7251
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Aspers P, Bengtsson P, Dobeson A. Market Fashioning. THEORY AND SOCIETY 2020; 49:417-438. [PMID: 32624636 PMCID: PMC7319428 DOI: 10.1007/s11186-020-09379-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
How do markets come about? This article offers a first systematic analysis of three different ideal types of market fashioning: mutual adjustment, organization, and fields. Although aspects of these are identifiable in most empirical markets, these three ideal types provide analytic tools for students of real markets and marketplaces. After going through this comprehensive literature, it is argued that mutual adjustment, which refers to non-planned processes, is affinity with markets in which products are differentiated, for example, producer markets. Organization refers to process driven by attempts to decide for others and shows affinity with markets for standardized and homogenous products, for example, stock exchanges. Organization also accounts for the making of marketplaces. The broader notion of fields does not refer to any specific process, but accounts for the context of market fashioning and its respective power struggles.
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7252
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De Saegher T, Lauwaert J, Hanssen J, Bruneel E, Van Zele M, Van Geem K, De Buysser K, Verberckmoes A. Monometallic Cerium Layered Double Hydroxide Supported Pd-Ni Nanoparticles as High Performance Catalysts for Lignin Hydrogenolysis. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E691. [PMID: 32033090 PMCID: PMC7040693 DOI: 10.3390/ma13030691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/29/2020] [Accepted: 02/01/2020] [Indexed: 02/03/2023]
Abstract
Monometallic cerium layered double hydroxides (Ce-LDH) supports were successfully synthesized by a homogeneous alkalization route driven by hexamethylenetetramine (HMT). The formation of the Ce-LDH was confirmed and its structural and compositional properties studied by XRD, SEM, XPS, iodometric analyses and TGA. HT-XRD, N2-sorption and XRF analyses revealed that by increasing the calcination temperature from 200 to 800 °C, the Ce-LDH material transforms to ceria (CeO2) in four distinct phases, i.e., the loss of intramolecular water, dehydroxylation, removal of nitrate groups and removal of sulfate groups. When loaded with 2.5 wt% palladium (Pd) and 2.5 wt% nickel (Ni) and calcined at 500 °C, the PdNi-Ce-LDH-derived catalysts strongly outperform the PdNi-CeO2 benchmark catalyst in terms of conversion as well as selectivity for the hydrogenolysis of benzyl phenyl ether (BPE), a model compound for the α-O-4 ether linkage in lignin. The PdNi-Ce-LDH catalysts showed full selectivity towards phenol and toluene while the PdNi-CeO2 catalysts showed additional oxidation of toluene to benzoic acid. The highest BPE conversion was observed with the PdNi-Ce-LDH catalyst calcined at 600 °C, which could be related to an optimum in morphological and compositional characteristics of the support.
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7253
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Mastrucci A, Min J, Usubiaga-Liaño A, Rao ND. A Framework for Modelling Consumption-Based Energy Demand and Emission Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1799-1807. [PMID: 31909605 DOI: 10.1021/acs.est.9b05968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Energy demand in global climate scenarios is typically derived for sectors - such as buildings, transportation, and industry - rather than from underlying services that could drive energy use in all sectors. This limits the potential to model household consumption and lifestyles as mitigation options through their impact on economy-wide energy demand. We present a framework to estimate the economy-wide energy requirements and carbon emissions associated with future household consumption, by linking Industrial Ecology tools and Integrated Assessment Models (IAM). We apply the framework to assess final energy and emission pathways for meeting three essential and energy-intensive dimensions of basic well-being in India: food, housing and mobility. We show, for example, that nutrition-enhancing dietary changes can reduce emissions by a similar amount as meeting future basic mobility in Indian cities with public transportation. The relative impact of energy demand reduction measures compared to decarbonization differs across these services, with housing having the lowest and food the highest. This framework provides complementary insights to those obtained from IAM by considering a broader set of consumption and well-being-related interventions, and illustrating trade-offs between demand and supply-side options in climate stabilization scenarios.
