bluuebunny/crossref_metadata_2025_split huggingface dataset:
A frame orientation optimisation method for consistent interpretation of kinematic signals
Authors: Ortigas Vásquez Ariana , Taylor William R. , Maas Allan , Woiczinski Matthias , Grupp Thomas M. , Sauer Adrian 
Published: June 2023

AbstractIn clinical movement biomechanics, kinematic data are often depicted as waveforms (i.e. signals), characterising the motion of articulating joints. Clinically meaningful interpretations of the underlying joint kinematics, however, require an objective understanding of whether two different kinematic signals actually represent two different underlying physical movement patterns of the joint or not. Previously, the accuracy of IMU-based knee joint angles was assessed using a six-degrees-of-freedom joint simulator guided by fluoroscopy-based signals. Despite implementation of sensor-to-segment corrections, observed errors were clearly indicative of cross-talk, and thus inconsistent reference frame orientations. Here, we address these limitations by exploring how minimisation of dedicated cost functions can harmonise differences in frame orientations, ultimately facilitating consistent interpretation of articulating joint kinematic signals. In this study, we present and investigate a frame orientation optimisation method (FOOM) that aligns reference frames and corrects for cross-talk errors, hence yielding a consistent interpretation of the underlying movement patterns. By executing optimised rotational sequences, thus producing angular corrections around each axis, we enable a reproducible frame definition and hence an approach for reliable comparison of kinematic data. Using this approach, root-mean-square errors between the previously collected (1) IMU-based data using functional joint axes, and (2) simulated fluoroscopy-based data relying on geometrical axes were almost entirely eliminated from an initial range of 0.7°–5.1° to a mere 0.1°–0.8°. Our results confirm that different local segment frames can yield different kinematic patterns, despite following the same rotation convention, and that appropriate alignment of reference frame orientation can successfully enable consistent kinematic interpretation.
Shape optimization design of the offset mirror in FEL-1 beamline at S3FEL
Authors: Xu Zhongmin , Zhang Weiqing , Yang Chuan , Zhong Yinpeng 
Published: June 2023

AbstractNowadays, due to the advantages of high peak power, high average power, ultra-short pulse, and fully coherent characteristics, the high-repetition-rate free-electron laser (FEL) is thriving in many countries around the world. The thermal load caused by high-repetition-rate FEL poses a great challenge to the mirror surface shape. Especially in the case of high average power, how to perfectly control the mirror shape to maintain the coherence of the beam has become a difficult problem in beamline design. In addition to multi-segment PZT, when multiple resistive heaters are used to compensate for the mirror shape, the heat flux (or power) generated by each heater must be optimized to obtain sub-nanometer height error. This article establishes MHCKF model for the mirror surface deformation under the combined effect of the mirror initial deformation, the thermal deformation caused by X-rays, and the deformation compensated by multiple heaters. By searching the perturbation term in the mathematical model, the least squares solution of the heat fluxes generated by all heaters can be obtained. This method can not only set multiple constraints on the heat fluxes but also quickly obtain their values when minimizing the mirror shape error. It overcomes the problem of time-consuming optimization processes encountered by traditional finite element analysis software, especially in the context of multi-parameter optimization. This article focuses on the offset mirror in the FEL-1 beamline at S3FEL. Using this method, the optimization of 25 heat fluxes generated by all resistive heaters was accomplished within a few seconds utilizing an ordinary laptop. The results indicate that the height error RMS decreased from 40 nm to 0.009 nm, and the slope error RMS reduced from 192.7nrad to 0.4nrad. Wave-optics simulations show that the wavefront quality has been significantly improved. In addition, some factors affecting mirror shape error, such as the number of heaters, higher repetition rate, film coefficient, and the length of copper tube, were analyzed. The results show that the MHCKF model and optimization algorithm can effectively solve the optimization problem of compensating for the mirror shape with multiple heaters.
Physiological and transcriptomic analysis of a yellow leaf mutant in watermelon
Authors: Xu Binghua , Zhang Chaoyang , Gu Yan , Cheng Rui , Huang Dayue , Liu Xin , Sun Yudong 
Published: June 2023

