bluuebunny/crossref_metadata_2025_split huggingface dataset:
nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography
Authors: Liu Hsuan-Fu , Zhou Ye , Huang Qinwen , Piland Jonathan , Jin Weisheng , Mandel Justin , Du Xiaochen , Martin Jeffrey , Bartesaghi Alberto 
Published: October 2023

AbstractSingle-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP (http://nextpyp.app).
Indoor UWB Positioning and Position Tracking Data Set
Authors: Bregar Klemen 
Published: October 2023

AbstractIndoor positioning has become a hot topic in various fields, such as industry, healthcare, and commerce. Ultra-wideband (UWB) radio technology provides a cost-effective solution for range-based positioning, offering exceptionally high accuracy and precision. Its ultra-high temporal resolution enables range measurements with accuracy of a few centimeters. To develop and evaluate range-based positioning systems, we collected measurements in four different indoor environments using eight fixed devices and one mobile positioning device. To eliminate the fluctuation of walking speed from the data, we pre-defined a path in each indoor environment, similar to the human walking path, which was sampled at equidistant positions. We collected multiple range measurements and channel impulse response (CIR) data at each tag position on the path. The resulting dataset supports the development of range-based positioning and position tracking algorithms with various combinations of network topologies and anchor-tag combinations. We have also provided a full set of data analysis tools that enable the reproducibility of results and serve as a basis for further development of range-based UWB positioning algorithms.
An experimental investigation into whether choice architecture interventions are considered ethical
Authors: Turetski Daniella , Rondina Renante , Hutchings Jordan , Feng Bing , Soman Dilip 
Published: October 2023

Abstract
Despite their increasing use, choice architecture interventions have faced criticism for being possibly manipulative and unethical. We empirically explore how an intervention’s acceptability differs by the type of intervention used, by the domain, and by the way in which its implementation and benefits are explained. We employ a 5 × 5 × 5 factorial design with three fully crossed predictor variables: domain, type of intervention, and explanation. We measure participants’ acceptance of the proposed intervention, perceived threat to autonomy and freedom of choice, and belief that the intervention will be successful. We hypothesized that acceptability of the intervention and perceived threat to autonomy will change as a function of the type of intervention used, the domain in which it is implemented, and the rationale for which its use is presented. We find that acceptability of the intervention, perceived threat to autonomy, and belief that the intervention will be successful differ by the type of intervention used and by the domain in which it is implemented. The rationale for the use of the intervention appears to change acceptability of the intervention depending on the type of intervention that is being used, and the domain in which it is implemented. Exploratory analyses were conducted to investigate differences between specific levels within factors, and interactions between factors. Given the variation in acceptability across the three factors, we believe that the discourse about the ethics of choice architecture should avoid generalizations and should instead be at the level of individual interventions in a specific situation. We conclude with a discussion about areas for future research.

Protocol registration
The stage 1 protocol for this Registered Report was accepted in principle on 14 October 2022. The protocol, as accepted by the journal, can be found at: https://doi.org/10.6084/m9.figshare.21758666.
Hydrodynamics of a cold circulating fluidized bed for methanol-to-olefins (MTO) process: experimental and computational investigation
Authors: Babaei Mojtaba , Movahedirad Salman 
Published: October 2023

AbstractThe present study aims to investigate the hydrodynamic behavior of gas–solid flow in a pseudo-two-dimensional cold circulation fluidized bed specifically designed to mimic a plane cut of an industrial methanol-to-olefins (MTO) bed. The solid velocity pattern was experimentally examined using the Particle Image Velocimetry with Digital Image Analysis (PIV-DIA) technique. The hydrodynamics of this pseudo-2D bed were studied using the twoPhaseEulerFoam solver in OpenFOAM, and the adjusted solver was validated through solid particle velocity and solid volume fraction comparisons, showing good agreement with experimental data. Additionally, the study explores different geometries, including symmetric and asymmetric baffles, to understand their impact on the mixing characteristics of the circulating fluidized bed for MTO. The findings highlight the significant role of asymmetric baffles in enhancing mixing behavior. Furthermore, the DIA technique was employed to study the effects of bubbles on gas–solid mixing, revealing that the low mixing region of the bed limited the diameter of bubbles.
Enhancement of electrical conductivity associated with non-bridged oxygen defects in molybdenum phosphate oxide glass via doping of SrO
Authors: Fayad A. M. , Ouis M. A. , Morsi R. M. M. , Elwan R. L. 
Published: October 2023

