bluuebunny/crossref_metadata_2025_split huggingface dataset:
cGAS guards against chromosome end-to-end fusions during mitosis and facilitates replicative senescence
Authors: Li Xiaocui , Li Xiaojuan , Xie Chen , Cai Sihui , Li Mengqiu , Jin Heping , Wu Shu , Cui Jun , Liu Haiying , Zhao Yong 
Published: October 2021

AbstractAs a sensor of cytosolic DNA, the role of cyclic GMP-AMP synthase (cGAS) in innate immune response is well established, yet how its functions in different biological conditions remain to be elucidated. Here, we identify cGAS as an essential regulator in inhibiting mitotic DNA double-strand break (DSB) repair and protecting short telomeres from end-to-end fusion independent of the canonical cGAS-STING pathway. cGAS associates with telomeric/subtelomeric DNA during mitosis when TRF1/TRF2/POT1 are deficient on telomeres. Depletion of cGAS leads to mitotic chromosome end-to-end fusions predominantly occurring between short telomeres. Mechanistically, cGAS interacts with CDK1 and positions them to chromosome ends. Thus, CDK1 inhibits mitotic non-homologous end joining (NHEJ) by blocking the recruitment of RNF8. cGAS-deficient human primary cells are defective in entering replicative senescence and display chromosome end-to-end fusions, genome instability and prolonged growth arrest. Altogether, cGAS safeguards genome stability by controlling mitotic DSB repair to inhibit mitotic chromosome end-to-end fusions, thus facilitating replicative senescence.
Layered Double Hydroxide-Based MRI/CT Dual Modal Contrasting Agent With Homogeneous Particle Size
Authors: Jung Sang-Yong , Park Jin Kuen , Oh Jae-Min 
Published: October 2021

AbstractThe development of nanoparticles incorporating Gd3+ has attracted interest in the field of contrasting nanomedicine for magnetic resonance (MR) and computed tomography (CT). In order to achieve an effective contrasting performance, the amount and stability of Gd incorporated as well as particle-size control of the nanoparticles should be considered simultaneously. In the current study, Gd-diethylenetriaminepentaacetate(Gd-DTPA) was incorporated into layered double hydroxide (LDH) to meet the physicochemical properties required for MR-CT dual contrasting nanomedicine. Strategically, the particle size and nanometer incorporation of Gd-DTPA into LDH (GL-R hybrid) were controlled homogeneously using the reverse micelle method. X-ray diffraction showed that the hybrid obtained possessed a hydrotalcite phase. Dynamic light scattering and electron microscopic analyses showed that the hybrid had a controlled size of <200 nm with significant homogeneity. Fast Fourier-transform of transmission electron microscopy confirmed that the platelets of the GL-R hybrids were oriented randomly to form inter-particle space, enabling the Gd-DTPA moiety to be encapsulated stably. The encapsulation efficiency of Gd-DTPA was 20.8%, which was sufficiently high compared with other Gd-DTPA-incorporatedLDH. According to X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy, Gd-DTPA incorporated in the hybrid preserved its structure intact. Its potential as a dual modal contrast agent was demonstrated by measuring the concentration-dependent Hounsfield unit and magnetic resonance relaxivity, which were determined to be 230 at 2 mg/mL and 5.8 in the range ~0.2–1 mM-Gd, respectively.
Analysis and prediction of the impact of technological parameters on cutting force components in rough milling of AZ31 magnesium alloy
Authors: Kulisz M. , Zagórski I. , Weremczuk A. , Rusinek R. , Korpysa J. 
Published: October 2021

