| 1. |
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| 2. |
- Cho, Soohyun, et al.
(författare)
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Observation of Dresselhaus type spin splitting of zinc blende structure semiconductors by circular dichroic photoemission study
- 2021
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Ingår i: Current Applied Physics. - : Elsevier BV. - 1567-1739. ; 30, s. 96-101
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Tidskriftsartikel (refereegranskat)abstract
- Material family of zinc blende structure semiconductors (ZBSSs) is important for novel technique such as spintronics. A study of the ZBSS spin-splitting structure in momentum space is essential when seeking to understand the exotic properties of the material. The Dresselhaus field predominates in the bulk, but the Rashba field plays important roles in states near the surface. Here, we used circular dichroism in angle-resolved photoemission spectroscopy (CD-ARPES) to explore the spin-splitting structure of bulk ZBSS in momentum space. The observed structure was well-explained by a Dresselhaus field attributable to the lack of inversion symmetry in ZBSS crystals. We show that CD-ARPES usefully reveals spin-splitting in momentum space. CD-ARPES combined with hard x-ray incident-beam would be useful to investigate the spin-splitting structures of the interface states in the ZBSS heterostructure.
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| 3. |
- Jung, Minyong, et al.
(författare)
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The AGORA High-resolution Galaxy Simulations Comparison Project. V. Satellite Galaxy Populations in a Cosmological Zoom-in Simulation of a Milky Way-Mass Halo
- 2024
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Ingår i: Astrophysical Journal. - 0004-637X. ; 964:2
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Tidskriftsartikel (refereegranskat)abstract
- We analyze and compare the satellite halo populations at z ∼ 2 in the high-resolution cosmological zoom-in simulations of a 1012 M ⊙ target halo (z = 0 mass) carried out on eight widely used astrophysical simulation codes (Art-I, Enzo, Ramses, Changa, Gadget-3, Gear, Arepo-t, and Gizmo) for the AGORA High-resolution Galaxy Simulations Comparison Project. We use slightly different redshift epochs near z = 2 for each code (hereafter “z ∼ 2”) at which the eight simulations are in the same stage in the target halo’s merger history. After identifying the matched pairs of halos between the CosmoRun simulations and the DMO simulations, we discover that each CosmoRun halo tends to be less massive than its DMO counterpart. When we consider only the halos containing stellar particles at z ∼ 2, the number of satellite galaxies is significantly fewer than that of dark matter halos in all participating AGORA simulations and is comparable to the number of present-day satellites near the Milky Way or M31. The so-called “missing satellite problem” is fully resolved across all participating codes simply by implementing the common baryonic physics adopted in AGORA and the stellar feedback prescription commonly used in each code, with sufficient numerical resolution (≲100 proper pc at z = 2). We also compare other properties such as the stellar mass-halo mass relation and the mass-metallicity relation. Our work highlights the value of comparison studies such as AGORA, where outstanding problems in galaxy formation theory are studied simultaneously on multiple numerical platforms.
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| 4. |
- Kim, Ji-Hoon, et al.
(författare)
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Assessing the impact of freshwater discharge on the fluid chemistry in the Svalbard fjords
- 2022
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 835
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Tidskriftsartikel (refereegranskat)abstract
- Changes in the cryosphere extent (e.g., glacier, ice sheet, permafrost, and snow) have been speculated to impact (bio)geochemical interactions and element budgets of seawater and pore fluids in Arctic regions. However, this process has rarely been documented in Arctic fjords, which leads to a poor systematic understanding of land-ocean interactions in such a warming-susceptible region. Here, we present the chemical and isotopic (δ18O, δD, δ11B, and 87Sr/86Sr) compositions of seawater and pore fluids from five fjords in the Svalbard archipelago. Compared to bottom seawater, the low Cl− concentrations and depleted water isotopic signatures (δ18O and δD) of surface seawater and pore fluids delineate freshwater discharge originating from precipitation and/or meltwater of the cryosphere (i.e., glacier, snow, and permafrost). In contrast, the high Cl− concentrations with light water isotopic values in pore fluids from Dicksonfjorden indicate a brine probably resulted from submarine permafrost formation during the late Holocene, a timing supported by the numerical simulation of dissolved Cl− concentration.The freshwater is influenced by the local diagenetic processes such as ion exchanges indicated by δ11B signatures as well as interactions with bedrock during fluid migration inferred from pore fluid 87Sr/86Sr ratios. The interactions with bedrock significantly alter the hydrogeochemical properties of pore fluids in each fjord, yielding spatiotemporal variations. Consequently, land-ocean interactions in combination with the hydrosphere-cryosphere-lithosphere are critical factors for understanding and predicting the hydrology and elemental cycling during global climate change periods in the past, present, and future of the Svalbard archipelago.