AbstractBased on the attractive properties of phosphate glass, improved molybdenum phosphate glasses of composition 40P2O5, 20MoO3, 15MgO, (25-x)Li2O, xSrO, [x = 0, 5, 10, 15 and 20 mol %] were prepared via the melt-quench technique. They were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), UV–visible reflectance and Electron spin resonance (ESR). FTIR confirmed the existence of several structural phosphate groups other than MoO4 and MoO6 units. Optical analysis revealed the active species of molybdenum ions. SrO addition decreases the bandgap energy, converting the glass insulator features into semiconductor properties. The measured AC electrical conductivity (σac) increased within the temperature range of 298–473(K) and decreased in the frequency range of 0.042 kHz–1 MHz. The estimated DC electrical conductivity increased with temperature, suggesting the semiconducting behavior. The highest electrical conductivity was found in base and 5% SrO samples. Therefore, it appears that the prepared glasses are viable candidates for opto-electronic applications.
Increasing rectum–prostate distance using a hydrogel spacer to reduce radiation exposure during proton beam therapy for prostate cancer
Authors: Narukawa Tsukasa , Aibe Norihiro , Tsujimoto Masashi , Shiraishi Takumi , Kimoto Takuya , Suzuki Gen , Ueda Takashi , Fujihara Atsuko , Yamazaki Hideya , Ukimura Osamu 
Published: October 2023

AbstractSpaceOAR, a polyethylene-glycol hydrogel, reduces rectal radiation exposure during radiation therapy for prostate cancer. Previously, our group reported the modified technique of hydrogel insertion, which achieves greater separated distance at prostate-apex. This study aimed to investigate the impact of separated distance at prostate-apex and our modifier technique, on radiation exposure reduction during proton beam therapy (PBT). We included 330 patients undergoing PBT with the relative biological effectiveness (RBE) of 63 Gray (Gy) for localized prostate cancer, and categorized them into groups 0 (no spacer, n = 141), 1 (separated distance of spacer at the prostate-apex level < 7.5 mm, n = 81), and 2 (distance ≥ 7.5 mm, n = 108). The rectal volumes to receive 30–60 Gy (RBE), was estimated and described as Rectal V30–60 (ml) in 10 Gy increments. The Rectal V30–60 (ml) was significantly lower in group 2 than in group 1, and in group 1 than in group 0. After propensity score matching, the multivariate logistic regression analysis revealed that the most significant factor to reduce radiation exposure was our modified technique of hydrogel insertion. Therefore, using a hydrogel spacer to expand the prostate–rectum distance not only at prostate-mid to prostate-base level but also at the prostate-apex level can reduce the radiation exposure in PBT for prostate cancer.
Assessment of hybrid population immunity to SARS-CoV-2 following breakthrough infections of distinct SARS-CoV-2 variants by the detection of antibodies to nucleoprotein
Authors: den Hartog Gerco , Andeweg Stijn P. , Hoeve Christina E. , Smits Gaby , Voordouw Bettie , Eggink Dirk , Knol Mirjam J. , van Binnendijk Robert S. 
Published: October 2023

AbstractImmunity induced by vaccination and infection, referred to as hybrid immunity, provides better protection against SARS-CoV-2 infections compared to immunity induced by vaccinations alone. To assess the development of hybrid immunity we investigated the induction of Nucleoprotein-specific antibodies in PCR-confirmed infections by Delta or Omicron in vaccinated individuals (n = 520). Eighty-two percent of the participants with a breakthrough infection reached N-seropositivity. N-seropositivity was accompanied by Spike S1 antibody boosting, and independent of vaccination status or virus variant. Following the infection relatively more antibodies to the infecting virus variant were detected. In conclusion, these data show that hybrid immunity through breakthrough infections is hallmarked by Nucleoprotein antibodies and broadening of the Spike antibody repertoire. Exposure to future SARS-CoV-2 variants may therefore continue to maintain and broaden vaccine-induced population immunity.
Over-expression of GhACTIN1 under the control of GhSCFP promoter improves cotton fiber and yield
Authors: Iqbal Adnan , Aslam Sibgha , Akhtar Sidra , Ali Qurban , Rao Abdul Qayyum , Husnain Tayyab 
Published: October 2023

AbstractActin dynamics is pivotal in controlling cotton fiber elongation and the onset of secondary wall biosynthesis. We report that overexpression of GhACTIN1 under fiber fiber-specific promoter, GhSCFP, improves cotton fiber length, strength, and micronaire value. However, the effect of transgene has a more positive effect on fiber strength and micronaire value than fiber length. F-actin quantification and cellulose contents measurement in transgenic developing cotton fiber during the elongation phase showed an increase of up to 8.7% and 4.7% respectively. Additionally, physiological factors such as water use efficiency showed no significant change in transgenic cotton lines, while stomatal conductance and photosynthetic rate were significantly increased. Moreover, agronomical data determined that lint percentage (GOT) and seed cotton yield also increased up to 4.6% and 29.5% respectively, in transgenic cotton lines compared to the control lines. Our data demonstrate that the GhACTIN1 gene is a strong candidate gene for cotton fiber and yield improvement.
Unraveling surface and bulk dynamics of iron(III) molybdate during oxidative dehydrogenation using operando and transient spectroscopies
Authors: Schumacher Leon , Radtke Mariusz , Welzenbach Jan , Hess Christian 
Published: October 2023

