bluuebunny/crossref_metadata_2025_split huggingface dataset:
HVEM Cryomicroscopy of Frozen Hydrated PTK1 Cells
Authors: O’Toole E.T. , Wray G.P. , Kremer J.R. , Mcintosh J.R. 
Published: June 2020

Ultrarapid freezing and cryomicroscopy of frozen hydrated material makes it possible to visualize samples that have never been exposed to chemical fixatives, dehydration, or stains. In principle, freezing and cryoimaging methods avoid artifacts associated with chemical fixation and processing and allow one to visualize the specimen in a condition that is close to its native state. Here we describe a way to use a high voltage electron microscope (HVEM) for the cryoimaging of frozen hydrated PTK1 cells.PTK1 cells were cultured on formvar-coated, carbon stabilized gold grids. After three days in culture, the grids were removed from the culture medium and blotted in a humidity chamber at 35° C. In some instances, the grids were rinsed briefly in 0.16 M ammonium acetate buffer (pH 7.2) prior to blotting. After blotting, the grids were transferred to a plunging apparatus and plunged into liquid ethane held directly above its freezing point. The plunging apparatus consists of a vertical slide rail that guides the fall of a mounted pair of forceps that clamp the specimen. The forceps are surrounded by a plexiglass humidity chamber mounted over a dewar of liquid nitrogen containing an ethane chamber. After freezing, the samples were transferred to liquid nitrogen and viewed in a JEOL JEM 1000 equipped with a top entry cold stage designed and built by Mr. George Wray (Univ. Colorado). The samples were routinely exposed to electron doses of 1 e/Å2/sec, and viewed at a temperature of −150° C. A GATAN video system was used to enhance contrast and to estimate the correct amount of underfocus needed to obtain phase contrast at various magnifications. Low dose micrographs were taken using two second exposures of Kodak 4463 film. The state of the solid water in the specimen was determined by diffraction using a 30/μm field limiting aperture and a camera length of 1 meter.
Observations of Frozen-Hydrated Microtubules
Authors: Chrétien D. , Job D. , Wade R.H. 
Published: June 2020

Microtubules are filamentary structures found in the cytoplasm of eukaryotic cells, where, together with actin and intermediate filaments, they form the components of the cytoskeleton. They have many functions and show various levels of structural complexity as witnessed by the singlet, doublet and triplet structures involved in the architecture of centrioles, basal bodies, cilia and flagella. The accepted microtubule model consists of a 25 nm diameter hollow tube with a wall made up of 13 paraxial protofilaments (pf). Each pf is a string of aligned tubulin dimers. Some results have suggested that the pfs follow a superhelix. To understand how microtubules function in the cell an accurate model of the surface lattice is one of the requirements. For example the 9x2 architecture of the axoneme will depend on the organisation of its component microtubules. We should also note that microtubules with different numbers of pfs have been observed in thin sections of cellular and of in-vitro material. An outstanding question is how does the surface lattice adjust to these different pf numbers?We have been using cryo-electron microscopy of frozen-hydrated samples to study in-vitro assembled microtubules. The experimental conditions are described in detail in this reference. The results obtained in conjunction with thin sections of similar specimens and with axoneme outer doublet fragments have already allowed us to characterise the image contrast of 13, 14 and 15 pf microtubules on the basis of the measured image widths, of the the image contrast symmetry and of the amplitude and phase behaviour along the equator in the computed Fourier transforms. The contrast variations along individual microtubule images can be interpreted in terms of the geometry of the microtubule surface lattice. We can extend these results and make some reasonable predictions about the probable surface lattices in the case of other pf numbers, see Table 1. Figure 1 shows observed images with which these predictions can be compared.
Possibilities of the Bend-Contour Method in the Analysis of the Lattice Disorientations in Crystals on Thin-Film Transformations
Authors: Yu. Kolosov V. 
Published: June 2020