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| 5. |
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| 6. |
- Lee, Hyun-Seob, et al.
(författare)
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Foxa2 and Nurr1 Synergistically Yield A9 Nigral Dopamine Neurons Exhibiting Improved Differentiation, Function, and Cell Survival
- 2010
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Ingår i: Stem Cells. - : Oxford University Press (OUP). - 1549-4918 .- 1066-5099. ; 28:3, s. 501-512
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Tidskriftsartikel (refereegranskat)abstract
- Effective dopamine (DA) neuron differentiation from neural precursor cells (NPCs) is prerequisite for precursor/stem cell-based therapy of Parkinson's disease (PD). Nurr1, an orphan nuclear receptor, has been reported as a transcription factor that can drive DA neuron differentiation from non-dopaminergic NPCs in vitro. However, Nurr1 alone neither induces full neuronal maturation nor expression of proteins found specifically in midbrain DA neurons. In addition, Nurr1 expression is inefficient in inducing DA phenotype expression in NPCs derived from certain species such as mouse and human. We show here that Foxa2, a forkhead transcription factor whose role in midbrain DA neuron development was recently revealed, synergistically cooperates with Nurr1 to induce DA phenotype acquisition, midbrain-specific gene expression, and neuronal maturation. Thus, the combinatorial expression of Nurr1 and Foxa2 in NPCs efficiently yielded fully differentiated nigral (A9)-type midbrain neurons with clearly detectable DA neuronal activities. The effects of Foxa2 in DA neuron generation were observed regardless of the brain regions or species from which NPCs were derived. Furthermore, DA neurons generated by ectopic Foxa2 expression were more resistant to toxins. Importantly, Foxa2 expression resulted in a rapid cell cycle exit and reduced cell proliferation. Consistently, transplantation of NPCs transduced with Nurr1 and Foxa2 generated grafts enriched with midbrain-type DA neurons but reduced number of proliferating cells, and significantly reversed motor deficits in a rat PD model. Our findings can be applied to ongoing attempts to develop an efficient and safe precursor/stem cell-based therapy for PD. STEM CELLS 2010; 28: 501-512
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| 7. |
- Roca-Fàbrega, Santi, et al.
(författare)
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The AGORA High-resolution Galaxy Simulations Comparison Project. IV. Halo and Galaxy Mass Assembly in a Cosmological Zoom-in Simulation at z ≤ 2
- 2024
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Ingår i: Astrophysical Journal. - 0004-637X. ; 968:2
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Tidskriftsartikel (refereegranskat)abstract
- In this fourth paper from the AGORA Collaboration, we study the evolution down to redshift z = 2 and below of a set of cosmological zoom-in simulations of a Milky Way mass galaxy by eight of the leading hydrodynamic simulation codes. We also compare this CosmoRun suite of simulations with dark matter-only simulations by the same eight codes. We analyze general properties of the halo and galaxy at z = 4 and 3, and before the last major merger, focusing on the formation of well-defined rotationally supported disks, the mass-metallicity relation, the specific star formation rate, the gas metallicity gradients, and the nonaxisymmetric structures in the stellar disks. Codes generally converge well to the stellar-to-halo mass ratios predicted by semianalytic models at z ∼ 2. We see that almost all the hydro codes develop rotationally supported structures at low redshifts. Most agree within 0.5 dex with the observed mass-metallicity relation at high and intermediate redshifts, and reproduce the gas metallicity gradients obtained from analytical models and low-redshift observations. We confirm that the intercode differences in the halo assembly history reported in the first paper of the collaboration also exist in CosmoRun, making the code-to-code comparison more difficult. We show that such differences are mainly due to variations in code-dependent parameters that control the time stepping strategy of the gravity solver. We find that variations in the early stellar feedback can also result in differences in the timing of the low-redshift mergers. All the simulation data down to z = 2 and the auxiliary data will be made publicly available.
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| 8. |
- Strawn, Clayton, et al.