AbstractIron(III) molybdate (Fe2(MoO4)3) is a commercial catalyst for the oxidative dehydrogenation (ODH) of methanol, but it has recently been shown to be relevant for other substrates as well. Despite its commercial use, a detailed mechanistic understanding of Fe2(MoO4)3 catalysts at the surface and in the bulk has been lacking, largely hampered by the lack of suitable spectroscopic methods, directly applicable under reaction conditions. Using propane ODH as an example, we highlight the potential of operando Raman and impedance spectroscopy combined with transient IR spectroscopy, to identify surface active sites and monitor the hydrogen transfer and oxygen dynamics. By comparison with the behavior of reference compounds (MoO3, MoOx/Fe2O3) a mechanistic model is proposed. The presence of iron greatly influences the reactivity behavior via oxygen diffusion but is moderated in its oxidative capacity by surface MoOx. Our approach directly elucidates fundamental properties of Fe2(MoO4)3 of general importance to selective oxidation catalysis.
Design of prime-editing guide RNAs with deep transfer learning
Authors: Liu Feng , Huang Shuhong , Hu Jiongsong , Chen Xiaozhou , Song Ziguo , Dong Junguo , Liu Yao , Huang Xingxu , Wang Shengqi , Wang Xiaolong , Shu Wenjie 
Published: October 2023

AbstractPrime editors (PEs) are promising genome-editing tools, but effective optimization of prime-editing guide RNA (pegRNA) design remains a challenge owing to the lack of accurate and broadly applicable approaches. Here we develop Optimized Prime Editing Design (OPED), an interpretable nucleotide language model that leverages transfer learning to improve its accuracy and generalizability for the efficiency prediction and design optimization of pegRNAs. Comprehensive validations on various published datasets demonstrate its broad applicability in efficiency prediction across diverse scenarios. Notably, pegRNAs with high OPED scores consistently show significantly increased editing efficiencies. Furthermore, the versatility and efficacy of OPED in design optimization are confirmed by efficiently installing various ClinVar pathogenic variants using optimized pegRNAs in the PE2, PE3/PE3b and ePE editing systems. OPED consistently outperforms existing state-of-the-art approaches. We construct the OPEDVar database of optimized designs from over two billion candidates for all pathogenic variants and provide a user-friendly web application of OPED for any desired edit.
An adaptive fuzzy control technique for a high‐speed vehicular platoon experiencing communication delays
Authors: Li Handong , Wu Haimeng , Gulati Ishita , Ali Saleh A. , Pickert Volker , Dlay Satnam 
Published: October 2023

AbstractVehicle platooning is seen as an enabler to improve driving safety, traffic congestion and stress‐free driving. A platoon is a highly non‐linear system and fuzzy control is able to deal with those systems. This paper presents a pioneering solution to the complex problem of vehicle platooning. Our adaptive controller seamlessly integrates fuzzy logic with conventional PID control technology, thereby ensuring safe and efficient travel for vehicles within a platoon. The key objectives of this controller encompass the maintenance of a consistent inter‐vehicle time gap and the consideration of time‐varying parameter uncertainties and communication delays between vehicles. It provides mathematical proof of the stability of the platoon formation using the Routh–Hurwitz theorem and a set of equations that describe the platoon's overall performance. Simulation results show that the proposed controller is effective in controlling vehicle platoons, even in the presence of random communication delays, resulting in improved driving safety and reduced traffic congestion.
Constraining the magnetic field geometry of the millisecond pulsar PSR J0030+0451 from joint radio, thermal X-ray, andγ-ray emission
Authors: Pétri J. , Guillot S. , Guillemot L. , Cognard I. , Theureau G. , Grießmeier J.-M. , Bondonneau L. , González-Caniulef D. , Webb N. , Jankowski F. , Kravtsov I. P. , McKee J. W. , Carozzi T. D. , Cecconi B. , Serylak M. , Zarka P. 
Published: October 2023