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7254
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Hewitt LM, Roy JW, Rowland SJ, Bickerton G, DeSilva A, Headley JV, Milestone CB, Scarlett AG, Brown S, Spencer C, West CE, Peru KM, Grapentine L, Ahad JM, Pakdel H, Frank RA. Advances in Distinguishing Groundwater Influenced by Oil Sands Process-Affected Water (OSPW) from Natural Bitumen-Influenced Groundwaters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1522-1532. [PMID: 31906621 PMCID: PMC7003248 DOI: 10.1021/acs.est.9b05040] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 05/22/2023]
Abstract
The objective of this study was to advance analytical methods for detecting oil sands process-affected water (OSPW) seepage from mining containments and discriminating any such seepage from the natural bitumen background in groundwaters influenced by the Alberta McMurray formation. Improved sampling methods and quantitative analyses of two groups of monoaromatic acids were employed to analyze OSPW and bitumen-affected natural background groundwaters for source discrimination. Both groups of monoaromatic acids showed significant enrichment in OSPW, while ratios of O2/O4 containing heteroatomic ion classes of acid extractable organics (AEOs) did not exhibit diagnostic differences. Evaluating the monoaromatic acids to track a known plume of OSPW-affected groundwater confirmed their diagnostic abilities. A secondary objective was to assess anthropogenically derived artificial sweeteners and per- and polyfluoroalkyl substances (PFAS) as potential tracers for OSPW. Despite the discovery of acesulfame and PFAS in most OSPW samples, trace levels in groundwaters influenced by general anthropogenic activities preclude them as individual robust tracers. However, their inclusion with the other metrics employed in this study served to augment the tiered, weight of evidence methodology developed. This methodology was then used to confirm earlier findings of OSPW migrations into groundwater reaching the Athabasca River system adjacent to the reclaimed pond at Tar Island Dyke.
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7255
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Abstract
Regulatory landscapes have been defined in vertebrates as large DNA segments containing diverse enhancer sequences that produce coherent gene transcription. These genomic platforms integrate multiple cellular signals and hence can trigger pleiotropic expression of developmental genes. Identifying and evaluating how these chromatin regions operate may be difficult as the underlying regulatory mechanisms can be as unique as the genes they control. In this brief article and accompanying poster, we discuss some of the ways in which regulatory landscapes operate, illustrating these mechanisms using genes important for vertebrate development as examples. We also highlight some of the techniques available to researchers for analysing regulatory landscapes.
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7256
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Ferdous MR, Di Baldassarre G, Brandimarte L, Wesselink A. The interplay between structural flood protection, population density, and flood mortality along the Jamuna River, Bangladesh. REGIONAL ENVIRONMENTAL CHANGE 2020; 20:5. [PMID: 32089642 PMCID: PMC6997260 DOI: 10.1007/s10113-020-01600-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
Levees protect floodplain areas from frequent flooding, but they can paradoxically contribute to more severe flood losses. The construction or reinforcement of levees can attract more assets and people in flood-prone area, thereby increasing the potential flood damage when levees eventually fail. Moreover, structural protection measures can generate a sense of complacency, which can reduce preparedness, thereby increasing flood mortality rates. We explore these phenomena in the Jamuna River floodplain in Bangladesh. In this study area, different levels of flood protection have co-existed alongside each other since the 1960s, with a levee being constructed only on the right bank and its maintenance being assured only in certain places. Primary and secondary data on population density, human settlements, and flood fatalities were collected to carry out a comparative analysis of two urban areas and two rural areas with different flood protection levels. We found that the higher the level of flood protection, the higher the increase of population density over the past decades as well as the number of assets exposed to flooding. Our results also show that flood mortality rates associated with the 2017 flooding in Bangladesh were lower in the areas with lower protection level. This empirical analysis of the unintended consequences of structural flood protection is relevant for the making of sustainable policies of disaster risk reduction and adaptation to climate change in rapidly changing environments.