(författare)
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The AGORA High-resolution Galaxy Simulations Comparison Project. VI. Similarities and Differences in the Circumgalactic Medium
- 2024
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Ingår i: Astrophysical Journal. - 0004-637X. ; 962:1
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Tidskriftsartikel (refereegranskat)abstract
- We analyze the circumgalactic medium (CGM) for eight commonly-used cosmological codes in the AGORA collaboration. The codes are calibrated to use identical initial conditions, cosmology, heating and cooling, and star formation thresholds, but each evolves with its own unique code architecture and stellar feedback implementation. Here, we analyze the results of these simulations in terms of the structure, composition, and phase dynamics of the CGM. We show properties such as metal distribution, ionization levels, and kinematics are effective tracers of the effects of the different code feedback and implementation methods, and as such they can be highly divergent between simulations. This is merely a fiducial set of models, against which we will in the future compare multiple feedback recipes for each code. Nevertheless, we find that the large parameter space these simulations establish can help disentangle the different variables that affect observable quantities in the CGM, e.g., showing that abundances for ions with higher ionization energy are more strongly determined by the simulation’s metallicity, while abundances for ions with lower ionization energy are more strongly determined by the gas density and temperature.
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| 9. |
- Cho, Hyunsoo, et al.
(författare)
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YAP and TAZ Negatively Regulate Prox1 During Developmental and Pathologic Lymphangiogenesis
- 2019
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Ingår i: Circulation Research. - : Lippincott Williams & Wilkins. - 0009-7330 .- 1524-4571. ; 124:2, s. 225-242
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Tidskriftsartikel (refereegranskat)abstract
- Rationale: The Hippo pathway governs cellular differentiation, morphogenesis, and homeostasis, but how it regulates these processes in lymphatic vessels is unknown. Objective: We aimed to reveal the role of the final effectors of the Hippo pathway, YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif), in lymphatic endothelial cell (LEC) differentiation, morphogenesis, and homeostasis. Methods and Results: During mouse embryonic development, LEC-specific depletion of Yap/Taz disturbed both plexus patterning and valve initiation with upregulated Prox1 (prospero homeobox 1). Conversely, LEC-specific YAP/TAZ hyperactivation impaired lymphatic specification and restricted lymphatic sprouting with profoundly downregulated Prox1. Notably, lymphatic YAP/TAZ depletion or hyperactivation aggravated or attenuated pathological lymphangiogenesis in mouse cornea. Mechanistically, VEGF (vascular endothelial growth factor)-C activated canonical Hippo signaling pathway in LECs. Indeed, repression of PROX1 transcription by YAP/TAZ hyperactivation was mediated by recruitment of NuRD (nucleosome remodeling and histone deacetylase) complex and endogenous binding activity of TEAD (TEA domain family members) to the PROX1 promoter. Furthermore, YAP/TAZ hyperactivation enhanced MYC signaling and inhibited CDKN1C, leading to cell cycle dysregulation and aberrant proliferation. Conclusions: We find that YAP and TAZ play promoting roles in remodeling lymphatic plexus patterning and postnatal lymphatic valve maintenance by negatively regulating Prox1 expression. We further show that YAP and TAZ act as plastic regulators of lymphatic identity and define the Hippo signaling-mediated PROX1 transcriptional programing as a novel dynamic checkpoint underlying LEC plasticity and pathophysiology.
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| 10. |
- Hosseini, Seyed Mehdi, et al.
(författare)
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Lipase-immobilized chitosan-crosslinked magnetic nanoparticle as a biocatalyst for ring opening esterification of itaconic anhydride
- 2019
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Ingår i: Biochemical Engineering Journal. - : Elsevier BV. - 1369-703X. ; 143, s. 141-150
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Tidskriftsartikel (refereegranskat)abstract
- Nano-magnetic biocatalyst particles, lipase-immobilized chitosan-crosslinked magnetic nanoparticles (LCMNs) were prepared by a new approach integrated from magnetic nanoparticle preparation, in situ thin layer coating and crosslinking of chitosan, and enzyme immobilization method. Thin layer coating of magnetic (Fe3O4) by crosslinked chitosan nanoparticles were prepared by reacting FeCl3.6H2O and sodium acetate in ethylene glycol, followed by suspension cross-linking using citric acid on the hydroxyl and amine group of chitosan at neutral pH. The resulting nanoparticles were used to immobilize the lipase from Candida antarctica Lipase B by linking using glutaraldehyde. The particles in each step were characterized by Fourier transform infrared spectrometry (FT-IR), vibrating-sample magnetometer measurements (VSM), and transmission electron microscopy (TEM). The magnetic biocatalyst, LCMN was found to have high storage stability and reusability due to the tightly crosslinked structure of chitosan and covalent bond immobilization. LCMNs were used for the oligomerization of itaconic anhydride by ring opening esterification, and the results were compared with those from free lipase and commercial immobilized lipase. The molecular mass of the products obtained with the biocatalysts showed similar Mn profiles with 308–381. This process represents a green approach for the preparation of both biobased magnetic biocatalysts and functional oligo-esters, and can be applied for both the immobilization of other enzymes and the utilization of photo-curable functional esters as biobased functional materials.
