bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergent many-body composite excitations of interacting spin-1/2 trimers
Authors: Bera Anup Kumar , Yusuf S. M. , Saha Sudip Kumar , Kumar Manoranjan , Voneshen David , Skourski Yurii , Zvyagin Sergei A. 
Published: November 2022

AbstractUnderstanding exotic forms of magnetism in quantum spin systems is an emergent topic of modern condensed matter physics. Quantum dynamics can be described by particle-like carriers of information, known-as quasiparticles that appear from the collective behaviour of the underlying system. Spinon excitations, governing the excitations of quantum spin-systems, have been accurately calculated and precisely verified experimentally for the antiferromagnetic chain model. However, identification and characterization of novel quasiparticles emerging from the topological excitations of the spin system having periodic exchange interactions are yet to be obtained. Here, we report the identification of emergent composite excitations of the novel quasiparticles doublons and quartons in spin-1/2 trimer-chain antiferromagnet Na2Cu3Ge4O12 (having periodic intrachain exchange interactions J1-J1-J2) and its topologically protected quantum 1/3 magnetization-plateau state. The characteristic energies, dispersion relations, and dynamical structure factor of neutron scattering as well as macroscopic quantum 1/3 magnetization-plateau state are in good agreement with the state-of-the-art dynamical density matrix renormalization group calculations.
Real-time brain-machine interface in non-human primates achieves high-velocity prosthetic finger movements using a shallow feedforward neural network decoder
Authors: Willsey Matthew S. , Nason-Tomaszewski Samuel R. , Ensel Scott R. , Temmar Hisham , Mender Matthew J. , Costello Joseph T. , Patil Parag G. , Chestek Cynthia A. 
Published: November 2022

AbstractDespite the rapid progress and interest in brain-machine interfaces that restore motor function, the performance of prosthetic fingers and limbs has yet to mimic native function. The algorithm that converts brain signals to a control signal for the prosthetic device is one of the limitations in achieving rapid and realistic finger movements. To achieve more realistic finger movements, we developed a shallow feed-forward neural network to decode real-time two-degree-of-freedom finger movements in two adult male rhesus macaques. Using a two-step training method, a recalibrated feedback intention–trained (ReFIT) neural network is introduced to further improve performance. In 7 days of testing across two animals, neural network decoders, with higher-velocity and more natural appearing finger movements, achieved a 36% increase in throughput over the ReFIT Kalman filter, which represents the current standard. The neural network decoders introduced herein demonstrate real-time decoding of continuous movements at a level superior to the current state-of-the-art and could provide a starting point to using neural networks for the development of more naturalistic brain-controlled prostheses.
Lipid-mediated prestin organization in outer hair cell membranes and its implications in sound amplification
Authors: Dehghani-Ghahnaviyeh Sepehr , Zhao Zhiyu , Tajkhorshid Emad 
Published: November 2022

AbstractPrestin is a high-density motor protein in the outer hair cells (OHCs), whose conformational response to acoustic signals alters the shape of the cell, thereby playing a major role in sound amplification by the cochlea. Despite recent structures, prestin’s intimate interactions with the membrane, which are central to its function remained unresolved. Here, employing a large set (collectively, more than 0.5 ms) of coarse-grained molecular dynamics simulations, we demonstrate the impact of prestin’s lipid-protein interactions on its organization at densities relevant to the OHCs and its effectiveness in reshaping OHCs. Prestin causes anisotropic membrane deformation, which mediates a preferential membrane organization of prestin where deformation patterns by neighboring copies are aligned constructively. The resulting reduced membrane rigidity is hypothesized to maximize the impact of prestin on OHC reshaping. These results demonstrate a clear case of protein-protein cooperative communication in membrane, purely mediated by interactions with lipids.
Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking
Authors: Vogel Karin , Bläske Tobias , Nagel Marie-Kristin , Globisch Christoph , Maguire Shane , Mattes Lorenz , Gude Christian , Kovermann Michael , Hauser Karin , Peter Christine , Isono Erika 
Published: November 2022

