bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global‐MHD Simulations Using MagPIE: Impact of Flux Transfer Events on the Ionosphere
Authors: Paul Arghyadeep , Strugarek Antoine , Vaidya Bhargav 
Published: November 2023

AbstractThis study presents a recently developed two‐way coupled magnetosphere‐ionosphere model named “MagPIE” that enables the investigation of the impact of flux transfer events (FTEs) on the ionosphere. Our findings highlight the prominent role of cusp‐FTE reconnection in influencing the ionosphere. The typical morphology of an FTE signal, represented by field‐aligned currents (FACs) on the ionosphere, is shown to exhibit a distinct pattern characterized by an “I”‐shaped patch surrounded by a “U”‐shaped patch. Furthermore, we demonstrate that the effects of FACs resulting from FTEs may extend well into the region of closed field lines on the ionosphere. These FACs are seen to exhibit a remarkable resemblance to discrete dayside auroral arcs, providing further evidence that FTEs can be considered as a probable cause of such phenomena. Additionally, FTEs generate vortex‐like patterns of ionospheric flow, which can manifest as either twin vortices or a combination of multiple vortices, depending on the characteristics of the FACs producing them. Furthermore, we present compelling evidence of morphological similarities between the simulated ionospheric signatures obtained from the MagPIE model and an observation made by the SWARM satellites. The agreement between our model and observational data further strengthens the credibility of our model and opens up new avenues to theoretically explore the complex ionospheric effects caused by FTEs.
Anomalous Long‐Distance Propagation of ILS LOC Signals by the Es Layer and Its Impact on Aviation Receivers
Authors: Saito S. , Hosokawa K. , Sakai J. , Tomizawa I. 
Published: November 2023

AbstractAnomalous long‐distance propagation of Very High Frequency radio waves of aeronautical navigation systems was investigated by an airborne Instrument Landing System (ILS) localizer (ILS LOC) receiver installed on the ground at Kure, Japan (34.245°N, 132.528°E). Intense ILS LOC type signals were observed and the received power was strong enough for the aviation receiver to output course deviation. The radio source was identified by receiving the Morse Code for identification as the localizer‐type directional aid (LDA) serving the Runway‐21 of the Hualien Airport, Taiwan (24.0396°N, 121.6221°E) of which beam pointed close to the receiver. This result supports that the source of the signals often observed at the same frequency at the same location is most probably the LDA at the Hualien Airport. The maximum received power was −99 dBm for an omni‐directional antenna. It was strong enough to cause co‐channel interference. Considering stronger power (−70 dBm) found in previous observations at the same frequency at the same location, anomalous propagation of ILS LOC signals by the Es layer could be a cause of interference when a receiver was near the center of the ILS LOC beam. The course deviation output was consistent with the geometry between the beam of Runway‐21 LDA at the Hualien Airport and the receiver. However, the observed course deviation fluctuated remarkably even when the received power was strong enough. The fluctuation of the course deviation may indicate the structure of the Es layer, and observation of the course deviation could be used to diagnose the Es layer structure.
Variability in home blood pressure and its association with renal function and pulse pressure in patients with treated hypertension in primary care
Authors: Andersson Ulrika , Nilsson Peter M. , Kjellgren Karin , Harris Katie , Chalmers John , Ekholm Mikael , Midlöv Patrik 
Published: November 2023