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| 11. |
- Huang, Tzu-Hao, et al.
(författare)
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Separating Si phases from diagenetically-modified sediments through sequential leaching.
- 2023
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Ingår i: Chemical Geology. - 0009-2541 .- 1872-6836.
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Tidskriftsartikel (refereegranskat)abstract
- Silicon (Si) phases such as biogenic silica, lithogenic silicate and authigenic silica/silicate in marine sediments provide valuable information about past Si cycling. Wet-chemical sequential leaching methods are often applied to extract different Si phases from marine sediments to study Si diagenetic processes in shallow subsurface. The potential of this method to separate Si phases from deeply-buried and diagenetically-modified sediments has not been systematically examined. We applied a sequential leaching protocol to drill core sediments retrieved from the Ulleung Basin, East/Japan Sea. We performed geochemical (elemental abundance and stable Si isotopes, δ30Si) and microscopic (X-ray diffraction and scanning electron microscope) analyses to monitor leaching efficiency in separating different Si phases. We show that, prior to alkaline leaching, applying weak acid is able to remove metal oxide and/or clay-like phases. The following Na2CO3 leaching, based on a commonly-adopted protocol, is able to dissolve some but not all diatoms. The results of elemental contents and δ30Si values of leachates suggest that, in diagenetically-modified sediments, either a longer digesting time or a harsher alkaline leaching is needed to dissolve all diatoms. This is attributed to increased resistance of diatoms to Na2CO3 leaching as a result of reduced surface area and/or improved SiO2 tetrahedron ordering during diagenetic processes over time and burial depths. Lithogenic silicate minerals can be dissolved by NaOH and potentially separated from diatoms if the latter is completely removed in the preceding leaching steps. Even if a trace amount of diatom is left undissolved in the NaOH leaching, it is still possible to separate the two through a mass balance calculation given the knowledge of composition for the two end-members. We conclude that a successful separation of Si phases in diagenetically modified sediments relies on the knowledge of elemental abundance and even δ30Si values of the leachates, as well as information such as species of Si-skeleton organisms, contents and maturation degree of biogenic silica.
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| 12. |
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| 13. |
- Kim, HoUng, et al.
(författare)
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The Future of Biosimilars : Maximizing Benefits Across Immune-Mediated Inflammatory Diseases
- 2020
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Ingår i: Drugs. - : Adis International. - 0012-6667 .- 1179-1950. ; 80:2, s. 99-113
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Tidskriftsartikel (refereegranskat)abstract
- Biologics have transformed the treatment of immune-mediated inflammatory diseases such as rheumatoid arthritis (RA) and inflammatory bowel disease (IBD). Biosimilars-biologic medicines with no clinically meaningful differences in safety or efficacy from licensed originators-can stimulate market competition and have the potential to expand patient access to biologics within the parameters of treatment recommendations. However, maximizing the benefits of biosimilars requires cooperation between multiple stakeholders. Regulators and developers should collaborate to ensure biosimilars reach patients rapidly without compromising stringent quality, safety, or efficacy standards. Pharmacoeconomic evaluations and payer policies should be updated following biosimilar market entry, minimizing the risk of imposing nonmedical barriers to biologic treatment. In RA, disparities between treatment guidelines and national reimbursement criteria could be addressed to ensure more uniform patient access to biologics and enable rheumatologists to effectively implement treat-to-target strategies. In IBD, the cost-effectiveness of biologic treatment earlier in the disease course is likely to improve when biosimilars are incorporated into pharmacoeconomic analyses. Patient understanding of biosimilars is crucial for treatment success and avoiding nocebo effects. Full understanding of biosimilars by physicians and carefully considered communication strategies can help support patients initiating or switching to biosimilars. Developers must operate efficiently to be sustainable, without undermining product quality, the reliability of the supply chain, or pharmacovigilance. Developers should also facilitate information sharing to meet the needs of other stakeholders. Such collaboration will help to ensure a sustainable future for both the biosimilar market and healthcare systems, supporting the availability of effective treatments for patients.