AbstractThe abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.
Durability and cross-reactivity of immune responses induced by a plant-based virus-like particle vaccine for COVID-19
Authors: Gobeil Philipe , Pillet Stéphane , Boulay Iohann , Charland Nathalie , Lorin Aurélien , Cheng Matthew P. , Vinh Donald C. , Boutet Philippe , Van Der Most Robbert , Roman François , Ceregido Maria Angeles , Landry Nathalie , D’Aoust Marc-André , Ward Brian J. 
Published: November 2022

AbstractAs the SARS-CoV-2 pandemic evolves, vaccine evaluation needs to include consideration of both durability and cross-reactivity. This report expands on previously reported results from a Phase 1 trial of an AS03-adjuvanted, plant-based coronavirus-like particle (CoVLP) displaying the spike (S) glycoprotein of the ancestral SARS-CoV-2 virus in healthy adults (NCT04450004). Humoral and cellular responses against the ancestral strain were evaluated 6 months post-second dose (D201) as secondary outcomes. Independent of dose, all vaccinated individuals retain binding antibodies, and ~95% retain neutralizing antibodies (NAb). Interferon gamma and interleukin-4 responses remain detectable in ~94% and ~92% of vaccinees respectively. In post-hoc analyses, variant-specific (Alpha, Beta, Delta, Gamma and Omicron) NAb were assessed at D42 and D201. Using a live virus neutralization assay, broad cross-reactivity is detectable against all variants at D42. At D201, cross-reactive antibodies are detectable in almost all participants against Alpha, Gamma and Delta variants (94%) and the Beta variant (83%) and in a smaller proportion against Omicron (44%). Results are similar with the pseudovirion assay. These data suggest that two doses of 3.75 µg CoVLP+AS03 elicit a durable and cross-reactive response that persists for at least 6 months post-vaccination.
Machine-learning-based intelligent framework for discovering refractory high-entropy alloys with improved high-temperature yield strength
Authors: Giles Stephen A. , Sengupta Debasis , Broderick Scott R. , Rajan Krishna 
Published: November 2022

AbstractRefractory high-entropy alloys (RHEAs) show significant elevated-temperature yield strengths and have potential to use as high-performance materials in gas turbine engines. Exploring the vast RHEA compositional space experimentally is challenging, and a small fraction of this space has been explored to date. This work demonstrates the development of a state-of-the-art machine learning framework coupled with optimization methods to intelligently explore the vast compositional space and drive the search in a direction that improves high-temperature yield strengths. Our yield strength model is shown to have a significantly improved predictive accuracy relative to the state-of-the-art approach, and also provides inherent uncertainty quantification through the use of repeatedk-fold cross-validation. Upon developing and validating a robust yield strength prediction model, the coupled framework is used to discover RHEAs with superior high temperature yield strength. We have shown that RHEA compositions can be customized to have maximum yield strength at a specific temperature.
Temporal and spatial evolution of enzymatic degradation of amorphous PET plastics
Authors: Lippold Holger , Kahle Laura , Sonnendecker Christian , Matysik Jörg , Fischer Cornelius 
Published: November 2022

AbstractBiocatalytic degradation is an emerging strategy aiming for energy-efficient recycling of poly(ethylene terephthalate) (PET), the most commonly used thermoplastic polyester. Besides material composition and physico-chemical parameters, the degradation kinetics is co-determined by the evolving nanotopography. In this study, the 3-dimensional development of the surface characteristics of an amorphous PET film, reacted with a highly effective hydrolase enzyme for up to 24 h, was explored by vertical scanning interferometry and confocal microscopy. The spatio-temporal analysis unveiled that the degradation process is not uniform with respect to reaction time and spatial reactivity distribution. An early phase of an unspecific roughness evolution is followed by an advanced phase characterized by a circular degradation pattern, consisting of shallow pits that are steadily renewed over time. The data suggest a hindrance of degradation during the initial roughening process, demonstrating the potential role of targeted surface modification in the large-scale treatment of plastic waste.
Plasma p-tau181, neurofilament light chain and association with cognition in Parkinson’s disease
Authors: Batzu Lucia , Rota Silvia , Hye Abdul , Heslegrave Amanda , Trivedi Dhaval , Gibson Lucy L. , Farrell Chloe , Zinzalias Pavlos , Rizos Alexandra , Zetterberg Henrik , Chaudhuri K. Ray , Aarsland Dag 
Published: November 2022