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7257
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Garita-Hernandez M, Routet F, Guibbal L, Khabou H, Toualbi L, Riancho L, Reichman S, Duebel J, Sahel JA, Goureau O, Dalkara D. AAV-Mediated Gene Delivery to 3D Retinal Organoids Derived from Human Induced Pluripotent Stem Cells. Int J Mol Sci 2020; 21:ijms21030994. [PMID: 32028585 PMCID: PMC7036814 DOI: 10.3390/ijms21030994] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 01/01/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) promise a great number of future applications to investigate retinal development, pathophysiology and cell therapies for retinal degenerative diseases. Specific approaches to genetically modulate hiPSC would be valuable for all of these applications. Vectors based on adeno-associated virus (AAV) have shown the ability for gene delivery to retinal organoids derived from hiPSCs. Thus far, little work has been carried out to investigate mechanisms of AAV-mediated gene delivery and the potential advantages of engineered AAVs to genetically modify retinal organoids. In this study, we compared the early transduction efficiency of several recombinant and engineered AAVs in hiPSC-derived RPE cells and retinal organoids in relation to the availability of their cell-surface receptors and as a function of time. The genetic variant AAV2-7m8 had a superior transduction efficiency when applied at day 44 of differentiation on retinal organoids and provided long-lasting expressions for at least 4 weeks after infection without compromising cell viability. All of the capsids we tested transduced the hiPSC-RPE cells, with the AAV2-7m8 variant being the most efficient. Transduction efficiency was correlated with the presence of primary cell-surface receptors on the hiPS-derived organoids. Our study explores some of the mechanisms of cell attachment of AAVs and reports long-term gene expression resulting from gene delivery in retinal organoids.
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7258
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Schaefer GO. Context is Needed When Assessing Fair Subject Selection. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2020; 20:20-22. [PMID: 31990254 DOI: 10.1080/15265161.2019.1701742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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7259
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Sunko V, Mazzola F, Kitamura S, Khim S, Kushwaha P, Clark OJ, Watson MD, Marković I, Biswas D, Pourovskii L, Kim TK, Lee TL, Thakur PK, Rosner H, Georges A, Moessner R, Oka T, Mackenzie AP, King PDC. Probing spin correlations using angle-resolved photoemission in a coupled metallic/Mott insulator system. SCIENCE ADVANCES 2020; 6:eaaz0611. [PMID: 32128385 PMCID: PMC7032925 DOI: 10.1126/sciadv.aaz0611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
A nearly free electron metal and a Mott insulating state can be thought of as opposite ends of the spectrum of possibilities for the motion of electrons in a solid. Understanding their interaction lies at the heart of the correlated electron problem. In the magnetic oxide metal PdCrO2, nearly free and Mott-localized electrons exist in alternating layers, forming natural heterostructures. Using angle-resolved photoemission spectroscopy, quantitatively supported by a strong coupling analysis, we show that the coupling between these layers leads to an "intertwined" excitation that is a convolution of the charge spectrum of the metallic layer and the spin susceptibility of the Mott layer. Our findings establish PdCrO2 as a model system in which to probe Kondo lattice physics and also open new routes to use the a priori nonmagnetic probe of photoemission to gain insights into the spin susceptibility of correlated electron materials.
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7260
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Li Y, Haarhuis JHI, Sedeño Cacciatore Á, Oldenkamp R, van Ruiten MS, Willems L, Teunissen H, Muir KW, de Wit E, Rowland BD, Panne D. The structural basis for cohesin-CTCF-anchored loops. Nature 2020; 578:472-476. [PMID: 31905366 PMCID: PMC7035113 DOI: 10.1038/s41586-019-1910-z] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022]
Abstract
Cohesin catalyses the folding of the genome into loops that are anchored by CTCF1. The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of human cohesin. We report a crystal structure of SA2-SCC1 in complex with CTCF at a resolution of 2.7 Å, which reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF binding sites. A similar motif is present in a number of established and newly identified cohesin ligands, including the cohesin release factor WAPL2,3. Our data suggest that CTCF enables the formation of chromatin loops by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables the dynamic regulation of chromatin folding by cohesin and CTCF.
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7261
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Rezzoagli C, Granato ET, Kümmerli R. Harnessing bacterial interactions to manage infections: a review on the opportunistic pathogen Pseudomonas aeruginosa as a case example. J Med Microbiol 2020; 69:147-161. [PMID: 31961787 PMCID: PMC7116537 DOI: 10.1099/jmm.0.001134] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During infections, bacterial pathogens can engage in a variety of interactions with each other, ranging from the cooperative sharing of resources to deadly warfare. This is especially relevant in opportunistic infections, where different strains and species often co-infect the same patient and interact in the host. Here, we review the relevance of these social interactions during opportunistic infections using the human pathogen Pseudomonas aeruginosa as a case example. In particular, we discuss different types of pathogen-pathogen interactions, involving both cooperation and competition, and elaborate on how they impact virulence in multi-strain and multi-species infections. We then review evolutionary dynamics within pathogen populations during chronic infections. We particuarly discuss how local adaptation through niche separation, evolutionary successions and antagonistic co-evolution between pathogens can alter virulence and the damage inflicted on the host. Finally, we outline how studying bacterial social dynamics could be used to manage infections. We show that a deeper appreciation of bacterial evolution and ecology in the clinical context is important for understanding microbial infections and can inspire novel treatment strategies.
