment transport intermittency in the geological past
Authors: Lyster Sinéad J. , Whittaker Alexander C. , Farnsworth Alex , Hampson Gary J.
Published: September 2023

Quantitative investigations of ancient rivers usually provide insights into either instantaneous or mean flow conditions. There is a critical gap between these time scales of investigation, which reflects the intermittency of flow and sediment transport, and closing this gap is crucial to fully explore the dynamics and evolution of ancient fluvial landscapes. Here, we combined fluvial stratigraphic data sets, flow and sediment transport models, and paleoclimate general circulation model (GCM) results to develop new methods to estimate intermittency in the geological past, specifically flow intermittency factors (Iw) and sediment transport intermittency factors (Is), and we show how they can be used to explore past hydrograph shapes. We illustrated these methods using the Upper Cretaceous Last Chance Ferron Sandstone in Utah, western United States. For sand-transporting flow conditions in Last Chance Ferron rivers, we estimated Iw values of 0.54−0.90, which imply that channel-forming conditions were sustained for the majority of the year, consistent with perennial systems in which relatively large discharges were sustained. In contrast, for gravel-transporting flow conditions, Iw values of 0.28−0.38 suggest that the largest formative flows may have occupied Last Chance Ferron rivers for nearly a third of the year, which could be explained by a monsoonal system in which high-magnitude discharge events were sustained, or a subtropical system in which high-magnitude discharge events had short durations but high frequencies. Meanwhile, Is values of 0.075−0.15 suggest that annual sediment budgets could have been transported in as little as 10 days and up to 2 months, if channel-forming conditions were sustained, and these values highlight that small changes in the duration of channel-forming conditions could significantly impact sediment budgets. Our results are consistent with independent facies- and proxy-based insights into Last Chance Ferron rivers, which point to a perennially wet system characterized by a monsoonal or subtropical discharge regime. Further, our results highlight new opportunities to use paleoclimate GCMs to constrain intermittency factors in the geological past. Going forward, paleoclimate GCMs will be particularly useful where the rock record is incomplete or inaccessible, or where stratigraphic approaches are limited, and they will enable us to tackle pertinent research questions pertaining to past surface processes on both Earth and other planets.
Controls on upstream-migrating bed forms in sandy submarine channels
Authors: Englert Rebecca G. , Vellinga Age J. , Cartigny Matthieu J.B. , Clare Michael A. , Eggenhuisen Joris T. , Hubbard Stephen M.
Published: September 2023

Submarine channels parallel river channels in their ability to transport sediment. However, in contrast to rivers, sediment transport and bed-form development in submarine channels are less well understood. Many steep (>1°), sandy submarine channels are dominated by upstream-migrating bed forms. The flow conditions required to form these upstream-migrating bed forms remain debated because the interactions between turbidity currents and active bed forms are difficult to measure directly. Consequently, we used a depth-resolved numerical model to test the role of flow parameters that are hypothesized to control the formation of upstream-migrating bed forms in submarine channels. While our modeling results confirmed the importance of previously identified flow parameters (e.g., densiometric Froude number), we found that basal sediment concentration in turbidity currents is the strongest predictor of upstream-migrating bed-form formation. Our model shows how locally steep gradients enable high sediment concentrations (average >5 vol%) in the basal parts of flows, which allow the development of cyclic step instabilities and their associated bed forms. This new insight explains the previously puzzling observation that upstream-migrating bed forms are abundant in proximal, steep, sandy reaches of submarine channels, while their occurrence becomes more intermittent downslope.
Best practice recommendations for body composition considerations in sport to reduce health and performance risks: a critical review, original survey and expert opinion by a subgroup of the IOC consensus on Relative Energy Deficiency in Sport (REDs)
Authors: Mathisen Therese Fostervold , Ackland Timothy , Burke Louise M , Constantini Naama , Haudum Judith , Macnaughton Lindsay S , Meyer Nanna L , Mountjoy Margo , Slater Gary , Sundgot-Borgen Jorunn
Published: September 2023

Background

The assessment of body composition (BC) in sport raises concern for athlete health, especially where an overfocus on being lighter or leaner increases the risk of Relative Energy Deficiency in Sport (REDs) and disordered eating.

Methods

We undertook a critical review of the effect of BC on performance (29 longitudinal, prospective or intervention studies) and explored current practice related to BC considerations via a follow-up to a 2013 internationally distributed survey.

Results

The review found that a higher level of body fat was negatively associated with endurance performance, while a gain in muscle mass resulted in performance benefits across sports. BC did not contribute to early talent identification, and no unique cut-off to signify a performance advantage for BC was identified. BC appears to be one of an array of variables impacting performance, and its influence should not be overstated. The survey (125 practitioners, 61 sports and 26 countries) showed subtle changes in BC considerations over time, such as an increased role for sport dietitian/nutrition practitioners as BC measurers (2013: 54%, 2022: 78%); less emphasis on reporting of body fat percentage (2013: 68%, 2022: 46%) and reduced frequency of BC assessment if ≥every fourth week (2013: 18%, 2022: 5%). Respondents remained concerned about a problematic focus on BC (2013: 69%, 2022: 78%). To address these findings, we provide detailed recommendations for BC considerations, including an overview of preferable BC methodology.