The paper summarized some of the authors data on the transmission electron microscope (TEM) investigations using bend-contours(BC)the transformations of crystal lattice orientations on crystallization of amorphous films and recrystallization. Most investigations were made in situ in JEOL and TESLA microscopes under the influence of the electron beam, Fig.3-5, 8,9. In some cases the video record was produced, some clippings supposed to be demonstrated.1. The possibilities of BC method were outlined earlier (e.g.1). In particular they are similar to Kikuchi lines method and sometimes are more powerful. However these and some other options are rarely used in practice though BC patterns often present on the TEM images and carry the unique diffraction information written in the image plane. The merits of BC method in the evaluation of the lattice orientation, if compared with traditional selected area diffraction(SAD)-high locality, the possibilities of simultaneous analysis of large areas(fields of orientations) and visual ability, the demerits - fitness only to crystals with large orientation gradients(more than 10−2rad/μm).
The Regional Earth System Model RegCM‐ES: Evaluation of the Mediterranean Climate and Marine Biogeochemistry
Authors: Reale Marco , Giorgi Filippo , Solidoro Cosimo , Di Biagio Valeria , Di Sante Fabio , Mariotti Laura , Farneti Riccardo , Sannino Gianmaria 
Published: June 2020

AbstractWe introduce a new version of the Earth System Regional Climate model RegCM‐ES and evaluate its performances for the first time over the Mediterranean region. The novel aspect of this coupled system is the possibility to simulate the dynamics of the marine ecosystem through a biogeochemical model, BFM (Biogeochemical Flux Model), coupled online with the ocean circulation model MITgcm (MIT general circulation model). The validation of atmosphere and ocean components has shown that the model is able to capture interannual and intermonthly variabilities of the atmospheric heat fluxes and spatial patterns of land surface temperature, precipitation, evaporation, and sea surface temperature with a general improvement compared to previous versions. At the same time, we diagnosed some prominent deficiencies as a warm and dry bias associated in summer with the resolution of the atmospheric module and the tuning of the boundary layer and convective precipitation scheme. On the biogeochemical side, RegCM‐ES shows good skills in reproducing mean values and spatial patterns of net primary production, phosphate, and horizontal/vertical patterns of chlorophyll‐a. Limitations in this case include deficiencies mainly in the simulation of mean values of nitrate and dissolved oxygen in the basin which have been associated with too large vertical mixing throughout the water column, deficiencies in the boundary conditions, and solubility computations. Overall, RegCM‐ES has the potential to become a suitable tool for the analysis of the impacts of climate change on the ocean and marine biogeochemistry in the Mediterranean region and many other domains.
Evaluating Precipitation Features and Rainfall Characteristics in a Multi‐Scale Modeling Framework
Authors: Chern Jiun‐Dar , Tao Wei‐Kuo , Lang Stephen E. , Li Xiaowen , Matsui Toshihisa 
Published: June 2020

AbstractCloud and precipitation systems are simulated with a multi‐scale modeling framework (MMF) and compared over the Tropics and Subtropics against the Tropical Rainfall Measuring Mission (TRMM) Radar‐defined Precipitation Features (RPFs) product. A methodology, in close analogy to the TRMM RPFs, is developed to produce simulated precipitation features (PFs) from the output of the embedded two‐dimensional (2D) cloud‐resolving models (CRMs) within an MMF. Despite the limitations of 2D CRMs, the simulated population distribution, horizontal and vertical structure of PFs, and the geographical location and local rainfall contribution of mesoscale convective systems (MCSs) are in good agreement with the TRMM observations. However, some model discrepancies are found and can be identified and quantified within the PF distributions. Using model biases in relative population and rainfall contributions, PFs can be characterized into four size categories: small, medium to large, very large, and extremely large. Four different major mechanisms might account for the model biases in each different category: (1) the two‐dimensionality of the CRMs, (2) a positive convection‐wind‐evaporation feedback loop, (3) an artificial dynamic constraint in a bounded CRM domain with cyclic boundaries, and (4) the limited CRM domain size. The second and fourth mechanisms tend to contribute to the excessive tropical precipitation biases commonly found in most MMFs, whereas the other mechanisms reduce rainfall contributions from small and very large PFs. MMF sensitivity experiments with various CRM domain sizes and grid spacings showed that larger domains (higher resolutions) tend to shift PF populations toward larger (smaller) sizes.
Strong Intensification of Hourly Rainfall Extremes by Urbanization
Authors: Li Yafei , Fowler Hayley J. , Argüeso Daniel , Blenkinsop Stephen , Evans Jason P. , Lenderink Geert , Yan Xiaodong , Guerreiro Selma B. , Lewis Elizabeth , Li Xiao‐Feng 
Published: June 2020