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7262
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Gaspar VM, Lavrador P, Borges J, Oliveira MB, Mano JF. Advanced Bottom-Up Engineering of Living Architectures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1903975. [PMID: 31823448 DOI: 10.1002/adma.201903975] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/30/2019] [Indexed: 05/08/2023]
Abstract
Bottom-up tissue engineering is a promising approach for designing modular biomimetic structures that aim to recapitulate the intricate hierarchy and biofunctionality of native human tissues. In recent years, this field has seen exciting progress driven by an increasing knowledge of biological systems and their rational deconstruction into key core components. Relevant advances in the bottom-up assembly of unitary living blocks toward the creation of higher order bioarchitectures based on multicellular-rich structures or multicomponent cell-biomaterial synergies are described. An up-to-date critical overview of long-term existing and rapidly emerging technologies for integrative bottom-up tissue engineering is provided, including discussion of their practical challenges and required advances. It is envisioned that a combination of cell-biomaterial constructs with bioadaptable features and biospecific 3D designs will contribute to the development of more robust and functional humanized tissues for therapies and disease models, as well as tools for fundamental biological studies.
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7263
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Loetgering L, Baluktsian M, Keskinbora K, Horstmeyer R, Wilhein T, Schütz G, Eikema KSE, Witte S. Generation and characterization of focused helical x-ray beams. SCIENCE ADVANCES 2020; 6:eaax8836. [PMID: 32110725 PMCID: PMC7021491 DOI: 10.1126/sciadv.aax8836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/26/2019] [Indexed: 05/06/2023]
Abstract
The phenomenon of orbital angular momentum (OAM) affects a variety of important applications in visible optics, including optical tweezers, free-space communication, and 3D localization for fluorescence imaging. The lack of suitable wavefront shaping optics such as spatial light modulators has inhibited the ability to impart OAM on x-ray and electron radiation in a controlled way. Here, we report the experimental observation of helical soft x-ray beams generated by holographically designed diffractive optical elements. We demonstrate that these beams rotate as a function of propagation distance and measure their vorticity and coherent mode structure using ptychography. Our results establish an approach for controlling and shaping of complex focused beams for short wavelength scanning microscopy and OAM-driven applications.
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7264
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Seoane PI, Taylor-Smith LM, Stirling D, Bell LCK, Noursadeghi M, Bailey D, May RC. Viral infection triggers interferon-induced expulsion of live Cryptococcus neoformans by macrophages. PLoS Pathog 2020; 16:e1008240. [PMID: 32106253 PMCID: PMC7046190 DOI: 10.1371/journal.ppat.1008240] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/25/2019] [Indexed: 11/19/2022] Open
Abstract
Cryptococcus neoformans is an opportunistic human pathogen, which causes serious disease in immunocompromised hosts. Infection with this pathogen is particularly relevant in HIV+ patients, where it leads to around 200,000 deaths per annum. A key feature of cryptococcal pathogenesis is the ability of the fungus to survive and replicate within the phagosome of macrophages, as well as its ability to be expelled from host cells via a novel non-lytic mechanism known as vomocytosis. Here we show that cryptococcal vomocytosis from macrophages is strongly enhanced by viral coinfection, without altering phagocytosis or intracellular proliferation of the fungus. This effect occurs with distinct, unrelated human viral pathogens and is recapitulated when macrophages are stimulated with the anti-viral cytokines interferon alpha or beta (IFNα or IFNβ). Importantly, the effect is abrogated when type-I interferon signalling is blocked, thus underscoring the importance of type-I interferons in this phenomenon. Lastly, our data help resolve previous, contradictory animal studies on the impact of type I interferons on cryptococcal pathogenesis and suggest that secondary viral stimuli may alter patterns of cryptococcal dissemination in the host.