AbstractLeaf color mutants are important materials for studying chloroplast and photomorphogenesis, and can function as basic germplasms for genetic breeding. In an ethylmethanesulfonate mutagenesis population of watermelon cultivar “703”, a chlorophyll-deficient mutant with yellow leaf (Yl2) color was identified. The contents of chlorophyll a, chlorophyll b, and carotenoids in Yl2 leaves were lower than those in wild-type (WT) leaves. The chloroplast ultrastructure in the leaves revealed that the chloroplasts in Yl2 were degraded. The numbers of chloroplasts and thylakoids in the Yl2 mutant were lower, resulting in lower photosynthetic parameters. Transcriptomic analysis identified 1292 differentially expressed genes, including1002 upregulated and 290 downregulated genes. The genes involved in chlorophyll biosynthesis (HEMA, HEMD, CHL1, CHLM, and CAO) were significantly downregulated in the Yl2 mutant, which may explain why chlorophyll pigment content was lower than that in the WT. Chlorophyll metabolism genes such as PDS, ZDS and VDE, were upregulated, which form the xanthophyll cycle and may protect the yellow‒leaves plants from photodamage. Taken together, our findings provide insight into the molecular mechanisms of leading to leaf color formation and chloroplast development in watermelon.
Detecting stress caused by nitrogen deficit using deep learning techniques applied on plant electrophysiological data
Authors: González I Juclà Daniel , Najdenovska Elena , Dutoit Fabien , Raileanu Laura Elena 
Published: June 2023

AbstractPlant electrophysiology carries a strong potential for assessing the health of a plant. Current literature for the classification of plant electrophysiology generally comprises classical methods based on signal features that portray a simplification of the raw data and introduce a high computational cost. The Deep Learning (DL) techniques automatically learn the classification targets from the input data, overcoming the need for precalculated features. However, they are scarcely explored for identifying plant stress on electrophysiological recordings. This study applies DL techniques to the raw electrophysiological data from 16 tomato plants growing in typical production conditions to detect the presence of stress caused by a nitrogen deficiency. The proposed approach predicts the stressed state with an accuracy of around 88%, which could be increased to over 96% using a combination of the obtained prediction confidences. It outperforms the current state-of-the-art with over 8% higher accuracy and a potential for a direct application in production conditions. Moreover, the proposed approach demonstrates the ability to detect the presence of stress at its early stage. Overall, the presented findings suggest new means to automatize and improve agricultural practices with the aim of sustainability.
Single neonatal estrogen implant sterilizes female animals by decreasing hypothalamic KISS1 expression
Authors: Park Chan Jin , Minabe Shiori , Hess Rex A. , Lin Po-Ching Patrick , Zhou Sherry , Bashir Shah Tauseef , Barakat Radwa , Gal Arnon , Ko CheMyong Jay 
Published: June 2023

AbstractReproductive sterilization by surgical gonadectomy is strongly advocated to help manage animal populations, especially domesticated pets, and to prevent reproductive behaviors and diseases. This study explored the use of a single-injection method to induce sterility in female animals as an alternative to surgical ovariohysterectomy. The idea was based on our recent finding that repetitive daily injection of estrogen into neonatal rats disrupted hypothalamic expression of Kisspeptin (KISS1), the neuropeptide that triggers and regulates pulsatile secretion of GnRH. Neonatal female rats were dosed with estradiol benzoate (EB) either by daily injections for 11 days or by subcutaneous implantation of an EB-containing silicone capsule designed to release EB over 2–3 weeks. Rats treated by either method did not exhibit estrous cyclicity, were anovulatory, and became infertile. The EB-treated rats had fewer hypothalamic Kisspeptin neurons, but the GnRH-LH axis remained responsive to Kisspeptin stimulation. Because it would be desirable to use a biodegradable carrier that is also easier to handle, an injectable EB carrier was developed from PLGA microspheres to provide pharmacokinetics comparable to the EB-containing silicone capsule. A single neonatal injection of EB-microspheres at an equivalent dosage resulted in sterility in the female rat. In neonatal female Beagle dogs, implantation of an EB-containing silicone capsule also reduced ovarian follicle development and significantly inhibited KISS1 expression in the hypothalamus. None of the treatments produced any concerning health effects, other than infertility. Therefore, further development of this technology for sterilization in domestic female animals, such as dogs and cats is worthy of investigation.
Erythroid lineage chromatin accessibility maps facilitate identification and validation of NFIX as a fetal hemoglobin repressor
Authors: Chaand Mudit , Fiore Chris , Johnston Brian , D’Ippolito Anthony , Moon Diane H. , Carulli John P. , Shearstone Jeffrey R. 
Published: June 2023