Abstract
This paper presents the results of experimental study of the AZ31 magnesium alloy milling process. Dry milling was carried out under high-speed machining conditions. First, a stability lobe diagram was determined using CutPro software. Next, experimental studies were carried out to verify the stability lobe diagram. The tests were carried out for different feed per tooth and cutting speed values using two types of tools. During the experimental investigations, cutting forces in three directions were recorded. The obtained time series were subjected to general analysis and analysis using composite multiscale entropy. Modelling and prediction were performed using Statistica Neural Network software, in which two types of neural networks were applied: multi-layered perceptron and radial basis function. It was observed that milling with high cutting speed values allows for component values of cutting force to be lowered as a result of the transition into the high-speed machining conditions range. In most cases, the highest values for the analysed parameters were recorded for the component F

x
, whereas the lowest were recorded for F

y
. Additionally, the paper shows that a prediction (with the use of artificial neural networks) of the components of cutting force can be made, both for the amplitudes of components of cutting force F

amp
and for root mean square F

rms
.
The Emperor's New Markov Blankets
Authors: Bruineberg Jelle , Dołęga Krzysztof , Dewhurst Joe , Baltieri Manuel 
Published: October 2021

AbstractThe free energy principle, an influential framework in computational neuroscience and theoretical neurobiology, starts from the assumption that living systems ensure adaptive exchanges with their environment by minimizing the objective function of variational free energy. Following this premise, it claims to deliver a promising integration of the life sciences. In recent work, Markov blankets, one of the central constructs of the free energy principle, have been applied to resolve debates central to philosophy (such as demarcating the boundaries of the mind). The aim of this paper is twofold. First, we trace the development of Markov blankets starting from their standard application in Bayesian networks, via variational inference, to their use in the literature on active inference. We then identify a persistent confusion in the literature between the formal use of Markov blankets as an epistemic tool for Bayesian inference, and their novel metaphysical use in the free energy framework to demarcate the physical boundary between an agent and its environment. Consequently, we propose to distinguish between “Pearl blankets” to refer to the original epistemic use of Markov blankets and “Friston blankets” to refer to the new metaphysical construct. Second, we use this distinction to critically assess claims resting on the application of Markov blankets to philosophical problems. We suggest that this literature would do well in differentiating between two different research programmes: “inference with a model” and “inference within a model.” Only the latter is capable of doing metaphysical work with Markov blankets, but requires additional philosophical premises and cannot be justified by an appeal to the success of the mathematical framework alone.
Iron Isotope Biogeochemical Cycling in the Western Arctic Ocean
Authors: Zhang Ruifeng , Jensen Laramie , Fitzsimmons Jessica , Sherrell Robert M. , Lam Phoebe , Xiang Yang , John Seth 
Published: October 2021

AbstractThe Arctic Ocean is unique, connecting the Atlantic and Pacific basins and being especially vulnerable to the impacts of a changing climate. Iron stable isotopes (δ56Fe) provide a unique window into the biogeochemical cycling of Fe in the Arctic. Here we present the first seawater δ56Fe for the Western Arctic Ocean, from the 2015 U.S. GEOTRACES GN01 transect. Samples analyzed for δ56Fe include seawater dissolved (<0.2 μm), soluble (<∼0.003 μm), and leachable particulate phases. Several key processes were explored using Fe isotopes, each characterized by a distinct combination of δ56Fe and Fe concentrations. Input of Fe from reducing continental shelf sediments was characterized by high dissolved Fe concentrations (6.18 ± 4.84 nmol kg−1) and low δ56Fe (−1.57 ± 0.66‰). Riverine Fe input observed in the Transpolar Drift Current was characterized by high Fe concentrations corresponding to a riverine end‐member Fe concentration of 19 nM, and near‐zero δ56Fe (0.02 ± 0.23‰) that was similar to that of average crustal material. The deep Arctic was mostly characterized by low Fe concentrations (0.33 ± 0.14 nmol kg−1) and slightly higher δ56Fe (0.05 ± 0.30‰), except for samples taken near continental slopes that were affected by sedimentary Fe input with lower δ56Fe, and in the Amundsen Basin which showed possible hydrothermal Fe input. Our data thus illuminate Fe biogeochemical cycling processes in the modern Arctic Ocean, and serve as a baseline for understanding how the Arctic Fe cycle responds to climate change.
Modulation of Magnetosonic Waves by Background Plasma Density in a Dipole Magnetic Field: 2‐D PIC Simulation
Authors: Sun Jicheng , Lu Quanming , Wang Xueyi , Liu Xu , Gao Xinliang , Yang Huigen 
Published: October 2021