AbstractBlood pressure variability (BPV) represents a cardiovascular risk factor, regardless of mean level of blood pressure (BP). In this post-hoc analysis from the PERson-centredness in Hypertension management using Information Technology (PERHIT) study, we aimed to explore BPV in daily home measurements in hypertensive patients from primary care, to identify factors associated with high BPV and to investigate whether estimated glomerular filtration rate (eGFR) and pulse pressure, as markers of target organ damage (TOD), are associated with BPV. For eight consecutive weeks, 454 participants reported their daily BP and heart rate in their mobile phone, along with reports of lifestyle and hypertension-related factors. Systolic BP (SBP) values were used to calculate BPV with coefficient of variation (CV) as primary estimate. Background characteristics and self-reports were tested between fifths of CV in a linear regression model, adjusted for age and sex. Associations between BPV and eGFR and pulse pressure were tested with linear and logistic regression models. Higher home BPV was associated with higher age, BP, heart rate, and smoking. BPV was lower for participants with low alcohol consumption and treatment with calcium channel blockers. There was a significant association between BPV and pulse pressure (P = 0.015), and between BPV and eGFR (P = 0.049). Participants with high BPV reported more dizziness and palpitations. In conclusion, pulse pressure and eGFR were significantly associated with home BPV. Older age, high BP, heart rate, and smoking were associated with high BPV, but treatment with calcium channel blockers and low alcohol consumption was associated with low BPV. Trial registration: The study was registered with ClinicalTrials.gov [NCT03554382].
Research progress and application of single-cell sequencing in head and neck malignant tumors
Authors: Qu Siyuan , Gong Mengdan , Deng Yongqin , Xiang Yizhen , Ye Dong 
Published: November 2023

AbstractSingle-cell sequencing (SCS) is a technology that separates thousands of cells from the organism and accurately analyzes the genetic material expressed in each cell using high-throughput sequencing technology. Unlike the traditional bulk sequencing approach, which can only provide the average value of a cell population and cannot obtain specific single-cell data, single-cell sequencing can identify the gene sequence and expression changes of a single cell, and reflects the differences between genetic material and protein between cells, and ultimately the role played by the tumor microenvironment. single-cell sequencing can further explore the pathogenesis of head and neck malignancies from the single-cell biological level and provides a theoretical basis for the clinical diagnosis and treatment of head and neck malignancies. This article will systematically introduce the latest progress and application of single-cell sequencing in malignant head and neck tumors.
Liquid-liquid phase separation in DNA double-strand breaks repair
Authors: Wang Yun-Long , Zhao Wan-Wen , Shi Jie , Wan Xiang-Bo , Zheng Jian , Fan Xin-Juan 
Published: November 2023

AbstractDNA double-strand breaks (DSBs) are the fatal type of DNA damage mostly induced by exposure genome to ionizing radiation or genotoxic chemicals. DSBs are mainly repaired by homologous recombination (HR) and nonhomologous end joining (NHEJ). To repair DSBs, a large amount of DNA repair factors was observed to be concentrated at the end of DSBs in a specific spatiotemporal manner to form a repair center. Recently, this repair center was characterized as a condensate derived from liquid-liquid phase separation (LLPS) of key DSBs repair factors. LLPS has been found to be the mechanism of membraneless organelles formation and plays key roles in a variety of biological processes. In this review, the recent advances and mechanisms of LLPS in the formation of DSBs repair-related condensates are summarized.
Engineering chirality at wafer scale with ordered carbon nanotube architectures
Authors: Doumani Jacques , Lou Minhan , Dewey Oliver , Hong Nina , Fan Jichao , Baydin Andrey , Zahn Keshav , Yomogida Yohei , Yanagi Kazuhiro , Pasquali Matteo , Saito Riichiro , Kono Junichiro , Gao Weilu 
Published: November 2023

AbstractCreating artificial matter with controllable chirality in a simple and scalable manner brings new opportunities to diverse areas. Here we show two such methods based on controlled vacuum filtration - twist stacking and mechanical rotation - for fabricating wafer-scale chiral architectures of ordered carbon nanotubes (CNTs) with tunable and large circular dichroism (CD). By controlling the stacking angle and handedness in the twist-stacking approach, we maximize the CD response and achieve a high deep-ultraviolet ellipticity of 40 ± 1 mdeg nm−1. Our theoretical simulations using the transfer matrix method reproduce the experimentally observed CD spectra and further predict that an optimized film of twist-stacked CNTs can exhibit an ellipticity as high as 150 mdeg nm−1, corresponding to agfactor of 0.22. Furthermore, the mechanical rotation method not only accelerates the fabrication of twisted structures but also produces both chiralities simultaneously in a single sample, in a single run, and in a controllable manner. The created wafer-scale objects represent an alternative type of synthetic chiral matter consisting of ordered quantum wires whose macroscopic properties are governed by nanoscopic electronic signatures and can be used to explore chiral phenomena and develop chiral photonic and optoelectronic devices.
Accelerating multielectron reduction at CuxO nanograins interfaces with controlled local electric field
Authors: Guo Weihua , Zhang Siwei , Zhang Junjie , Wu Haoran , Ma Yangbo , Song Yun , Cheng Le , Chang Liang , Li Geng , Liu Yong , Wei Guodan , Gan Lin , Zhu Minghui , Xi Shibo , Wang Xue , Yakobson Boris I. , Tang Ben Zhong , Ye Ruquan 
Published: November 2023