AbstractHuman genetics has validated de-repression of fetal gamma globin (HBG) in adult erythroblasts as a powerful therapeutic paradigm in diseases involving defective adult beta globin (HBB)1. To identify factors involved in the switch from HBG to HBB expression, we performed Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq)2 on sorted erythroid lineage cells derived from bone marrow (BM) or cord blood (CB), representing adult and fetal states, respectively. BM to CB cell ATAC-seq profile comparisons revealed genome-wide enrichment of NFI DNA binding motifs and increased NFIX promoter chromatin accessibility, suggesting that NFIX may repress HBG. NFIX knockdown in BM cells increased HBG mRNA and fetal hemoglobin (HbF) protein levels, coincident with increased chromatin accessibility and decreased DNA methylation at the HBG promoter. Conversely, overexpression of NFIX in CB cells reduced HbF levels. Identification and validation of NFIX as a new target for HbF activation has implications in the development of therapeutics for hemoglobinopathies.
A mutation-induced drug resistance database (MdrDB)
Authors: Yang Ziyi , Ye Zhaofeng , Qiu Jiezhong , Feng Rongjun , Li Danyu , Hsieh Changyu , Allcock Jonathan , Zhang Shengyu 
Published: June 2023

AbstractMutation-induced drug resistance is a significant challenge to the clinical treatment of many diseases, as structural changes in proteins can diminish drug efficacy. Understanding how mutations affect protein-ligand binding affinities is crucial for developing new drugs and therapies. However, the lack of a large-scale and high-quality database has hindered the research progresses in this area. To address this issue, we have developed MdrDB, a database that integrates data from seven publicly available datasets, which is the largest database of its kind. By integrating information on drug sensitivity and cell line mutations from Genomics of Drug Sensitivity in Cancer and DepMap, MdrDB has substantially expanded the existing drug resistance data. MdrDB is comprised of 100,537 samples of 240 proteins (which encompass 5119 total PDB structures), 2503 mutations, and 440 drugs. Each sample brings together 3D structures of wild type and mutant protein-ligand complexes, binding affinity changes upon mutation (ΔΔG), and biochemical features. Experimental results with MdrDB demonstrate its effectiveness in significantly enhancing the performance of commonly used machine learning models when predicting ΔΔG in three standard benchmarking scenarios. In conclusion, MdrDB is a comprehensive database that can advance the understanding of mutation-induced drug resistance, and accelerate the discovery of novel chemicals.
Magma reservoir growth and ground deformation preceding the 79 CE Plinian eruption of Vesuvius
Authors: Doronzo Domenico M. , Trasatti Elisa , Arienzo Ilenia , Balcone-Boissard Hélène , Barra Diana , Aiello Giuseppe , Amato Vincenzo , Di Vito Mauro A. 
Published: June 2023

AbstractThe 79 CE eruption of Vesuvius is the first documented Plinian eruption, also famous for the archaeological ruins of Pompeii and Herculaneum. Although much is known regarding the eruption dynamics and magma reservoir, little is known about the reservoir shape and growth, and related ground deformation. Numerical modelling by Finite Element Method was carried out, aimed at simulating the reservoir growth and ground deformation with respect to the reservoir shape (prolate, spherical, oblate) and magma overpressure. The modelling was tuned with volcanological, petrological and paleoenvironmental ground deformation constraints. Results indicate that the highest magma overpressure is achieved considering a prolate reservoir, making it as the most likely shape that led to eruption. Similar deformations but lower overpressures are obtained considering spherical and oblate reservoirs. These results demonstrate that ground deformation may not be indicative of eruption probability, style/size, and this has direct implications on surveillance at active explosive volcanoes.
Circadian regulation of pulmonary disease: the importance of timing
Authors: Cunningham Peter S. , Jackson Callum , Chakraborty Amlan , Cain Jafar , Durrington Hannah J. , Blaikley John F. 
Published: June 2023