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7265
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Aceto N. Bring along your friends: Homotypic and heterotypic circulating tumor cell clustering to accelerate metastasis. Biomed J 2020; 43:18-23. [PMID: 32200952 PMCID: PMC7090281 DOI: 10.1016/j.bj.2019.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 11/23/2022] Open
Abstract
Metastasis formation is a hallmark of invasive cancers and it is achieved through the shedding of circulating tumor cells (CTCs) from the primary site into the blood circulation. There, CTCs are found as single cells or as multicellular clusters, with clusters carrying an elevated ability to survive within the bloodstream and initiate new metastatic lesions at distant sites. Clusters of CTCs include homotypic clusters made of cancer cells only, as well as heterotypic clusters that incorporate stromal or immune cells along with cancer cells. Both homotypic and heterotypic CTC clusters are characterized by a high metastasis-forming capability, high proliferation rate and by distinct molecular features compared to single CTCs, and their presence in the peripheral circulation of cancer patients is generally associated with a poor prognosis. In this short review, we summarize the current literature that describes homotypic and heterotypic CTC clusters, both in the context of their molecular characteristics as well as their value in the clinical setting. While CTC clusters have only recently emerged as key players in the metastatic process and many aspects of their biology remain to be investigated, a detailed understanding of their vulnerabilities may pave the way towards the generation of new metastasis-suppressing agents.
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7266
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Le Möel F, Wystrach A. Opponent processes in visual memories: A model of attraction and repulsion in navigating insects' mushroom bodies. PLoS Comput Biol 2020; 16:e1007631. [PMID: 32023241 PMCID: PMC7034919 DOI: 10.1371/journal.pcbi.1007631] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 02/21/2020] [Accepted: 01/04/2020] [Indexed: 11/19/2022] Open
Abstract
Solitary foraging insects display stunning navigational behaviours in visually complex natural environments. Current literature assumes that these insects are mostly driven by attractive visual memories, which are learnt when the insect's gaze is precisely oriented toward the goal direction, typically along its familiar route or towards its nest. That way, an insect could return home by simply moving in the direction that appears most familiar. Here we show using virtual reconstructions of natural environments that this principle suffers from fundamental drawbacks, notably, a given view of the world does not provide information about whether the agent should turn or not to reach its goal. We propose a simple model where the agent continuously compares its current view with both goal and anti-goal visual memories, which are treated as attractive and repulsive respectively. We show that this strategy effectively results in an opponent process, albeit not at the perceptual level-such as those proposed for colour vision or polarisation detection-but at the level of the environmental space. This opponent process results in a signal that strongly correlates with the angular error of the current body orientation so that a single view of the world now suffices to indicate whether the agent should turn or not. By incorporating this principle into a simple agent navigating in reconstructed natural environments, we show that it overcomes the usual shortcomings and produces a step-increase in navigation effectiveness and robustness. Our findings provide a functional explanation to recent behavioural observations in ants and why and how so-called aversive and appetitive memories must be combined. We propose a likely neural implementation based on insects' mushroom bodies' circuitry that produces behavioural and neural predictions contrasting with previous models.
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7267
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Le P, Kunold E, Macsics R, Rox K, Jennings MC, Ugur I, Reinecke M, Chaves-Moreno D, Hackl MW, Fetzer C, Mandl FAM, Lehmann J, Korotkov VS, Hacker SM, Kuster B, Antes I, Pieper DH, Rohde M, Wuest WM, Medina E, Sieber SA. Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms. Nat Chem 2020; 12:145-158. [PMID: 31844194 PMCID: PMC6994260 DOI: 10.1038/s41557-019-0378-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022]
Abstract
New drugs are desperately needed to combat methicillin-resistant Staphylococcus aureus (MRSA) infections. Here, we report screening commercial kinase inhibitors for antibacterial activity and found the anticancer drug sorafenib as major hit that effectively kills MRSA strains. Varying the key structural features led to the identification of a potent analogue, PK150, that showed antibacterial activity against several pathogenic strains at submicromolar concentrations. Furthermore, this antibiotic eliminated challenging persisters as well as established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance, and shows oral bioavailability and in vivo efficacy. Analysis of the mode of action using chemical proteomics revealed several targets, which included interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltransferase and the stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this target hypothesis. The associated antibiotic effects, especially the lack of resistance development, probably stem from the compound's polypharmacology.