Conclusions

The ‘best practice’ guidelines stress the importance of a multidisciplinary athlete health and performance team, and the treatment of BC data as confidential medical information. The guidelines provide a health focus around BC, aiming to reduce the associated burden of disordered eating, problematic low energy availability and REDs.
Review of the scientific rationale, development and validation of the International Olympic Committee Relative Energy Deficiency in Sport Clinical Assessment Tool: V.2 (IOC REDs CAT2)—by a subgroup of the IOC consensus on REDs
Authors: Stellingwerff Trent , Mountjoy Margo , McCluskey Walter TP , Ackerman Kathryn E , Verhagen Evert , Heikura Ida A
Published: September 2023

Relative Energy Deficiency in Sport (REDs) has various different risk factors, numerous signs and symptoms and is heavily influenced by one’s environment. Accordingly, there is no singular validated diagnostic test. This 2023 International Olympic Committee’s REDs Clinical Assessment Tool—V.2 (IOC REDs CAT2) implements a three-step process of: (1) initial screening; (2) severity/risk stratification based on any identified REDs signs/symptoms (primary and secondary indicators) and (3) a physician-led final diagnosis and treatment plan developed with the athlete, coach and their entire health and performance team. The CAT2 also introduces a more clinically nuanced four-level traffic-light (green, yellow, orange and red) severity/risk stratification with associated sport participation guidelines. Various REDs primary and secondary indicators have been identified and ‘weighted’ in terms of scientific support, clinical severity/risk and methodological validity and usability, allowing for objective scoring of athletes based on the presence or absence of each indicator. Early draft versions of the CAT2 were developed with associated athlete-testing, feedback and refinement, followed by REDs expert validation via voting statements (ie, online questionnaire to assess agreement on each indicator). Physician and practitioner validity and usability assessments were also implemented. The aim of the IOC REDs CAT2 is to assist qualified clinical professionals in the early and accurate diagnosis of REDs, with an appropriate clinical severity and risk assessment, in order to protect athlete health and prevent prolonged and irreversible outcomes of REDs.
Primary, secondary and tertiary prevention of Relative Energy Deficiency in Sport (REDs): a narrative review by a subgroup of the IOC consensus on REDs
Authors: Torstveit Monica Klungland , Ackerman Kathryn E , Constantini Naama , Holtzman Bryan , Koehler Karsten , Mountjoy Margo L , Sundgot-Borgen Jorunn , Melin Anna
Published: September 2023

Relative Energy Deficiency in Sport (REDs) is common among female and male athletes representing various sports at different performance levels, and the underlying cause is problematic low energy availability (LEA). It is essential to prevent problematic LEA to decrease the risk of serious health and performance consequences. This narrative review addresses REDs primary, secondary and tertiary prevention strategies and recommends best practice prevention guidelines targeting the athlete health and performance team, athlete entourage (eg, coaches, parents, managers) and sport organisations. Primary prevention of REDs seeks to minimise exposure to and reduce behaviours associated with problematic LEA. Some of the important strategies are educational initiatives and de-emphasising body weight and leanness, particularly in young and subelite athletes. Secondary prevention encourages the early identification and management of REDs signs or symptoms to facilitate early treatment to prevent development of more serious REDs outcomes. Recommended strategies for identifying athletes at risk are self-reported screening instruments, individual health interviews and/or objective assessment of REDs markers. Tertiary prevention (clinical treatment) seeks to limit short-term and long-term severe health consequences of REDs. The cornerstone of tertiary prevention is identifying the source of and treating problematic LEA. Best practice guidelines to prevent REDs and related consequences include a multipronged approach targeting the athlete health and performance team, the athlete entourage and sport organisations, who all need to ensure a supportive and safe sporting environment, have sufficient REDs knowledge and remain observant for the early signs and symptoms of REDs.
2023 International Olympic Committee’s (IOC) consensus statement on Relative Energy Deficiency in Sport (REDs)
Authors: Mountjoy Margo , Ackerman Kathryn E , Bailey David M , Burke Louise M , Constantini Naama , Hackney Anthony C , Heikura Ida Aliisa , Melin Anna , Pensgaard Anne Marte , Stellingwerff Trent , Sundgot-Borgen Jorunn Kaiander , Torstveit Monica Klungland , Jacobsen Astrid Uhrenholdt , Verhagen Evert , Budgett Richard , Engebretsen Lars , Erdener Uğur
Published: September 2023