Context.With the advent of multi-wavelength electromagnetic observations of neutron stars – spanning many decades in photon energies – from radio wavelengths up to X-rays andγ-rays, it has become possible to significantly constrain the geometry and the location of the associated emission regions.Aims.In this work, we use results from the modelling of thermal X-ray observations of PSR J0030+0451 from the Neutron Star Interior Composition Explorer (NICER) mission and phase-aligned radio andγ-ray pulse profiles to constrain the geometry of an off-centred dipole that is able to reproduce the light curves in these respective bands simultaneously.Methods.To this aim, we deduced a configuration with a simple dipole off-centred from the location of the centre of the thermal X-ray hot spots. We show that the geometry is compatible with independent constraints from radio andγ-ray pulsations only, leading to a fixed magnetic obliquity ofα ≈ 75° and a line-of-sight inclination angle ofζ ≈ 54°.Results.We demonstrate that an off-centred dipole cannot be rejected by accounting for the thermal X-ray pulse profiles. Moreover, the crescent shape of one spot is interpreted as the consequence of a small-scale surface dipole on top of the large-scale off-centred dipole.
Age-dating the young open cluster UBC 1 with g-mode asteroseismology, gyrochronology, and isochrone fitting
Authors: Fritzewski D. J. , Van Reeth T. , Aerts C. , Van Beeck J. , Gossage S. , Li G. 
Published: October 2023

Aims. UBC 1 is an open cluster discovered in Gaia data and located near the edge of the Transiting Exoplanet Survey Satellite’s (TESS) continuous viewing zone. We aim to provide age constraints for this poorly studied open cluster from the combination of gravity-mode (g-mode) asteroseismology, gyrochronology, and isochrone fitting.
Methods. We established the members of UBC 1 from a spatial-kinematic filtering and estimate the cluster age and its parameters. Firstly, we fitted rotating isochrones to the single star cluster sequence. Secondly, using TESS time-series photometry, we explored the variability of the upper main sequence members and identified potential g-mode pulsators. For one star, we found a clear period spacing pattern that we used to deduce the buoyancy travel time, the near-core rotation rate, and an asteroseismic age. For a third independent age estimate, we employed the rotation periods of low-mass members of UBC 1.
Results. Based on isochrone fitting, we find log t = 8.1 ± 0.4, where the large uncertainty occurs because UBC 1 does not host evolved stars. From asteroseismology of one g-mode pulsator, we find a constrained age of log t = 8.24−0.14+0.43. From gyrochronology based on 17 cool star cluster members, we estimate log t = 8.35−0.25+0.16. Combined, all three methods lead to a consistent age in the range of 150 − 300 Myr.
Conclusions. Our results show that even a single cluster member with identified g modes can improve age-dating of young open clusters. Combining the gyrochronology of low-mass members with asteroseismology of intermediate-mass members is a powerful tool for young open cluster modelling, including high-precision age-dating.
Prolonged Deep Hypothermia
Authors: Rygg I.H. , Borgeskov Sv. , Arnfred I 
Published: October 2023

Observations made during and after prolonged deep hypothermia (7 hours between 6-20° C) are reported in a case operated for a rhinopharyngeal haemangioma with severe blood loss during cardiopulmonary bypass. Near normal numerical values of the acid-base parameters when corrected to the current temperature were aimed at. No organic damages could with certainty be described to the hypothermia itself or to the prolonged perfusion.
A case of prolonged, deep hypothermia during the application of cardiopulmonary bypass will be reported. For literature and for the theoretical background of using deep hypothermia the reader is referred to a review by I. H. Rygg (1969).
Bridging the Gap: A Systematic Review on Reporting Baseline Characteristics, Process, and Outcome Parameters in Rectosigmoid Hirschsprung's Disease
Authors: Rossi Daniel , Löf Granström Anna , Teunissen Nadine M. , Wijnen René M.H. , Wester Tomas , Sloots Cornelius E.J. 
Published: October 2023

AbstractThe variation in standardized, well-defined parameters in Hirschsprung's disease (HSCR) research hinders overarching comparisons and complicates evaluations of care quality across healthcare settings. This review addresses the significant variability observed in these parameters as reported in recent publications. The goal is to compile a list of commonly described baseline characteristics, process and outcome measures, and to investigate disparities in their utilization and definitions. A systematic review of literature on the primary care process for HSCR was performed according to PRISMA guidelines. Relevant literature published between 2015 and 2021 was obtained by combining the search term “Hirschsprung's disease” with “treatment outcome,” “complications,” “mortality,” “morbidity,” and “survival” in Medline, Embase, and the Cochrane Library. We extracted study characteristics, reported process and outcome parameters, and patient and disease characteristics. We extracted 1,026 parameters from 200 publications and categorized these into patient characteristics (n = 226), treatment and care process characteristics (n = 199), and outcomes (n = 601). A total of 116 parameters were reported in more than 5% of publications. The most frequently reported characteristics were sex (88%), age at the time of surgery (66%), postoperative Hirschsprung-associated enterocolitis (64%), type of repair (57%), fecal incontinence (54%), and extent of aganglionosis (51%). This review underscores the pronounced variation in reported parameters within HSCR studies, highlighting the necessity for consistent, well-defined measures and reporting systems to foster improved data interpretability. Moreover, it advocates for the use of these findings in the development of a Core Indicator Set, complementing the recently developed Core Outcome Set. This will facilitate quality assessments across pediatric surgical centers throughout Europe.