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| 14. |
- Kim, Hae Young, et al.
(författare)
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CT in Differentiating Complicated From Uncomplicated Appendicitis: Presence of Any of 10 CT Features Versus Radiologists Gestalt Assessment
- 2019
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Ingår i: American Journal of Roentgenology. - : AMER ROENTGEN RAY SOC. - 0361-803X .- 1546-3141. ; 213:5, s. W218-W226
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE. The purpose of this study is to propose a sensitive CT criterion (the presence of any of 10 CT features) for complicated appendicitis that could be used in the nonoperative management of appendicitis and to compare the diagnostic performance of this sensitive CT criterion with that of gestalt assessment. MATERIALS AND METHODS. This retrospective study, which was conducted in a tertiary teaching hospital, included 100 patients with suspected appendicitis on CT. Complicated appendicitis, defined as gangrenous or perforated appendicitis, was pathologically or surgically confirmed in 32 patients. Six radiologists independently determined the presence of 10 previously reported CT features of complicated appendicitis (contrast enhancement defect of the appendiceal wall, abscess, extraluminal air, intraluminal air, extraluminal appendicolith, intraluminal appendicolith, moderate-to-severe periappendiceal fat stranding, periappendiceal fluid, ileus, and ascites) and rated the likelihood score for complicated appendicitis using gestalt assessment. The sensitivity and specificity of CT for complicated appendicitis were measured by the presence of any of 10 CT features (the any-of-10-features criterion) and by the radiologists gestalt assessment. Pooled sensitivity and specificity were compared using a generalized linear mixed model. RESULTS. The pooled sensitivity of the presence of any of 10 CT features was higher than that of gestalt assessment (92% vs 64%; difference, 28% [95% CI, 10-46%]; p amp;lt; 0.001), although the pooled specificity was lower (43% vs 76%; difference, -33% [95% CI, -48% to -17%]; p amp;lt; 0.001). CONCLUSION. The pooled sensitivity of the presence of any of 10 CT features was higher than that of gestalt assessment, at the cost of lower specificity. For prudent selection of patients who should receive nonoperative treatment of appendicitis, the any-of-10-features criterion may be used to decrease treatment failure associated with a false-negative diagnosis of complication.
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| 15. |
- Kim, Ji-Hoon, et al.
(författare)
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A Pulse of Meteoric Subsurface Fluid Discharging Into the Chukchi Sea During the Early Holocene Thermal Maximum (EHTM)
- 2021
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Ingår i: Geochemistry Geophysics Geosystems. - 1525-2027. ; 22:8
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Tidskriftsartikel (refereegranskat)abstract
- The response of Arctic Ocean biogeochemistry to subsurface flow driven by permafrost thaw is poorly understood. We present dissolved chloride and water isotopic data from the Chukchi Sea Shelf sediments that reveal the presence of a meteoric subsurface flow enriched in cations with a radiogenic Sr fingerprint. This subsurface fluid is also enriched in dissolved inorganic carbon and methane that bear isotopic compositions indicative of a carbon reservoir modified by reactions in a closed system. Such fluid characteristics are in stark contrast with those from other sites in the Chukchi Sea where the pore water composition shows no sign of meteoric input, but reflect typical biogeochemical reactions associated with early diagenetic sequences in marine sediment. The most likely source of the observed subsurface flow at the Chukchi Sea Shelf is from the degradation of permafrost that had extended to the shelf region during the Last Glacial Maximum. Our data suggest that the permafrost-driven subsurface flow most likely took place during the 2-3 degrees C warming in the Early Holocene Thermal Maximum. This time scale is supported by numerical simulation of pore water profiles, which indicate that a minimum of several thousand years must have passed since the cessation of the subsurface methane-bearing fluid flow.
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| 16. |
- Kim, Ji Hoon, et al.