AbstractRecent satellite observations, combined with instability analyses, have shown that the background plasma density variation can modulate the magnetosonic (MS) waves by controlling the wave excitation. However, the detailed modulation process needs to be identified since the MS waves propagate nearly perpendicular to the background magnetic field. In this study, we investigate the MS wave modulation by background plasma density using a 2‐D general curvilinear particle‐in‐cell simulation in the meridian plane of a dipole magnetic field. The simulation model consists of three plasma components: the background cold electrons and protons and ring distribution protons. We find that MS waves can be locally generated by ring distribution protons in the low plasma density region, while no MS wave is generated in the high density region. These MS waves are confined near the local source region since they are damped by the background cold plasma. The background protons gain more energy than background electrons, implying the plasmaspheric protons may dominate the modulation of MS waves. Moreover, we have also investigated the generation and propagation of MS waves in the plasmapause density structure. Our simulation results demonstrate that the background plasma density variation can modulate the MS waves and may play an important role in the spatial distribution of MS waves.
Reconstruction of the Electron Diffusion Region With Inertia and Compressibility Effects
Authors: Hasegawa H. , Nakamura T. K. M. , Denton R. E. 
Published: October 2021

AbstractA method based on electron magnetohydrodynamics (EMHD) for the reconstruction of steady, two‐dimensional plasma and magnetic field structures from data taken by a single spacecraft, first developed by Sonnerup et al. (2016), https://doi.org/10.1002/2016ja022430, is extended to accommodate inhomogeneity of the electron density and temperature, electron inertia effects, and guide magnetic field in and around the electron diffusion region (EDR), the central part of the magnetic reconnection region. The new method assumes that the electron density and temperature are constant along, but may vary across, the magnetic field lines. We present two models for the reconstruction of electron streamlines, one of which is not constrained by any specific formula for the electron pressure tensor term in the generalized Ohm's law that is responsible for electron unmagnetization in the EDR, and the other is a modification of the original model to include the inertia and compressibility effects. Benchmark tests using data from fully kinetic simulations show that our new method is applicable to both antiparallel and guide‐field (component) reconnection, and the electron velocity field can be better reconstructed by including the inertia effects. The new EMHD reconstruction technique has been applied to an EDR of magnetotail reconnection encountered by the Magnetospheric Multiscale spacecraft on 11 July 2017, reported by Torbert et al. (2018), https://doi.org/10.1126/science.aat2998 and reconstructed with the original inertia‐less version by Hasegawa et al. (2019), https://doi.org/10.1029/2018ja026051, which demonstrates that the new method better performs in recovering the electric field and electron streamlines than the original version.
Monthly and Interannual Variations in Winter Positive Surface‐Bottom Temperature Difference in Northeastern Coastal Waters of the Shandong Peninsula in the Yellow Sea
Authors: Zhai Fangguo , Liu Zizhou , Li Peiliang , Gu Yanzhen , Hu Luoyu , Sun Liyuan , Yang Baoqing 
Published: October 2021