AbstractAlthough observations and modeling studies show that heavy rainfall is increasing in many regions, how changes will manifest themselves on sub‐daily timescales remains highly uncertain. Here, for the first time, we combine observational analysis and high‐resolution modeling results to examine changes to extreme rainfall intensities in urbanized Kuala Lumpur, Malaysia. We find that hourly intensities of extreme rainfall have increased by ~35% over the last three decades, nearly 3 times more than in surrounding rural areas, with daily intensities showing much weaker increases. Our modeling results confirm that the urban heat island effect creates a more unstable atmosphere, increased vertical uplift and moisture convergence. This, combined with weak surface winds in the Tropics, causes intensification of rainfall extremes over the city, with reduced rainfall in the surrounding region.
Wind Wave Effects on Remote Sensing of Sea Surface Currents From SAR
Authors: Li Shuiqing , Liu Baochang , Shen Hui , Hou Yijun , Perrie Will 
Published: June 2020

AbstractWind waves contribute a significant component to the sea surface currents detected by synthetic aperture radar (SAR) systems via the orbital velocity; this component is typically referred to as the wind wave‐induced artifact surface velocity (WASV). Accordingly, it is essential to precisely describe the WASV effect, so that the real sea surface currents can be obtained from SAR measurements. In order to enhance our understanding about WASV, we carried out a numerical analysis of the sea state dependence of WASV under various radar configurations. The simulated WASV compares reasonably well with observations reported in the literature. It is found that WASV not only depends on the wind speed but also increases considerably with the development of the wind waves, as characterized by wave age. WASV may increase by two to three times, in fully developed wind wave conditions, as compared to young waves. The wave age dependence appears to largely account for the observed uncertainty in WASV at a given wind speed; moreover, swell is also found to significantly influence WASV through hydrodynamic modulation of wind wave properties. These effects are stronger at higher wind speeds and vary significantly with the different radar configurations that are possible, in terms of polarizations and incidence angles. The variations in WASV using different shortwave spectral functions and angular spreading functions are examined in this manuscript.
Antarctic Circumpolar Current Transport Through Drake Passage: What Can We Learn From Comparing High‐Resolution Model Results to Observations?
Authors: Xu Xiaobiao , Chassignet Eric P. , Firing Yvonne L. , Donohue Kathleen 
Published: June 2020

AbstractUncertainty exists in the time‐mean total transport of the Antarctic Circumpolar Current (ACC), the world's strongest ocean current. The two most recent observational programs in Drake Passage, DRAKE and cDrake, yielded transports of 141 and 173.3 Sv, respectively. In this paper, we use a realistic 1/12° global ocean simulation to interpret these observational estimates and reconcile their differences. We first show that the modeled ACC transport in the upper 1,000 m is in excellent agreement with repeat shipboard acoustic Doppler current profiler (SADCP) transects and that the exponentially decaying transport profile in the model is consistent with the profile derived from repeat hydrographic data. By further comparing the model results to the cDrake and DRAKE observations, we argue that the modeled 157.3 Sv transport, that is, approximately the average of the cDrake and DRAKE estimates, is actually representative of the time‐mean ACC transport through the Drake Passage. The cDrake experiment overestimated the barotropic contribution in part because the array undersampled the deep recirculation southwest of the Shackleton Fracture Zone, whereas the surface geostrophic currents used in the DRAKE estimate yielded a weaker near‐surface transport than implied by the SADCP data. We also find that the modeled baroclinic and barotropic transports are not correlated; thus, monitoring either baroclinic or barotropic transport alone may be insufficient to assess the temporal variability of the total ACC transport.
Berberine mediates root remodeling in an immature tooth with apical periodontitis by regulating stem cells from apical papilla differentiation
Authors: Cui Yujia , Xie Jing , Fu Yujie , Li Chuwen , Zheng Liwei , Huang Dingming , Zhou Changchun , Sun Jianxun , Zhou Xuedong 
Published: June 2020

