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Development of advanced artificial intelligence models for daily rainfall prediction 期刊论文
ATMOSPHERIC RESEARCH, 2020, 237
作者:  Binh Thai Pham;  Lu Minh Le;  Tien-Thinh Le;  Kien-Trinh Thi Bui;  Vuong Minh Le;  Hai-Bang Ly;  Prakash, Indra
收藏  |  浏览/下载:12/0  |  提交时间:2020/07/02
Rainfall  Artificial Neural Networks  Robustness analysis  Support Vector Machines  Adaptive Network based Fuzzy Inference System  Particle Swarm Optimization  
Nondispersive Drainage Direction Simulation Based on Flexible Triangular Facets 期刊论文
WATER RESOURCES RESEARCH, 2020, 56 (4)
作者:  Wu, Pengfei;  Liu, Jintao;  Han, Xiaole;  Liang, Zhongmin;  Liu, Yangyang;  Fei, Junyuan
收藏  |  浏览/下载:10/0  |  提交时间:2020/07/02
terrain analysis  nondispersive drainage direction  flexible triangular facet  flow aggregation  drainage network  
Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche 期刊论文
NATURE, 2020, 580 (7804) : 524-+
作者:  Poore, Gregory D.;  Kopylova, Evguenia;  Zhu, Qiyun;  Carpenter, Carolina;  Fraraccio, Serena;  Wandro, Stephen;  Kosciolek, Tomasz;  Janssen, Stefan;  Metcalf, Jessica;  Song, Se Jin;  Kanbar, Jad;  Miller-Montgomery, Sandrine;  Heaton, Robert;  Mckay, Rana;  Patel, Sandip Pravin;  Swafford, Austin D.;  Knight, Rob
收藏  |  浏览/下载:40/0  |  提交时间:2020/07/03

The initiation of an intestinal tumour is a probabilistic process that depends on the competition between mutant and normal epithelial stem cells in crypts(1). Intestinal stem cells are closely associated with a diverse but poorly characterized network of mesenchymal cell types(2,3). However, whether the physiological mesenchymal microenvironment of mutant stem cells affects tumour initiation remains unknown. Here we provide in vivo evidence that the mesenchymal niche controls tumour initiation in trans. By characterizing the heterogeneity of the intestinal mesenchyme using single-cell RNA-sequencing analysis, we identified a population of rare pericryptal Ptgs2-expressing fibroblasts that constitutively process arachidonic acid into highly labile prostaglandin E-2 (PGE(2)). Specific ablation of Ptgs2 in fibroblasts was sufficient to prevent tumour initiation in two different models of sporadic, autochthonous tumorigenesis. Mechanistically, single-cell RNA-sequencing analyses of a mesenchymal niche model showed that fibroblast-derived PGE(2) drives the expansion omicron f a population of Sca-1(+) reserve-like stem cells. These express a strong regenerative/tumorigenic program, driven by the Hippo pathway effector Yap. In vivo, Yap is indispensable for Sca-1(+) cell expansion and early tumour initiation and displays a nuclear localization in both mouse and human adenomas. Using organoid experiments, we identified a molecular mechanism whereby PGE(2) promotes Yap dephosphorylation, nuclear translocation and transcriptional activity by signalling through the receptor Ptger4. Epithelial-specific ablation of Ptger4 misdirected the regenerative reprogramming of stem cells and prevented Sca-1(+) cell expansion and sporadic tumour initiation in mutant mice, thereby demonstrating the robust paracrine control of tumour-initiating stem cells by PGE(2)-Ptger4. Analyses of patient-derived organoids established that PGE(2)-PTGER4 also regulates stem-cell function in humans. Our study demonstrates that initiation of colorectal cancer is orchestrated by the mesenchymal niche and reveals a mechanism by which rare pericryptal Ptgs2-expressing fibroblasts exert paracrine control over tumour-initiating stem cells via the druggable PGE(2)-Ptger4-Yap signalling axis.


Single-cell RNA-sequencing analysis of intestinal mesenchyme identified a population of fibroblasts that produce prostaglandin E-2, which, when disrupted, prevented initiation of intestinal tumours.


  
The role of local stakeholders in disseminating knowledge for supporting the circular economy: a network analysis approach 期刊论文
ECOLOGICAL ECONOMICS, 2020, 169
作者:  Ghinoi, Stefano;  Silvestri, Francesco;  Steiner, Bodo
收藏  |  浏览/下载:8/0  |  提交时间:2020/07/02
Circular economy  Knowledge networks  Local stakeholders  Brokerage  Social Network Analysis  
Policy integration: Do laws or actors integrate issues relevant to flood risk management in Switzerland? 期刊论文
GLOBAL ENVIRONMENTAL CHANGE-HUMAN AND POLICY DIMENSIONS, 2020, 61
作者:  Metz, Florence;  Angst, Mario;  Fischer, Manuel
收藏  |  浏览/下载:8/0  |  提交时间:2020/07/02
Policy integration  issue integration  flood risk management  adaptive governance  network analysis  bipartite network  
The strength and pattern of natural selection on gene expression in rice 期刊论文
NATURE, 2020, 578 (7796) : 572-+
作者:  Lipson, Mark;  Ribot, Isabelle;  Mallick, Swapan;  Rohland, Nadin;  Olalde, Inigo;  Adamski, Nicole;  Broomandkhoshbacht, Nasreen;  Lawson, Ann Marie;  Lopez, Saioa;  Oppenheimer, Jonas;  Stewardson, Kristin
收藏  |  浏览/下载:19/0  |  提交时间:2020/07/03