Abstract
Circadian regulation causes the activity of biological processes to vary over a 24-h cycle. The pathological effects of this variation are predominantly studied using two different approaches: pre-clinical models or observational clinical studies. Both these approaches have provided useful insights into how underlying circadian mechanisms operate and specifically which are regulated by the molecular oscillator, a key time-keeping mechanism in the body. This review compares and contrasts findings from these two approaches in the context of four common respiratory diseases (asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and respiratory infection). Potential methods used to identify and measure human circadian oscillations are also discussed as these will be useful outcome measures in future interventional human trials that target circadian mechanisms.
Optimal attitude consensus control for rigid spacecraft formation based on control Lyapunov functions
Authors: Wang Hui , Zhang Jinxiu , Zhou Qingrui , Sun Hui‐Jie , Wu Yu‐Yao 
Published: June 2023

AbstractIn this article, the optimal attitude consensus control problem of distributed spacecraft formation through local information exchange is solved in the presence of parameter uncertainty and disturbance. The attitude dynamics model of rigid spacecraft formation is established based on unit quaternion under an undirected graph. Then, the optimal attitude consensus control scheme based on control Lyapunov functions is adopted for rigid spacecraft formation. The approach to construct an appropriate Lyapunov function for multiple spacecraft is developed. Then the lumped disturbance is estimated by an extended state observer (ESO) and using the sliding mode control approach improves the robustness of the controller. The proposed optimal controller can not only ensure the global consensus convergence of the system but also make the preset performance index function achieve the minimum value. In addition, the mathematical proof is given for the stability analysis of the system by the Lyapunov stability theory. Finally, some simulations and comparisons are presented to demonstrate the validity and advantages of the proposed controller.
Toward a 3D kinetic tomography of Taurus clouds
Authors: Duchêne Q. , Hottier C. , Lallement R. , Vergely J. L. , Babusiaux C. , Marchal A. , Arenou F. 
Published: June 2023

Context. Three-dimensional (3D) kinetic maps of the Milky Way interstellar medium are an essential tool in studies of its structure and of star formation.
Aims. We aim to assign radial velocities to Galactic interstellar clouds now spatially localized based on starlight extinction and star distances from Gaia and stellar surveys.
Methods. We developed an automated search for coherent projections on the sky of clouds isolated in 3D extinction density maps on the one hand, and regions responsible for CO radio emissions at specific Doppler shifts on the other hand. The discrete dust structures were obtained by application of the Fellwalker algorithm to a recent 3D extinction density map. For each extinction cloud, a technique using a narrow sliding spectral window moved along the contour-bounded CO spectrum and geometrical criteria was used to select the most likely velocity interval.
Results. We applied the new contour-based technique to the 3D extinction density distribution within the volume encompassing the Taurus, Auriga, Perseus, and California molecular complexes. From the 45 clouds issued from the decomposition, 42 were assigned a velocity. The remaining structures correspond to very weak CO emission or extinction. We used the non-automated assignments of radial velocities to clouds of the same region presented in Paper I and based on KI absorption spectra as a validation test. The new fully automated determinations were found to be in good agreement with these previous measurements.
Conclusions. Our results show that an automated search based on cloud-contour morphology can be efficient and that this novel technique may be extended to wider regions of the Milky Way and at larger distance. We discuss its limitations and potential improvements after combination with other techniques.
Spiral-wave-driven accretion in quiescent dwarf novæ
Authors: Van den Bossche M. , Lesur G. , Dubus G. 
Published: June 2023