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7268
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Terrazzano G, Bruzzaniti S, Rubino V, Santopaolo M, Palatucci AT, Giovazzino A, La Rocca C, de Candia P, Puca A, Perna F, Procaccini C, De Rosa V, Porcellini C, De Simone S, Fattorusso V, Porcellini A, Mozzillo E, Troncone R, Franzese A, Ludvigsson J, Matarese G, Ruggiero G, Galgani M. T1D progression is associated with loss of CD3 +CD56 + regulatory T cells that control CD8 + T cell effector functions. Nat Metab 2020; 2:142-152. [PMID: 32500117 PMCID: PMC7272221 DOI: 10.1038/s42255-020-0173-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An unresolved issue in autoimmunity is the lack of surrogate biomarkers of immunological self-tolerance for disease monitoring. Here, we show that peripheral frequency of a regulatory T cell population, characterized by the co-expression of CD3 and CD56 molecules (TR3-56), is reduced in subjects with new-onset type 1 diabetes (T1D). In three independent T1D cohorts, we find that low frequency of circulating TR3-56 cells is associated with reduced β-cell function and with the presence of diabetic ketoacidosis. As autoreactive CD8+ T cells mediate disruption of insulin-producing β-cells1-3, we demonstrate that TR3-56 cells can suppress CD8+ T cell functions in vitro by reducing levels of intracellular reactive oxygen species. The suppressive function, phenotype and transcriptional signature of TR3-56 cells are also altered in T1D children. Together, our findings indicate that TR3-56 cells constitute a regulatory cell population that controls CD8+ effector functions, whose peripheral frequency may represent a traceable biomarker for monitoring immunological self-tolerance in T1D.
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7269
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Siemons M, Cloin BMC, Salas DM, Nijenhuis W, Katrukha EA, Kapitein LC. Comparing strategies for deep astigmatism-based single-molecule localization microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:735-751. [PMID: 32133221 PMCID: PMC7041481 DOI: 10.1364/boe.382023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 05/22/2023]
Abstract
Single-molecule localization microscopy (SMLM) enables fluorescent microscopy with nanometric resolution. While localizing molecules close to the coverslip is relatively straightforward using high numerical aperture (NA) oil immersion (OI) objectives, optical aberrations impede SMLM deeper in watery samples. Adaptive optics (AO) with a deformable mirror (DM) can be used to correct such aberrations and to induce precise levels of astigmatism to encode the z-position of molecules. Alternatively, the use of water immersion (WI) objectives might be sufficient to limit the most dominant aberrations. Here we compare SMLM at various depths using either WI or OI with or without AO. In addition, we compare the performance of a cylindrical lens and a DM for astigmatism-based z-encoding. We find that OI combined with adaptive optics improves localization precision beyond the performance of WI-based imaging and enables deep (>10 µm) 3D localization.
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7270
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Biagioli F. Ernst Cassirer's transcendental account of mathematical reasoning. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2020; 79:30-40. [PMID: 32072924 DOI: 10.1016/j.shpsa.2019.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/01/2018] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Cassirer's philosophical agenda revolved around what appears to be a paradoxical goal, that is, to reconcile the Kantian explanation of the possibility of knowledge with the conceptual changes of nineteenth and early twentieth-century science. This paper offers a new discussion of one way in which this paradox manifests itself in Cassirer's philosophy of mathematics. Cassirer articulated a unitary perspective on mathematics as an investigation of structures independently of the nature of individual objects making up those structures. However, this posed the problem of how to account for the applicability of abstract mathematical concepts to empirical reality. My suggestion is that Cassirer was able to address this problem by giving a transcendental account of mathematical reasoning, according to which the very formation of mathematical concepts provides an explanation of the extensibility of mathematical knowledge. In order to spell out what this argument entails, the first part of the paper considers how Cassirer positioned himself within the Marburg neo-Kantian debate over intellectual and sensible conditions of knowledge in 1902-1910. The second part compares what Cassirer says about mathematics in 1910 with some relevant examples of how structural procedures developed in nineteenth-century mathematics.