AbstractOnce pulp necrosis or apical periodontitis occurs on immature teeth, the weak root and open root apex are challenging to clinicians. Berberine (BBR) is a potential medicine for bone disorders, therefore, we proposed to apply BBR in root canals to enhance root repair in immature teeth. An in vivo model of immature teeth with apical periodontitis was established in rats, and root canals were filled with BBR, calcium hydroxide or sterilized saline for 3 weeks. The shape of the roots was analyzed by micro-computed tomography and histological staining. In vitro, BBR was introduced into stem cells from apical papilla (SCAPs). Osteogenic differentiation of stem cells from apical papilla was investigated by alkaline phosphatase activity, mineralization ability, and gene expression of osteogenic makers. The signaling pathway, which regulated the osteogenesis of SCAPs was evaluated by quantitative real time PCR, Western blot analysis, and immunofluorescence. In rats treated with BBR, more tissue was formed, with longer roots, thicker root walls, and smaller apex diameters. In addition, we found that BBR promoted SCAPs osteogenesis in a time-dependent and concentration-dependent manner. BBR induced the expression of β-catenin and enhanced β-catenin entering into the nucleus, to up-regulate more runt-related nuclear factor 2 downstream. BBR enhanced root repair in immature teeth with apical periodontitis by activating the canonical Wnt/β-catenin pathway in SCAPs.
Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers
Authors: Liu Shufeng , Wang Haiying , Chen Liming , Wang Jiawen , Zheng Maosheng , Liu Sitong , Chen Qian , Ni Jinren 
Published: June 2020

Abstract
The recent discovery of comammox Nitrospira as complete nitrifiers has fundamentally renewed perceptions of nitrogen cycling in natural and engineered systems, yet little is known about the environmental controls on these newly recognized bacteria. Based on improved phylogenetic resolution through successful assembly of ten novel genomes (71–96% completeness), we provided the first biogeographic patterns for planktonic and benthic comammox Nitrospira in the Yangtze River over a 6030 km continuum. Our study revealed the widespread distributions and relative abundance of comammox Nitrospira in this large freshwater system, constituting 30 and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira contributed more to nitrifier abundances (34–87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A) areas of the upper reach. The dominant position of planktonic comammox Nitrospira was replaced by canonical Nitrospira sublineages I/II and ammonia-oxidizing bacteria from the plateau to downstream plain due to environmental selection, while the dissimilarity of benthic comammox Nitrospira was moderately associated with geographic distance. A substantial decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, consistent with a similarly considerable decrease in overall sediment bacterial taxa. Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.
Induction of ASC pyroptosis requires gasdermin D or caspase-1/11-dependent mediators and IFNβ from pyroptotic macrophages
Authors: Zhang Cuiping , Zhao Caiqi , Chen Xiaoyan , Tao Rujia , Wang Sijiao , Meng Guangxun , Liu Xing , Shao Changzhou , Su Xiao 
Published: June 2020

AbstractMesenchymal stem cells (MSCs) have been used in cell-based therapies for a variety of disorders. Some factors such as inflammatory mediators in the diseased area might damage the survival of MSCs and affect their efficacy. Pyroptosis is a form of programmed necrosis as a response for immune cells to cytosolic pathogenic stimuli. Whether MSCs develop pyroptosis under pathological stimulation, its underlying mechanism and biological significance are still unclear. Here, we found that LPS, flagellin, dsDNA, nigericin (NIG), or LPS combined with nigericin (LPS/NIG) could not induce pyroptosis in adipose-tissue-derived mesenchymal stem cells (ASCs). However, when applied the culture media collected from LPS/NIG-induced pyroptotic bone marrow-derived macrophages (BMDMs) to incubate ASCs, ASCs developed pyroptosis. Inhibition of caspases or deletion of Caspase-1/11 in ASCs did not affect the pyroptotic macrophage media-triggered ASC pyroptosis while ablation of Caspase-1/11 abolished BMDM pyroptosis induced by LPS/NIG. Media collected from LPS/NIG stimulated Gsdmd−/− or Caspase-1/11−/− BMDMs could not induce pyroptosis of ASCs. In addition, RNA-seq analysis showed that interferon (IFN)-stimulated genes were upregulated in pyroptotic ASCs. Adding IFNβ could boost LPS/NIG stimulated BMDM media-induced ASC pyroptosis. Surprisingly, the pyroptotic ASCs had a lower bactericidal ability to P. Aeruginosa. Taken together, induction of ASC pyroptosis requires gasdermin D or caspase-1/11-dependent mediators and IFNβ from pyroptotic macrophages.
Control of electrical resistance and magnetoresistance by electric-field-driven oxygen ion migration in a single GdOx wire
Authors: Kang Jun-Ho , Lee Soogil , Lee Taek-Hyeon , Yang Ji-Seok , Lee Jae Wook , Tae Cheong Cheon , Jeong Jong-Ryul , Park Seung-Young , Park Byong-Guk , Kim Kab-Jin 
Published: June 2020