AbstractEarly identification of cognitive impairment in Parkinson’s disease (PD) has important clinical and research implications. The aim of our study was to investigate the role of plasma tau phosphorylated at amino acid 181 (p-tau181) and plasma neurofilament light chain (NfL) as biomarkers of cognition in PD. Baseline concentrations of plasma p-tau181 and NfL were measured in a cohort of 136 patients with PD and 63 healthy controls (HC). Forty-seven PD patients were followed up for up to 2 years. Cross-sectional and longitudinal associations between baseline plasma biomarkers and cognitive progression were investigated using linear regression and linear mixed effects models. At baseline, plasma p-tau181 concentration was significantly higher in PD subjects compared with HC (p = 0.026). In PD patients, higher plasma NfL was associated with lower MMSE score at baseline, after adjusting for age, sex and education (p = 0.027). Baseline plasma NfL also predicted MMSE decline over time in the PD group (p = 0.020). No significant association between plasma p-tau181 concentration and baseline or longitudinal cognitive performance was found. While the role of p-tau181 as a diagnostic biomarker for PD and its relationship with cognition need further elucidation, plasma NfL may serve as a feasible, non-invasive biomarker of cognitive progression in PD.
Parkin deficiency exacerbates fasting-induced skeletal muscle wasting in mice
Authors: Peker Nesibe , Sharma Mridula , Kambadur Ravi 
Published: November 2022

AbstractParkinson’s Disease (PD) is a chronic and progressive neurodegenerative disease manifesting itself with tremors, muscle stiffness, bradykinesia, dementia, and depression. Mutations of mitochondrial E3 ligase, PARKIN, have been associated with juvenile PD. Previous studies have characterized muscle atrophy and motor deficits upon loss of functional Parkin in fly and rodent models. However, the mechanisms behind pathophysiology of Parkin deficient muscle remains to be elusive. Here, results suggested that knock down of Parkin significantly increases proteolytic activities in skeletal muscle cell line, the C2C12 myotubes. However, the atrogene levels increase moderately in Parkin deficient cell line. To further investigate the role of Parkin in skeletal muscle atrophy, Parkin knock out (KO) and wild type mice were subjected to 48 h starvation. After 48 h fasting, a greater reduction in skeletal muscle weights was observed in Parkin KO mice as compared to age matched wild type control, suggesting elevated proteolytic activity in the absence of Parkin. Subsequent microarray analyses revealed further enhanced expression of FOXO and ubiquitin pathway in fasted Parkin KO mice. Furthermore, a greater reduction in the expression of cytoskeleton genes was observed in Parkin KO mice following 48 h fasting. Collectively, these results suggest that Parkin deficiency exacerbates fasting-induced skeletal muscle wasting, through upregulating genes involved in catabolic activities in skeletal muscle.
Electrical two-qubit gates within a pair of clock-qubit magnetic molecules
Authors: Ullah Aman , Hu Ziqi , Cerdá Jesús , Aragó Juan , Gaita-Ariño Alejandro 
Published: November 2022