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Richard MI, Cornelius TW, Lauraux F, Molin JB, Kirchlechner C, Leake SJ, Carnis J, Schülli TU, Thilly L, Thomas O. Variable-Wavelength Quick Scanning Nanofocused X-Ray Microscopy for In Situ Strain and Tilt Mapping. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905990. [PMID: 31962006 DOI: 10.1002/smll.201905990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/24/2019] [Indexed: 06/10/2023]
Abstract
Compression of micropillars is followed in situ by a quick nanofocused X-ray scanning microscopy technique combined with 3D reciprocal space mapping. Compared to other attempts using X-ray nanobeams, it avoids any motion or vibration that would lead to a destruction of the sample. The technique consists of scanning both the energy of the incident nanofocused X-ray beam and the in-plane translations of the focusing optics along the X-ray beam. Here, the approach by imaging the strain and lattice orientation of Si micropillars and their pedestals during in situ compression is demonstrated. Varying the energy of the incident beam instead of rocking the sample and mapping the focusing optics instead of moving the sample supplies a vibration-free measurement of the reciprocal space maps without removal of the mechanical load. The maps of strain and lattice orientation are in good agreement with the ones recorded by ordinary rocking-curve scans. Variable-wavelength quick scanning X-ray microscopy opens the route for in situ strain and tilt mapping toward more diverse and complex materials environments, especially where sample manipulation is difficult.
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Lee JH, Wang X, Bendor D. The role of adaptation in generating monotonic rate codes in auditory cortex. PLoS Comput Biol 2020; 16:e1007627. [PMID: 32069272 PMCID: PMC7048304 DOI: 10.1371/journal.pcbi.1007627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 02/28/2020] [Accepted: 01/02/2020] [Indexed: 11/19/2022] Open
Abstract
In primary auditory cortex, slowly repeated acoustic events are represented temporally by the stimulus-locked activity of single neurons. Single-unit studies in awake marmosets (Callithrix jacchus) have shown that a sub-population of these neurons also monotonically increase or decrease their average discharge rate during stimulus presentation for higher repetition rates. Building on a computational single-neuron model that generates stimulus-locked responses with stimulus evoked excitation followed by strong inhibition, we find that stimulus-evoked short-term depression is sufficient to produce synchronized monotonic positive and negative responses to slowly repeated stimuli. By exploring model robustness and comparing it to other models for adaptation to such stimuli, we conclude that short-term depression best explains our observations in single-unit recordings in awake marmosets. Together, our results show how a simple biophysical mechanism in single neurons can generate complementary neural codes for acoustic stimuli.
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Schipper AM, Hilbers JP, Meijer JR, Antão LH, Benítez‐López A, de Jonge MMJ, Leemans LH, Scheper E, Alkemade R, Doelman JC, Mylius S, Stehfest E, van Vuuren DP, van Zeist W, Huijbregts MAJ. Projecting terrestrial biodiversity intactness with GLOBIO 4. GLOBAL CHANGE BIOLOGY 2020; 26:760-771. [PMID: 31680366 PMCID: PMC7028079 DOI: 10.1111/gcb.14848] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 08/09/2019] [Indexed: 05/06/2023]
Abstract
Scenario-based biodiversity modelling is a powerful approach to evaluate how possible future socio-economic developments may affect biodiversity. Here, we evaluated the changes in terrestrial biodiversity intactness, expressed by the mean species abundance (MSA) metric, resulting from three of the shared socio-economic pathways (SSPs) combined with different levels of climate change (according to representative concentration pathways [RCPs]): a future oriented towards sustainability (SSP1xRCP2.6), a future determined by a politically divided world (SSP3xRCP6.0) and a future with continued global dependency on fossil fuels (SSP5xRCP8.5). To this end, we first updated the GLOBIO model, which now runs at a spatial resolution of 10 arc-seconds (~300 m), contains new modules for downscaling land use and for quantifying impacts of hunting in the tropics, and updated modules to quantify impacts of climate change, land use, habitat fragmentation and nitrogen pollution. We then used the updated model to project terrestrial biodiversity intactness from 2015 to 2050 as a function of land use and climate changes corresponding with the selected scenarios. We estimated a global area-weighted mean MSA of 0.56 for 2015. Biodiversity intactness declined in all three scenarios, yet the decline was smaller in the sustainability scenario (-0.02) than the regional rivalry and fossil-fuelled development scenarios (-0.06 and -0.05 respectively). We further found considerable variation in projected biodiversity change among different world regions, with large future losses particularly for sub-Saharan Africa. In some scenario-region combinations, we projected future biodiversity recovery due to reduced demands for agricultural land, yet this recovery was counteracted by increased impacts of other pressures (notably climate change and road disturbance). Effective measures to halt or reverse the decline of terrestrial biodiversity should not only reduce land demand (e.g. by increasing agricultural productivity and dietary changes) but also focus on reducing or mitigating the impacts of other pressures.