AbstractElectric-field-driven ion migration can significantly modulate the electric and magnetic properties of solids, creating novel functionalities useful for advanced electromagnetic devices. Earlier works have used vertically stacked structures for this purpose, in which the redox process results from ion migration driven by a vertical electric field through the interfaces. However, the existence of the interfaces between the dissimilar layers causes the oxidation and reduction processes to have high and asymmetric energy barriers, which means that a large electric field is required to control the devices. Here, we show that in a partially oxidized single GdOx wire using a lateral electric field configuration, low and symmetric energy barriers for the oxidation and reduction processes can be achieved. We provide evidence that the redox process is the result of the lateral motion of oxygen ions by directly visualizing the electric-field-driven real-time ionic motion using an optical microscope. An electric field as low as 105 V/m was able to drive oxygen ions at room temperature, allowing controllable modulation of the electrical resistance using a lateral electric field. A large negative magnetoresistance was also observed in the GdOx wire, and its magnitude was significantly enhanced up to 20% at 9 T through oxygen ion control. Our results suggest that the electrical and magnetic properties of single GdOx can be efficiently controlled through oxygen ion motion driven by a lateral electric field, which paves the way for fully functional electromagnetic devices such as artificial synapses.
Globalization and the rise and fall of cognitive control
Authors: Mosleh Mohsen , Kyker Katelynn , Cohen Jonathan D. , Rand David G. 
Published: June 2020

AbstractThe scale of human interaction is larger than ever before—people regularly interact with and learn from others around the world, and everyone impacts the global environment. We develop an evolutionary game theory model to ask how the scale of interaction affects the evolution of cognition. Our agents make decisions using automatic (e.g., reflexive) versus controlled (e.g., deliberative) cognition, interact with each other, and influence the environment (i.e., game payoffs). We find that globalized direct contact between agents can either favor or disfavor control, depending on whether controlled agents are harmed or helped by contact with automatic agents; globalized environment disfavors cognitive control, while also promoting strategic diversity and fostering mesoscale communities of more versus less controlled agents; and globalized learning destroys mesoscale communities and homogenizes the population. These results emphasize the importance of the scale of interaction for the evolution of cognition, and help shed light on modern challenges.
Metallic nanocrystals with low angle grain boundary for controllable plastic reversibility
Authors: Zhu Qi , Huang Qishan , Guang Cao , An Xianghai , Mao Scott X. , Yang Wei , Zhang Ze , Gao Huajian , Zhou Haofei , Wang Jiangwei 
Published: June 2020

AbstractAdvanced nanodevices require reliable nanocomponents where mechanically-induced irreversible structural damage should be largely prevented. However, a practical methodology to improve the plastic reversibility of nanosized metals remains challenging. Here, we propose a grain boundary (GB) engineering protocol to realize controllable plastic reversibility in metallic nanocrystals. Both in situ nanomechanical testing and atomistic simulations demonstrate that custom-designed low-angle GBs with controlled misorientation can endow metallic bicrystals with endurable cyclic deformability via GB migration. Such fully reversible plasticity is predominantly governed by the conservative motion of Shockley partial dislocation pairs, which fundamentally suppress damage accumulation and preserve the structural stability. This reversible deformation is retained in a broad class of face-centred cubic metals with low stacking fault energies when tuning the GB structure, external geometry and loading conditions over a wide range. These findings shed light on practical advances in promoting cyclic deformability of metallic nanomaterials.