(författare)
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THE AGORA HIGH-RESOLUTION GALAXY SIMULATIONS COMPARISON PROJECT. II. ISOLATED DISK TEST
- 2016
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 833:2
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Tidskriftsartikel (refereegranskat)abstract
- Using an isolated Milky Way-mass galaxy simulation, we compare results from nine state-of-the-art gravito-hydrodynamics codes widely used in the numerical community. We utilize the infrastructure we have built for the AGORA High-resolution Galaxy Simulations Comparison Project. This includes the common disk initial conditions, common physics models (e.g., radiative cooling and UV background by the standardized package Grackle) and common analysis toolkit yt, all of which are publicly available. Subgrid physics models such as Jeans pressure floor, star formation, supernova feedback energy, and metal production are carefully constrained across code platforms. With numerical accuracy that resolves the disk scale height, we find that the codes overall agree well with one another in many dimensions including: gas and stellar surface densities, rotation curves, velocity dispersions, density and temperature distribution functions, disk vertical heights, stellar clumps, star formation rates, and Kennicutt-Schmidt relations. Quantities such as velocity dispersions are very robust (agreement within a few tens of percent at all radii) while measures like newly formed stellar clump mass functions show more significant variation (difference by up to a factor of ∼3). Systematic differences exist, for example, between mesh-based and particle-based codes in the low-density region, and between more diffusive and less diffusive schemes in the high-density tail of the density distribution. Yet intrinsic code differences are generally small compared to the variations in numerical implementations of the common subgrid physics such as supernova feedback. Our experiment reassures that, if adequately designed in accordance with our proposed common parameters, results of a modern high-resolution galaxy formation simulation are more sensitive to input physics than to intrinsic differences in numerical schemes.
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| 17. |
- Kim, Ye-Jin, et al.
(författare)
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Femtosecond-resolved imaging of a single-particle phase transition in energy-filtered ultrafast electron microscopy
- 2023
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Using an energy filter in transmission electron microscopy has enabled elemental mapping at the atomic scale and improved the precision of structural determination by gating inelastic and elastic imaging electrons, respec-tively. Here, we use an energy filter in ultrafast electron microscopy to enhance the temporal resolution toward the domain of atomic motion. Visualizing transient structures with femtosecond temporal precision was achieved by selecting imaging electrons in a narrow energy distribution from dense chirped photoelectron packets with broad longitudinal momentum distributions and thus typically exhibiting picosecond durations. In this study, the heterogeneous ultrafast phase transitions of vanadium dioxide (VO2) nanoparticles, a repre-sentative strongly correlated system, were filmed and attributed to the emergence of a transient, low-symmetry metallic phase caused by different local strains. Our approach enables electron microscopy to access the time scale of elementary nuclear motion to visualize the onset of the structural dynamics of matter at the nanoscale.
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| 18. |
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| 19. |
- Li (李嘉轩), Jiaxuan, et al.
(författare)
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Beyond Ultra-diffuse Galaxies. I. Mass–Size Outliers among the Satellites of Milky Way Analogs
- 2023
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 955:1
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Tidskriftsartikel (refereegranskat)abstract
- Large diffuse galaxies are hard to find, but understanding the environments where they live, their numbers, and ultimately their origins, is of intense interest and importance for galaxy formation and evolution. Using Subaru's Hyper Suprime-Cam Strategic Survey Program, we perform a systematic search for low surface brightness galaxies and present novel and effective methods for detecting and modeling them. As a case study, we surveyed 922 Milky Way analogs in the nearby Universe (0.01 < z < 0.04) and built a large sample of satellite galaxies that are outliers in the mass–size relation. These "ultra-puffy" galaxies (UPGs), defined to be 1.5σ above the average mass–size relation, represent the tail of the satellite size distribution. We find that each MW analog hosts NUPG = 0.31 ± 0.05 UPGs on average, which is consistent with but slightly lower than the observed abundance at this halo mass in the Local Volume. We also construct a sample of ultra-diffuse galaxies (UDGs) in MW analogs and find an abundance of NUDG = 0.44 ± 0.05 per host. With literature results, we confirm that the UDG abundance scales with the host halo mass following a sublinear power law. We argue that our definition of UPGs, which is based on the mass–size relation, is more physically motivated than the common definition of UDGs, which depends on the surface brightness and size cuts and thus yields different surface mass density cuts for quenched and star-forming galaxies.
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| 20. |
- Pajarillo, Edward Alain B., et al.