AbstractTraditionally, the Yellow Sea (YS) is believed to be well mixed throughout the water column or to experience significant temperature inversions in winter. Recently, we found a significant positive surface‐bottom temperature difference (SBTD) as large as 3.7°C in northeastern coastal waters of the Shandong Peninsula in the YS in winter. By analyzing 4 years (June 2016–September 2020) of online in situ observations, this study examined monthly and interannual variations in winter positive SBTD and the underlying dynamics. The winter positive SBTD generally formed in November, peaked in December/January, and disappeared in March. At the interannual time scale, this SBTD was strongest in 2018 and weakest in 2020. The underlying dynamics involved the combined effects of prevailing winter monsoon winds and resultant surface heat loss and current heat advection. When the surface northerly wind was strong, strengthened southward advection of cold air over the ocean cooled the water column intensely, whereas wind‐enhanced southward advection of warm surface water partly offset the sea surface cooling and resulted in surface temperature cooling that was considerably slower than bottom temperature or even surface temperature warming. These processes together generated strong positive SBTDs. When the surface northerly wind was weak, all of the above processes became weak and resulted in weak positive SBTDs. The relationship with Yellow River runoff was also discussed. This study enriches our knowledge of winter thermal structure in the YS. More observations and coupled physical‐biogeochemical simulations are needed to further clarify the impacts on climate and marine ecology.
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley
Authors: Mahdi Lisa K , Miyauchi Shingo , Uhlmann Charles , Garrido-Oter Ruben , Langen Gregor , Wawra Stephan , Niu Yulong , Guan Rui , Robertson-Albertyn Senga , Bulgarelli Davide , Parker Jane E , Zuccaro Alga 
Published: October 2021

Abstract
Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.
Circular RNA circUBE2J2 acts as the sponge of microRNA-370-5P to suppress hepatocellular carcinoma progression
Authors: Zhang Lu , Liu Yachong , Tao Haisu , Zhu He , Pan Yonglong , Li Pengcheng , Liang Huifang , Zhang Bixiang , Song Jia 
Published: October 2021

AbstractAccumulating evidences indicate that circular RNAs (circRNAs), a class of non-coding RNAs, play important roles in tumorigenesis. However, the function of circRNAs in hepatocellular carcinoma is largely unknown. CircRNA microarray was performed to identify abnormally expressed circRNAs in HCC tissue samples. We conducted Kaplan–Meier survival analysis to explore the significance of circUBE2J2 in clinical prognosis. Then, we examined the functions of circUBE2J2 in HCC by cell proliferation, migration, and mouse xenograft assay. We identified miR-370-5P as a circUBE2J2-related microRNA by using biotin-labeled circUBE2J2 probe to perform RNA antisense purification (RAP) assay in HCC cells. The dual luciferase reporter assay and RNA pulldown assays were employed to verify the relationships among circUBE2J2, miRNA-370-5P, and KLF7. Microarray analysis and qRT-PCR verified a circRNA termed circUBE2J2 that was downregulated in HCC. Kaplan–Meier survival analysis showed that downregulated circUBE2J2 was correlated with poorer survival. CircUBE2J2 expression in HCC cells was selectively regulated via luciferase reporter assays; circUBE2J2 and KLF7 were observed to directly bind to miR-370-5P. Furthermore, knockdown of circUBE2J2 in HCC could downregulate KLF7, the target of miR-370-5P, thus promoting the proliferation and migration of HCC cells. Then the related experiment suggested that circUBE2J2 could regulate the expression of KLF7 by sponging miR-370-5p. In summary, we infer that circUBE2J2 may act as a competing endogenous RNA (ceRNA) to regulate KLF7 expression through sponging miR-370-5P and play a regulatory functions in HCC. CircUBE2J2 may be a diagnostic biomarker and potential target for HCC therapy.
Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21
Authors: Liu Jinfeng , Yang Jinrong , Zeng Xiao Cheng , Xantheas Sotiris S. , Yagi Kiyoshi , He Xiao 
Published: October 2021

AbstractThe spectroscopic features of protonated water species in dilute acid solutions have been long sought after for understanding the microscopic behavior of the proton in water with gas-phase water clusters H+(H2O)n extensively studied as bottom-up model systems. We present a new protocol for the calculation of the infrared (IR) spectra of complex systems, which combines the fragment-based Coupled Cluster method and anharmonic vibrational quasi-degenerate perturbation theory, and demonstrate its accuracy towards the complete and accurate assignment of the IR spectrum of the H+(H2O)21 cluster. The site-specific IR spectral signatures reveal two distinct structures for the internal and surface four-coordinated water molecules, which are ice-like and liquid-like, respectively. The effect of inter-molecular interaction between water molecules is addressed, and the vibrational resonance is found between the O-H stretching fundamental and the bending overtone of the nearest neighboring water molecule. The revelation of the spectral signature of the excess proton offers deeper insight into the nature of charge accommodation in the extended hydrogen-bonding network underpinning this aqueous cluster.
Geophysical constraints on the reliability of solar and wind power worldwide
Authors: Tong Dan , Farnham David J. , Duan Lei , Zhang Qiang , Lewis Nathan S. , Caldeira Ken , Davis Steven J. 
Published: October 2021