Relative Energy Deficiency in Sport (REDs) was first introduced in 2014 by the International Olympic Committee’s expert writing panel, identifying a syndrome of deleterious health and performance outcomes experienced by female and male athletes exposed to low energy availability (LEA; inadequate energy intake in relation to exercise energy expenditure). Since the 2018 REDs consensus, there have been >170 original research publications advancing the field of REDs science, including emerging data demonstrating the growing role of low carbohydrate availability, further evidence of the interplay between mental health and REDs and more data elucidating the impact of LEA in males. Our knowledge of REDs signs and symptoms has resulted in updated Health and Performance Conceptual Models and the development of a novel Physiological Model. This Physiological Model is designed to demonstrate the complexity of either problematic or adaptable LEA exposure, coupled with individual moderating factors, leading to changes in health and performance outcomes. Guidelines for safe and effective body composition assessment to help prevent REDs are also outlined. A new REDs Clinical Assessment Tool-Version 2 is introduced to facilitate the detection and clinical diagnosis of REDs based on accumulated severity and risk stratification, with associated training and competition recommendations. Prevention and treatment principles of REDs are presented to encourage best practices for sports organisations and clinicians. Finally, methodological best practices for REDs research are outlined to stimulate future high-quality research to address important knowledge gaps.
Methodology for studying Relative Energy Deficiency in Sport (REDs): a narrative review by a subgroup of the International Olympic Committee (IOC) consensus on REDs
Authors: Ackerman Kathryn E , Rogers Margot Anne , Heikura Ida A , Burke Louise M , Stellingwerff Trent , Hackney Anthony C , Verhagen Evert , Schley Stacey , Saville Grace H , Mountjoy Margo , Holtzman Bryan
Published: September 2023

In the past decade, the study of relationships among nutrition, exercise and the effects on health and athletic performance, has substantially increased. The 2014 introduction of Relative Energy Deficiency in Sport (REDs) prompted sports scientists and clinicians to investigate these relationships in more populations and with more outcomes than had been previously pursued in mostly white, adolescent or young adult, female athletes. Much of the existing physiology and concepts, however, are either based on or extrapolated from limited studies, and the comparison of studies is hindered by the lack of standardised protocols. In this review, we have evaluated and outlined current best practice methodologies to study REDs in an attempt to guide future research.

This includes an agreement on the definition of key terms, a summary of study designs with appropriate applications, descriptions of best practices for blood collection and assessment and a description of methods used to assess specific REDs sequelae, stratified as eitherPreferred,Used and RecommendedorPotential. Researchers can use the compiled information herein when planning studies to more consistently select the proper tools to investigate their domain of interest. Thus, the goal of this review is to standardise REDs research methods to strengthen future studies and improve REDs prevention, diagnosis and care.
Molecular portraits of patients with intrahepatic cholangiocarcinoma who diverge as rapid progressors or long survivors on chemotherapy
Authors: O'Rourke Colm J , Salati Massimiliano , Rae Colin , Carpino Guido , Leslie Holly , Pea Antonio , Prete Maria G , Bonetti Luca R , Amato Francesco , Montal Robert , Upstill-Goddard Rosie , Nixon Colin , Sanchon-Sanchez Paula , Kunderfranco Paolo , Sia Daniela , Gaudio Eugenio , Overi Diletta , Cascinu Stefano , Hogdall Dan , Pugh Sian , Domingo Enric , Primrose John N , Bridgewater John , Spallanzani Andrea , Gelsomino Fabio , Llovet Josep M , Calvisi Diego F , Boulter Luke , Caputo Francesco , Lleo Ana , Jamieson Nigel B , Luppi Gabriele , Dominici Massimo , Andersen Jesper B , Braconi Chiara
Published: September 2023

Objective

Cytotoxic agents are the cornerstone of treatment for patients with advanced intrahepatic cholangiocarcinoma (iCCA), despite heterogeneous benefit. We hypothesised that the pretreatment molecular profiles of diagnostic biopsies can predict patient benefit from chemotherapy and define molecular bases of innate chemoresistance.

Design

We identified a cohort of advanced iCCA patients with comparable baseline characteristics who diverged as extreme outliers on chemotherapy (survival <6 m in rapid progressors, RP; survival >23 m in long survivors, LS). Diagnostic biopsies were characterised by digital pathology, then subjected to whole-transcriptome profiling of bulk and geospatially macrodissected tissue regions. Spatial transcriptomics of tumour-infiltrating myeloid cells was performed using targeted digital spatial profiling (GeoMx). Transcriptome signatures were evaluated in multiple cohorts of resected cancers. Signatures were also characterised using in vitro cell lines, in vivo mouse models and single cell RNA-sequencing data.

Results

Pretreatment transcriptome profiles differentiated patients who would become RPs or LSs on chemotherapy. Biologically, this signature originated from altered tumour-myeloid dynamics, implicating tumour-induced immune tolerogenicity with poor response to chemotherapy. The central role of the liver microenviroment was confrmed by the association of the RPLS transcriptome signature with clinical outcome in iCCA but not extrahepatic CCA, and in liver metastasis from colorectal cancer, but not in the matched primary bowel tumours.

Conclusions

The RPLS signature could be a novel metric of chemotherapy outcome in iCCA. Further development and validation of this transcriptomic signature is warranted to develop precision chemotherapy strategies in these settings.