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Moretti A, Fonteyne L, Giesert F, Hoppmann P, Meier AB, Bozoglu T, Baehr A, Schneider CM, Sinnecker D, Klett K, Fröhlich T, Rahman FA, Haufe T, Sun S, Jurisch V, Kessler B, Hinkel R, Dirschinger R, Martens E, Jilek C, Graf A, Krebs S, Santamaria G, Kurome M, Zakhartchenko V, Campbell B, Voelse K, Wolf A, Ziegler T, Reichert S, Lee S, Flenkenthaler F, Dorn T, Jeremias I, Blum H, Dendorfer A, Schnieke A, Krause S, Walter MC, Klymiuk N, Laugwitz KL, Wolf E, Wurst W, Kupatt C. Somatic gene editing ameliorates skeletal and cardiac muscle failure in pig and human models of Duchenne muscular dystrophy. Nat Med 2020; 26:207-214. [PMID: 31988462 PMCID: PMC7212064 DOI: 10.1038/s41591-019-0738-2] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 12/11/2019] [Indexed: 11/09/2022]
Abstract
Frameshift mutations in the DMD gene, encoding dystrophin, cause Duchenne muscular dystrophy (DMD), leading to terminal muscle and heart failure in patients. Somatic gene editing by sequence-specific nucleases offers new options for restoring the DMD reading frame, resulting in expression of a shortened but largely functional dystrophin protein. Here, we validated this approach in a pig model of DMD lacking exon 52 of DMD (DMDΔ52), as well as in a corresponding patient-derived induced pluripotent stem cell model. In DMDΔ52 pigs1, intramuscular injection of adeno-associated viral vectors of serotype 9 carrying an intein-split Cas9 (ref. 2) and a pair of guide RNAs targeting sequences flanking exon 51 (AAV9-Cas9-gE51) induced expression of a shortened dystrophin (DMDΔ51-52) and improved skeletal muscle function. Moreover, systemic application of AAV9-Cas9-gE51 led to widespread dystrophin expression in muscle, including diaphragm and heart, prolonging survival and reducing arrhythmogenic vulnerability. Similarly, in induced pluripotent stem cell-derived myoblasts and cardiomyocytes of a patient lacking DMDΔ52, AAV6-Cas9-g51-mediated excision of exon 51 restored dystrophin expression and amelioreate skeletal myotube formation as well as abnormal cardiomyocyte Ca2+ handling and arrhythmogenic susceptibility. The ability of Cas9-mediated exon excision to improve DMD pathology in these translational models paves the way for new treatment approaches in patients with this devastating disease.
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Lee HG, Wang L, Si L, He X, Porter DG, Kim JR, Ko EK, Kim J, Park SM, Kim B, Wee ATS, Bombardi A, Zhong Z, Noh TW. Atomic-Scale Metal-Insulator Transition in SrRuO 3 Ultrathin Films Triggered by Surface Termination Conversion. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905815. [PMID: 31830343 DOI: 10.1002/adma.201905815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The metal-insulator transition (MIT) in transition-metal-oxide is fertile ground for exploring intriguing physics and potential device applications. Here, an atomic-scale MIT triggered by surface termination conversion in SrRuO3 ultrathin films is reported. Uniform and effective termination engineering at the SrRuO3 (001) surface can be realized via a self-limiting water-leaching process. As the surface termination converts from SrO to RuO2 , a highly insulating and nonferromagnetic phase emerges within the topmost SrRuO3 monolayer. Such a spatially confined MIT is corroborated by systematic characterizations on electrical transport, magnetism, and scanning tunneling spectroscopy. Density functional theory calculations and X-ray linear dichroism further suggest that the surface termination conversion breaks the local octahedral symmetry of the crystal field. The resultant modulation in 4d orbital occupancy stabilizes a nonferromagnetic insulating surface state. This work introduces a new paradigm to stimulate and tune exotic functionalities of oxide heterostructures with atomic precision.
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