AbstractRegulating electron transport rate and ion concentrations in the local microenvironment of active site can overcome the slow kinetics and unfavorable thermodynamics of CO2 electroreduction. However, simultaneous optimization of both kinetics and thermodynamics is hindered by synthetic constraints and poor mechanistic understanding. Here we leverage laser-assisted manufacturing for synthesizing CuxO bipyramids with controlled tip angles and abundant nanograins, and elucidate the mechanism of the relationship between electron transport/ion concentrations and electrocatalytic performance. Potassium/OH− adsorption tests and finite element simulations corroborate the contributions from strong electric field at the sharp tip. In situ Fourier transform infrared spectrometry and differential electrochemical mass spectrometry unveil the dynamic evolution of critical *CO/*OCCOH intermediates and product profiles, complemented with theoretical calculations that elucidate the thermodynamic contributions from improved coupling at the Cu+/Cu2+ interfaces. Through modulating the electron transport and ion concentrations, we achieve high Faradaic efficiency of 81% at ~900 mA cm−2 for C2+ products via CO2RR. Similar enhancement is also observed for nitrate reduction reaction (NITRR), achieving 81.83 mg h−1 ammonia yield rate per milligram catalyst. Coupling the CO2RR and NITRR systems demonstrates the potential for valorizing flue gases and nitrate wastes, which suggests a practical approach for carbon-nitrogen cycling.
Kinetic magnetism in triangular moiré materials
Authors: Ciorciaro L. , Smoleński T. , Morera I. , Kiper N. , Hiestand S. , Kroner M. , Zhang Y. , Watanabe K. , Taniguchi T. , Demler E. , İmamoğlu A. 
Published: November 2023

AbstractMagnetic properties of materials ranging from conventional ferromagnetic metals to strongly correlated materials such as cuprates originate from Coulomb exchange interactions. The existence of alternate mechanisms for magnetism that could naturally facilitate electrical control has been discussed theoretically1–7, but an experimental demonstration8 in an extended system has been missing. Here we investigate MoSe2/WS2 van der Waals heterostructures in the vicinity of Mott insulator states of electrons forming a frustrated triangular lattice and observe direct evidence of magnetic correlations originating from a kinetic mechanism. By directly measuring electronic magnetization through the strength of the polarization-selective attractive polaron resonance9,10, we find that when the Mott state is electron-doped, the system exhibits ferromagnetic correlations in agreement with the Nagaoka mechanism.
Embryo-scale reverse genetics at single-cell resolution
Authors: Saunders Lauren M. , Srivatsan Sanjay R. , Duran Madeleine , Dorrity Michael W. , Ewing Brent , Linbo Tor H. , Shendure Jay , Raible David W. , Moens Cecilia B. , Kimelman David , Trapnell Cole 
Published: November 2023