Levels of gene expression underpin organismal phenotypes(1,2), but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown(1,2). Here we assayed gene expression in rice (Oryza sativa)(3), and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts(4,5). Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions. Overall, more transcripts are conditionally neutral (2.83%) than are antagonistically pleiotropic(6) (0.04%), and transcripts that display lower levels of expression and stochastic noise(7-9) and higher levels of plasticity(9) are under stronger selection. Selection strength was further weakly negatively associated with levels of cis-regulation and network connectivity(9). Our multivariate analysis suggests that selection acts on the expression of photosynthesis genes(4,5), but that the efficacy of selection is genetically constrained under drought conditions(10). Drought selected for earlier flowering(11,12) and a higher expression of OsMADS18 (Os07g0605200), which encodes a MADS-box transcription factor and is a known regulator of early flowering(13)-marking this gene as a drought-escape gene(11,12). The ability to estimate selection strengths provides insights into how selection can shape molecular traits at the core of gene action.


Phenotypic selection analysis is used to estimate the type and strength of selection that acts on more than 15,000 transcripts in rice (Oryza sativa), which provides insight into the adaptive evolutionary role of selection on gene expression.


  
Hidden diversity of vacancy networks in Prussian blue analogues 期刊论文
NATURE, 2020, 578 (7794) : 256-+
作者:  Hendrickx, N. W.;  Franke, D. P.;  Sammak, A.;  Scappucci, G.;  Veldhorst, M.
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

Prussian blue analogues (PBAs) are a diverse family of microporous inorganic solids, known for their gas storage ability(1), metal-ion immobilization(2), proton conduction(3), and stimuli-dependent magnetic(4,5), electronic(6) and optical(7) properties. This family of materials includes the double-metal cyanide catalysts(8,9) and the hexacyanoferrate/ hexacyanomanganate battery materials(10,11). Central to the various physical properties of PBAs is their ability to reversibly transport mass, a process enabled by structural vacancies. Conventionally presumed to be random(12,13), vacancy arrangements are crucial because they control micropore-network characteristics, and hence the diffusivity and adsorption profiles(14,15). The long-standing obstacle to characterizing the vacancy networks of PBAs is the inaccessibility of single crystals(16). Here we report the growth of single crystals of various PBAs and the measurement and interpretation of their X-ray diffuse scattering patterns. We identify a diversity of non-random vacancy arrangements that is hidden from conventional crystallographic powder analysis. Moreover, we explain this unexpected phase complexity in terms of a simple microscopic model that is based on local rules of electroneutrality and centrosymmetry. The hidden phase boundaries that emerge demarcate vacancynetwork polymorphs with very different micropore characteristics. Our results establish a foundation for correlated defect engineering in PBAs as a means of controlling storage capacity, anisotropy and transport efficiency.


  
Structure of SAGA and mechanism of TBP deposition on gene promoters 期刊论文
NATURE, 2020, 577 (7792) : 711-+
作者:  Xue, Jenny Y.;  Zhao, Yulei;  Aronowitz, Jordan;  Mai, Trang T.;  Vides, Alberto;  Qeriqi, Besnik;  Kim, Dongsung;  Li, Chuanchuan;  de Stanchina, Elisa;  Mazutis, Linas;  Risso, Davide;  Lito, Piro
收藏  |  浏览/下载:33/0  |  提交时间:2020/07/03

SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes(1). Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 angstrom resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression.


Structural studies on the yeast transcription coactivator complex SAGA (Spt-Ada-Gcn5-acetyltransferase) provide insights into the mechanism of initiation of regulated transcription by this multiprotein complex, which is conserved among eukaryotes.


  
Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses 期刊论文
GLOBAL CHANGE BIOLOGY, 2019
作者:  Monteiro, Homere J. Alves;  Brahmi, Chloe;  Mayfield, Anderson B.;  Vidal-Dupiol, Jeremie;  Lapeyre, Bruno;  Le Luyer, Jeremy
收藏  |  浏览/下载:11/0  |  提交时间:2020/02/17
co-expression network analysis  giant clams  metabarcoding  RNA-Seq  Symbiodiniaceae  thermo-acclimation  
Alarm communication networks as a driver of community structure in African savannah herbivores 期刊论文
ECOLOGY LETTERS, 2020, 23 (2) : 293-304
作者:  Meise, Kristine;  Franks, Daniel W.;  Bro-Jorgensen, Jakob
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/02
Agent-based modelling  antipredator strategies  interspecific information transfer  mixed-species groups  resource competition  social affinity  social information use  social network analysis  spatial ecology  ungulates