AbstractEnhanced coherence in HoW10 molecular spin qubits has been demonstrated by use of clock-transitions (CTs). More recently it was shown that, while operating at the CTs, it was possible to use an electrical field to selectively address HoW10 molecules pointing in a given direction, within a crystal that contains two kinds of identical but inversion-related molecules. Herein we theoretically explore the possibility of employing the electric field to effect entangling two-qubit quantum gates within a 2-qubit Hilbert space resulting from dipolar coupling of two CT-protected HoW10 molecules in a diluted crystal. We estimate the thermal evolution of T1, T2, find that CTs are also optimal operating points from the point of view of phonons, and lay out how to combine a sequence of microwave and electric field pulses to achieve coherent control within a switchable two-qubit operating space between symmetric and asymmetric qubit states that are protected both from spin-bath and from phonon-bath decoherence. This two-qubit gate approach presents an elegant correspondence between physical stimuli and logical operations, meanwhile avoiding any spontaneous unitary evolution of the qubit states. Finally, we found a highly protected 1-qubit subspace resulting from the interaction between two clock molecules.
The ImSURE phantoms: a digital dataset for radiomic software benchmarking and investigation
Authors: Bettinelli Andrea , Marturano Francesca , Sarnelli Anna , Bertoldo Alessandra , Paiusco Marta 
Published: November 2022

AbstractIn radiology and oncology, radiomic models are increasingly employed to predict clinical outcomes, but their clinical deployment has been hampered by lack of standardisation. This hindrance has driven the international Image Biomarker Standardisation Initiative (IBSI) to define guidelines for image pre-processing, standardise the formulation and nomenclature of 169 radiomic features and share two benchmark digital phantoms for software calibration. However, to better assess the concordance of radiomic tools, more heterogeneous phantoms are needed. We created two digital phantoms, called ImSURE phantoms, having isotropic and anisotropic voxel size, respectively, and 90 regions of interest (ROIs) each. To use these phantoms, we designed a systematic feature extraction workflow including 919 different feature values (obtained from the 169 IBSI-standardised features considering all possible combinations of feature aggregation and intensity discretisation methods). The ImSURE phantoms will allow to assess the concordance of radiomic software depending on interpolation, discretisation and aggregation methods, as well as on ROI volume and shape. Eventually, we provide the feature values extracted from these phantoms using five open-source IBSI-compliant software.
Modeling community standards for metadata as templates makes data FAIR
Authors: Musen Mark A. , O’Connor Martin J. , Schultes Erik , Martínez-Romero Marcos , Hardi Josef , Graybeal John 
Published: November 2022

AbstractIt is challenging to determine whether datasets are findable, accessible, interoperable, and reusable (FAIR) because the FAIR Guiding Principles refer to highly idiosyncratic criteria regarding the metadata used to annotate datasets. Specifically, the FAIR principles require metadata to be “rich” and to adhere to “domain-relevant” community standards. Scientific communities should be able to define their ownmachine-actionable templatesfor metadata that encode these “rich,” discipline-specific elements. We have explored this template-based approach in the context of two software systems. One system is the CEDAR Workbench, which investigators use to author new metadata. The other is the FAIRware Workbench, which evaluates the metadata of archived datasets for their adherence to community standards. Benefits accrue when templates for metadata become central elements in an ecosystem of tools to manage online datasets—both because the templates serve as a community reference for what constitutes FAIR data, and because they embody that perspective in a form that can be distributed among a variety of software applications to assist with data stewardship and data sharing.
Ginsenoside Rh2 sensitizes the anti-cancer effects of sunitinib by inducing cell cycle arrest in renal cell carcinoma
Authors: Hwang Hyun Ji , Hong Seong Hwi , Moon Hong Sang , Yoon Young Eun , Park Sung Yul 
Published: November 2022