AbstractThe maturation of single-cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos1–4. A majority of these data, however, has been collected from wild-type embryos without an appreciation for the latent variation that is present in development. Here we present the ‘zebrafish single-cell atlas of perturbed embryos’: single-cell transcriptomic data from 1,812 individually resolved developing zebrafish embryos, encompassing 19 timepoints, 23 genetic perturbations and a total of 3.2 million cells. The high degree of replication in our study (eight or more embryos per condition) enables us to estimate the variance in cell type abundance organism-wide and to detect perturbation-dependent deviance in cell type composition relative to wild-type embryos. Our approach is sensitive to rare cell types, resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons, a cell population that comprises less than 1% of the embryo. Additionally, time-series profiling of individual mutants identified a group ofbrachyury-independent cells with strikingly similar transcriptomes to notochord sheath cells, leading to new hypotheses about early origins of the skull. We anticipate that standardized collection of high-resolution, organism-scale single-cell data from large numbers of individual embryos will enable mapping of the genetic dependencies of zebrafish cell types, while also addressing longstanding challenges in developmental genetics, including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals.
Stress granules plug and stabilize damaged endolysosomal membranes
Authors: Bussi Claudio , Mangiarotti Agustín , Vanhille-Campos Christian , Aylan Beren , Pellegrino Enrica , Athanasiadi Natalia , Fearns Antony , Rodgers Angela , Franzmann Titus M. , Šarić Anđela , Dimova Rumiana , Gutierrez Maximiliano G. 
Published: November 2023

AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host.
Illuminating protein space with a programmable generative model
Authors: Ingraham John B. , Baranov Max , Costello Zak , Barber Karl W. , Wang Wujie , Ismail Ahmed , Frappier Vincent , Lord Dana M. , Ng-Thow-Hing Christopher , Van Vlack Erik R. , Tie Shan , Xue Vincent , Cowles Sarah C. , Leung Alan , Rodrigues João V. , Morales-Perez Claudio L. , Ayoub Alex M. , Green Robin , Puentes Katherine , Oplinger Frank , Panwar Nishant V. , Obermeyer Fritz , Root Adam R. , Beam Andrew L. , Poelwijk Frank J. , Grigoryan Gevorg 
Published: November 2023

AbstractThree billion years of evolution has produced a tremendous diversity of protein molecules1, but the full potential of proteins is likely to be much greater. Accessing this potential has been challenging for both computation and experiments because the space of possible protein molecules is much larger than the space of those likely to have functions. Here we introduce Chroma, a generative model for proteins and protein complexes that can directly sample novel protein structures and sequences, and that can be conditioned to steer the generative process towards desired properties and functions. To enable this, we introduce a diffusion process that respects the conformational statistics of polymer ensembles, an efficient neural architecture for molecular systems that enables long-range reasoning with sub-quadratic scaling, layers for efficiently synthesizing three-dimensional structures of proteins from predicted inter-residue geometries and a general low-temperature sampling algorithm for diffusion models. Chroma achieves protein design as Bayesian inference under external constraints, which can involve symmetries, substructure, shape, semantics and even natural-language prompts. The experimental characterization of 310 proteins shows that sampling from Chroma results in proteins that are highly expressed, fold and have favourable biophysical properties. The crystal structures of two designed proteins exhibit atomistic agreement with Chroma samples (a backbone root-mean-square deviation of around 1.0 Å). With this unified approach to protein design, we hope to accelerate the programming of protein matter to benefit human health, materials science and synthetic biology.
Morphological changes in intraepithelial and stromal telocytes in Cyprinus carpio in response to salinity stress
Authors: Emeish Walaa F. A. , Abd-ElHafeez Hanan H. , Alghamdi Abdullah A. A. , Ahmed Madeha , Khalifa Mahmoud Osman , El-Mansi Ahmed A. , Abou-Elhamd Alaa S. , Khormi Mohsen M. , Alkashif Khalid , Soliman Soha A. 
Published: November 2023