(författare)
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Proteomic View of the Crosstalk between Lactobacillus mucosae and Intestinal Epithelial Cells in Co-culture Revealed by Q Exactive-Based Quantitative Proteomics
- 2017
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Lactobacilli are bacteria that are beneficial to host health, but information on communication between Lactobacilli and host cells in the intestine is lacking. In this study, we examined the proteomes of the Lactobacillus mucosae strain LM1, as a model of beneficial bacteria, and the intestinal porcine epithelial cell line (IPEC-J2) after co-culture. Label-free proteomics demonstrated the high-throughput capability of the technique, and robust characterization of the functional profiles and changes in the bacteria and intestinal cells was achieved in pure and mixed cultures. After co-culture, we identified totals of 376 and 653 differentially expressed proteins in the LM1 and IPEC-J2 proteomes, respectively. The major proteomic changes in the LM1 strain occurred in the functional categories of transcription, general function, and translation, whereas those in IPEC-J2 cells involved metabolic and cellular processes, and cellular component organization/biogenesis. Among them, elongation factor Tu, glyceraldehyde 3-phosphate dehydrogenase, and phosphocarrier protein HPr, which are known to be involved in bacterial adhesion, were upregulated in LM1. In contrast, proteins involved in tight junction assembly, actin organization, and genetic information processing (i.e., histones and signaling pathways) were significantly upregulated in IPEC-J2 cells. Furthermore, we identified functional pathways that are possibly involved in host–microbe crosstalk and response. These findings will provide novel insights into host–bacteria communication and the molecular mechanism of probiotic establishment in the intestine.
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| 21. |
- Pajarillo, Edward Alain, et al.
(författare)
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Quantitative Proteogenomics and the Reconstruction of the Metabolic Pathway in Lactobacillus mucosae LM1
- 2015
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Ingår i: Hangug chugsan sigpum haghoeji = Korean journal for food science of animal resources. - : Korean Society for Food Science of Animal Resources. - 1225-8563 .- 2234-246X. ; 35:5, s. 692-702
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Tidskriftsartikel (refereegranskat)abstract
- Lactobacillus mucosae is a natural resident of the gastrointestinal tract of humans and animals and a potential probiotic bacterium. To understand the global protein expression profile and metabolic features of L. mucosae LM1 in the early stationary phase, the QExactive™ Hybrid Quadrupole-Orbitrap Mass Spectrometer was used. Characterization of the intracellular proteome identified 842 proteins, accounting for approximately 35% of the 2,404 protein-coding sequences in the complete genome of L. mucosae LM1. Proteome quantification using QExactive™ Orbitrap MS detected 19 highly abundant proteins (> 1.0% of the intracellular proteome), including CysK (cysteine synthase, 5.41%) and EF-Tu (elongation factor Tu, 4.91%), which are involved in cell survival against environmental stresses. Metabolic pathway annotation of LM1 proteome using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database showed that half of the proteins expressed are important for basic metabolic and biosynthetic processes, and the other half might be structurally important or involved in basic cellular processes. In addition, glycogen biosynthesis was activated in the early stationary phase, which is important for energy storage and maintenance. The proteogenomic data presented in this study provide a suitable reference to understand the protein expression pattern of lactobacilli in standard conditions.
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| 22. |
- Park, Kwang-Hyun, et al.
(författare)
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RNA activation-independent DNA targeting of the Type III CRISPR-Cas system by a Csm complex
- 2017
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Ingår i: EMBO Reports. - : Wiley-VCH Verlagsgesellschaft. - 1469-221X .- 1469-3178. ; 18:5, s. 826-840
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Tidskriftsartikel (refereegranskat)abstract
- The CRISPR-Cas system is an adaptive and heritable immune response that destroys invading foreign nucleic acids. The effector complex of the Type III CRISPR-Cas system targets RNA and DNA in a transcription-coupled manner, but the exact mechanism of DNA targeting by this complex remains elusive. In this study, an effector Csm holocomplex derived from Thermococcus onnurineus is reconstituted with a minimalistic combination of Csm1(1)2(1)3(3)4(1)5(1), and shows RNA targeting and RNA-activated single-stranded DNA (ssDNA) targeting activities. Unexpectedly, in the absence of an RNA transcript, it cleaves ssDNA containing a sequence complementary to the bound crRNA guide region in a manner dependent on the HD domain of the Csm1 subunit. This nuclease activity is blocked by a repeat tag found in the host CRISPR loci. The specific cleavage of ssDNA without a target RNA suggests a novel ssDNA targeting mechanism of the Type III system, which could facilitate the efficient and complete degradation of foreign nucleic acids.
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