AbstractSunitinib, a VEGF blockade, is used to treat clear cell renal cell carcinoma (ccRCC). However, the anti-cancer treatment effects of sunitinib do not last long in ccRCC patients. Ginsenoside, a natural medicine extracted from ginseng, has been studied in cancer treatment and shown to have anti-tumor effects and low toxicity. We assessed cell viability and cell cycle analysis in ccRCC cell lines after treatment with ginsenoside and sunitinib. DNA damage was evaluated by measuring 8-OHdG levels and comet assay. ROS levels, reflecting the cause of oxidative stress, were also measured. Ginsenoside significantly enhanced the inhibition of cell viability by sunitinib, a result that was also confirmed in the xenograft model. In cell cycle analysis, combination treatment of ginsenoside and sunitinib enhanced G2M arrest in comparison with single-treatment groups. In addition, DNA damage was increased by ginsenoside and sunitinib according to the comet assay, and the level of 8-OHdG, which reflects oxidative DNA damage, also increased. We verified that ginsenoside enhances the efficacy of sunitinib to inhibit the proliferation of ccRCC cells via induction of oxidative DNA damage. The combination therapy of sunitinib and ginsenoside suggested the possibility of effectively treating ccRCC patients.
Cement augmentation for treatment of high to mid-thoracic osteoporotic compression fractures, high-viscosity cement percutaneous vertebroplasty versus balloon kyphoplasty
Authors: Wu Shiny Chih-Hsuan , Luo An-Jhih , Liao Jen-Chung 
Published: November 2022

AbstractWhilst the majority of the literature suggests that balloon kyphoplasty (BKP) can relieve pain associated with vertebral compression fractures (VCFs), evidence of high-viscosity cement (HVC) vertebroplasty (VP) or low viscosity cement (LVC) BKP for the treatment of VCFs at the levels of high and mid-thoracic vertebrae remains limited. The purpose of this study was to identify the different outcomes between HVC VP and LVC BKP used to repair high (T4–6) and mid (T7–9)-thoracic VCFs. A total of 114 patients with painful collapsed single-level vertebrae at high to mid-thoracic level who had undergone HVC VP or LVC BKP at a single tertiary medical center was reviewed retrospectively. All patients were divided into the HVC VP group (n = 72) and the LVC BKP group (n = 42). Clinical outcomes including demographic data and visual analogue scale (VAS) were compared. Radiographic data were collected preoperatively, postoperatively, and at final follow-up. More volume (ml) of cement injection was seen in the LVC BKP group (4.40 vs. 3.66, p < 0.001). The operation time (minutes) of the HVC VP group was significantly less than that of the LVC BKP group (33.34 vs. 39.05, p = 0.011). Leakage rate of cement was also fewer in the HVC VP group (26/72 vs. 27/42, p = 0.004). Compared with preoperative data, the VAS was improved after surgery in both groups. The LVC BKP group corrected more middle vertebral body height and local kyphosis angle than the HVC VP group. The outcomes of LVC BKP were not superior to that of HVC VP. HVC VP might be a good alternative to LVC BKP in the treatment of osteoporotic VCFs in high to mid-thoracic spine.
A digital twin for 64Cu production with cyclotron and solid target system
Authors: Isolan Lorenzo , Malinconico Mario , Tieu William , Hollis Courtney , Testa Marco , Melandri Matteo , Brunetti Alessandro , Sumini Marco 
Published: November 2022

AbstractOne method for finding reliable and cost-effective solutions for designing radioisotope production systems is represented by the “digital twin” philosophy of design. Looking at cyclotron solid targets, uncertainties of the particle beam, material composition and geometry play a crucial role in determining the results. The difference between what has been designed and what can be effectively manufactured, where processes such as electroplating are poorly controllable and generate large non-uniformities in deposition, must also be considered. A digital twin, where the target geometry is 3D scanned from real models, can represent a good compromise for connecting “ideal” and “real” worlds. Looking at the 64Ni(p,n)64Cu reaction, different Unstructured-Mesh MCNP6 models have been built starting from the 3D solid target system designed and put into operation by COMECER. A characterization has been performed considering the designed ideal target and a 3D scan of a real manufactured target measured with a ZEISS contact probe. Libraries and physics models have been also tested due to limited cross-section data. Proton spectra in the target volume, 3D proton-neutron-photon flux maps, average energies, power to be dissipated, shut-down dose-rate, 64Cu yield compared with various sources of experimental data and beam axial shifting impact, have been estimated. A digital twin of the 64Ni(p,n)64Cu production device has been characterized, considering the real measured target geometry, paving the way for a fully integrated model suitable also for thermal, structural or fluid-dynamic analyses.