AbstractTelocytes establish connections and communicate with various types of cells and structures. Few experimental studies have been performed on telocytes. In this study, we investigated the effect of salinity stress on telocytes in relation to osmoregulatory, immune, and stem cells. After exposing the common carp to 0.2 (control), 6, 10, or 14 ppt salinity, we extracted and fixed gill samples in glutaraldehyde, processed and embedded the samples in resin, and prepared semi-thin and ultrathin sections. Two types of telocytes were identified: intraepithelial and stromal telocytes. Intraepithelial telocytes were found to form part of the cellular lining of the lymphatic space and shed secretory vesicles into this space. Stromal telocytes were observed to shed their secretory vesicles into the secondary circulatory vessels. Both intraepithelial and stromal telocytes were enlarged and exhibited increased secretory activities as salinity increased. They exerted their effects via direct contact and paracrine signaling. The following changes were observed in samples from fish exposed to high salinity levels: chloride cells underwent hypertrophy, and their mitochondria became cigar-shaped; pavement cells were enlarged, and their micro-ridges became thin and elongated; stromal telocytes established contact with stem cells and skeletal myoblasts; skeletal muscle cells underwent hypertrophy; and macrophages and rodlet cells increased in number. In conclusion, our findings indicate that intraepithelial and stromal telocytes respond to salinity stress by activating cellular signaling and that they play major roles in osmoregulation, immunity, and regeneration.
Pulmonary artery catheter monitoring versus arterial waveform-based monitoring during liver transplantation: a retrospective cohort study
Authors: Jung Ji-Yoon , Sohn Jin Young , Lim Leerang , Cho Hyeyeon , Ju Jae-Woo , Yoon Hyun-Kyu , Yang Seong-Mi , Lee Ho-Jin , Kim Won Ho 
Published: November 2023

AbstractAlthough pulmonary artery catheter (PAC) has been used during liver transplantation surgery, the usefulness of PAC has rarely been investigated. We evaluated whether the use of PAC is associated with better clinical outcomes compared to arterial waveform-based monitoring after liver transplantation. A total of 1565 cases undergoing liver transplantation were reviewed. We determined whether patients received PAC or not and divided our cohort into the PAC with hemodynamic monitoring using PAC and the non-PAC with arterial waveform-based monitoring using FloTrac-Vigileo. Propensity score matching was performed. Acute kidney injury (AKI), early allograft dysfunction (EAD) and 1-year all-cause mortality or graft failure were compared in the matched cohorts. Logistic regression analysis was performed in the inverse probability of treatment-weighted (IPTW) cohort for postoperative EAD and AKI, respectively. Five-year overall survival was compared between the two groups. In the matched cohort, there was no significant difference in the incidence of AKI, EAD, length of hospital or ICU stay, and 1-year all-cause mortality between the groups. In the IPTW cohort, the use of PAC was not a significant predictor for AKI or EAD (AKI: odds ratio (95% confidence interval) of 1.20 (0.47–1.56), p = 0.229; EAD: 0.99 (0.38–1.14), p = 0.323). There was no significant difference in the survival between groups after propensity score matching (Log-rank test p = 0.578). In conclusion, posttransplant clinical outcomes were not significantly different between the groups with and without PAC. Anesthetic management without the use of PAC may be possible in low-risk patients during liver transplantation. The risk should be carefully assessed by considering MELD scores, ischemic time, surgical history, previous treatment of underlying liver disease, and degree of portal and pulmonary hypertension.Registration: https://clinicaltrials.gov/ct2/show/NCT05457114 (registration date: July 15, 2022).
Energy transfer in N-component nanosystems enhanced by pulse-driven vibronic many-body entanglement
Authors: Gómez-Ruiz Fernando J. , Acevedo Oscar L. , Rodríguez Ferney J. , Quiroga Luis , Johnson Neil F. 
Published: November 2023

AbstractThe processing of energy by transfer and redistribution, plays a key role in the evolution of dynamical systems. At the ultrasmall and ultrafast scale of nanosystems, quantum coherence could in principle also play a role and has been reported in many pulse-driven nanosystems (e.g. quantum dots and even the microscopic Light-Harvesting Complex II (LHC-II) aggregate). Typical theoretical analyses cannot easily be scaled to describe these general N-component nanosystems; they do not treat the pulse dynamically; and they approximate memory effects. Here our aim is to shed light on what new physics might arise beyond these approximations. We adopt a purposely minimal model such that the time-dependence of the pulse is included explicitly in the Hamiltonian. This simple model generates complex dynamics: specifically, pulses of intermediate duration generate highly entangled vibronic (i.e. electronic-vibrational) states that spread multiple excitons – and hence energy – maximally within the system. Subsequent pulses can then act on such entangled states to efficiently channel subsequent energy capture. The underlying pulse-generated vibronic entanglement increases in strength and robustness as N increases.