Context. In dwarf novæ (DNe) and low-mass X-ray binaries, the tidal potential excites spiral waves in the accretion disc. Spiral-wave-driven accretion may be important in quiescent discs, where the angular momentum transport mechanism has yet to be identified. Previous studies were limited to unrealistically high temperatures for numerical studies or to specific regimes for analytical studies.
Aims. We perform the first numerical simulation of spiral-wave-driven accretion in the cold temperature regime appropriate to quiescent discs, which have Mach numbers ≳100.
Methods. We used the new GPU-accelerated finite-volume code IDEFIX to produce global hydrodynamics 2D simulations of the accretion discs of DN systems with a sufficiently fine spatial resolution to capture the short scale-height of cold, quiescent discs with Mach numbers ranging from 80 to 370.
Results. Running the simulations on timescales of tens of binary orbits shows transient angular momentum transport that decays as the disc relaxes from its initial conditions. We find the angular momentum parameter α drops to values of ≪10−2, too weak to drive accretion in quiescence.
JWST MIRI flight performance: The Medium-Resolution Spectrometer
Authors: Argyriou Ioannis , Glasse Alistair , Law David R. , Labiano Alvaro , Álvarez-Márquez Javier , Patapis Polychronis , Kavanagh Patrick J. , Gasman Danny , Mueller Michael , Larson Kirsten , Vandenbussche Bart , Glauser Adrian M. , Royer Pierre , Dicken Daniel , Harkett Jake , Sargent Beth A. , Engesser Michael , Jones Olivia C. , Kendrew Sarah , Noriega-Crespo Alberto , Brandl Bernhard , Rieke George H. , Wright Gillian S. , Lee David , Wells Martyn 
Published: June 2023

Context. The Medium-Resolution Spectrometer (MRS) provides one of the four operating modes of the Mid-Infrared Instrument (MIRI) on board the James Webb Space Telescope (JWST). The MRS is an integral field spectrometer, measuring the spatial and spectral distributions of light across the 5–28 µm wavelength range with a spectral resolving power between 3700 and 1300.
Aims. We present the MRS’s optical, spectral, and spectro-photometric performance, as achieved in flight, and we report on the effects that limit the instrument’s ultimate sensitivity.
Methods. The MRS flight performance has been quantified using observations of stars, planetary nebulae, and planets in our Solar System. The precision and accuracy of this calibration was checked against celestial calibrators with well-known flux levels and spectral features.
Results. We find that the MRS geometric calibration has a distortion solution accuracy relative to the commanded position of 8 mas at 5 µm and 23 mas at 28 µm. The wavelength calibration is accurate to within 9 km s−1 at 5 µm and 27 km s−1 at 28 µm. The uncertainty in the absolute spectro-photometric calibration accuracy was estimated at 5.6 ± 0.7%. The MIRI calibration pipeline is able to suppress the amplitude of spectral fringes to below 1.5% for both extended and point sources across the entire wavelength range. The MRS point spread function (PSF) is 60% broader than the diffraction limit along its long axis at 5 µm and is 15% broader at 28 µm.
Conclusions. The MRS flight performance is found to be better than prelaunch expectations. The MRS is one of the most subscribed observing modes of JWST and is yielding many high-profile publications. It is currently humanity’s most powerful instrument for measuring the mid-infrared spectra of celestial sources and is expected to continue as such for many years to come.
An efficient multi parametric kernel function for large and small-update methods interior point algorithm for P*(κ)-horizontal linear complementarity problem
Authors: Mousaab Bouafia , Adnan Yassine 
Published: June 2023

In this paper, we propose the first efficient multi parametric kernel function with logarithmic barrier term. A class of polynomial interior-point algorithms for P*(κ)-horizontal linear complementarity problem based on this kernel function, with parameters pi > 0 for all i ∈ 1, 2, , m, are presented. Then by using some simple analysis tools, we present a primal-dual interior point method (IPM) for P*(κ)-horizontal linear complementarity problems based on this kernel function. At the same time, we derive the complexity bounds small and large-update methods, respectively. In particular, if we take many different values of the parameters, we obtain the best known iteration bounds for the algorithms with large- and small-update methods are derived, namely, O((1 + 2κ)√n(log n)log n/ϵ) and O((1 + 2κ)√n log n/ϵ) respectively. We illustrate the performance of the proposed kernel function by some numerical results that are derived by applying our algorithm.