AbstractIf future net-zero emissions energy systems rely heavily on solar and wind resources, spatial and temporal mismatches between resource availability and electricity demand may challenge system reliability. Using 39 years of hourly reanalysis data (1980–2018), we analyze the ability of solar and wind resources to meet electricity demand in 42 countries, varying the hypothetical scale and mix of renewable generation as well as energy storage capacity. Assuming perfect transmission and annual generation equal to annual demand, but no energy storage, we find the most reliable renewable electricity systems are wind-heavy and satisfy countries’ electricity demand in 72–91% of hours (83–94% by adding 12 h of storage). Yet even in systems which meet >90% of demand, hundreds of hours of unmet demand may occur annually. Our analysis helps quantify the power, energy, and utilization rates of additional energy storage, demand management, or curtailment, as well as the benefits of regional aggregation.
Engineering digitizer circuits for chemical and genetic screens in human cells
Authors: Wong Nicole M. , Frias Elizabeth , Sigoillot Frederic D. , Letendre Justin H. , Hild Marc , Wong Wilson W. 
Published: October 2021

AbstractCell-based transcriptional reporters are invaluable in high-throughput compound and CRISPR screens for identifying compounds or genes that can impact a pathway of interest. However, many transcriptional reporters have weak activities and transient responses. This can result in overlooking therapeutic targets and compounds that are difficult to detect, necessitating the resource-consuming process of running multiple screens at various timepoints. Here, we present RADAR, a digitizer circuit for amplifying reporter activity and retaining memory of pathway activation. Reporting on the AP-1 pathway, our circuit identifies compounds with known activity against PKC-related pathways and shows an enhanced dynamic range with improved sensitivity compared to a classical reporter in compound screens. In the first genome-wide pooled CRISPR screen for the AP-1 pathway, RADAR identifies canonical genes from the MAPK and PKC pathways, as well as non-canonical regulators. Thus, our scalable system highlights the benefit and versatility of using genetic circuits in large-scale cell-based screening.
Analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling in the activation of neural stem progenitor cells
Authors: Peñailillo Johany , Palacios Miriam , Mounieres Constanza , Muñoz Rosana , Slater Paula G. , De Domenico Elena , Patrushev Ilya , Gilchrist Mike , Larraín Juan 
Published: October 2021

AbstractXenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPCs). Here we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, aiming to identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC-specific ribosome biogenesis factors, and genes involved in stem cell proliferation. Western blot and immunofluorescence analysis showed that mTORC1 is rapidly and transiently activated after SCI, and its pharmacological inhibition impairs spinal cord regeneration and proliferation of NSPC through the downregulation of genes involved in the G1/S transition of cell cycle, with a strong effect on PCNA. We propose that the mTOR signaling pathway is a key player in the activation of NPSCs during the early steps of spinal cord regeneration.
Improving online and offline gain from repetitive practice using anodal tDCS at dorsal premotor cortex
Authors: Kim Taewon , Buchanan John J. , Bernard Jessica A. , Wright David L. 
Published: October 2021

AbstractAdministering anodal transcranial direct current stimulation at the left dorsal premotor cortex (PMd) but not right PMd throughout the repetitive practice of three novel motor sequences resulted in improved offline performance usually only observed after interleaved practice. This gain only emerged following overnight sleep. These data are consistent with the proposed proprietary role of left PMd for motor sequence learning and the more recent claim that PMd is central to sleep-related consolidation of novel skill memory.