Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma.

Primary liver cancer arises either from hepatocytic or biliary lineage cells, giving rise to hepatocellular carcinoma (HCC) or intrahepatic cholangiocarcinoma (ICCA). Combined hepatocellular- cholangiocarcinomas (cHCC-CCA) exhibit equivocal or mixed features of both, causing diagnostic uncertainty and difficulty in determining proper management. Here, we perform a comprehensive deep learning-based phenotyping of multiple cohorts of patients. We show that deep learning can reproduce the diagnosis of HCC vs. CCA with a high performance. We analyze a series of 405 cHCC-CCA patients and demonstrate that the model can reclassify the tumors as HCC or ICCA, and that the predictions are consistent with clinical outcomes, genetic alterations and in situ spatial gene expression profiling. This type of approach could improve treatment decisions and ultimately clinical outcome for patients with rare and biphenotypic cancers such as cHCC-CCA

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org)

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org)

Effect of interlayer cation and relative humidity on the hydration properties of a dioctahedral smectite

International audienceThis paper aims at characterizing the structural evolution of a dioctahedral smectite (i.e. Wyoming montmorillonite) saturated by Na+, Cu2+or Pb2+. Hydration properties of the <2μm size fraction of Wyoming montmorillonite smectite (SWy) source clay (low charge i.e. 0.35) were studied by modelling of X-ray diffraction (XRD) patterns recorded under controlled relative humidity (RH) conditions on Na, Cu or Pb saturated specimens. The Cation Exchange Capacity (CEC) of the starting sample was first Na+ saturated to guarantee better dispersion, followed by exchanges with the cations Cu2+ or Pb2+. The resulting complexes were respectively labelled Wy-Na, Wy-Cu and Wy-Pb. The qualitative analysis of XRD patterns obtained under room pressure and temperature conditions showed that all complexes have one water layer hydration state. In order to highlight the specific hydration properties of each complex, we studied the XRD patterns under controlled relative humidity (%RH). The quantitative analysis of XRD patterns is achieved using an indirect method based on the comparison of experimental XRD patterns with calculated ones. This quantitative study showed that for Wy-Na, Wy-Cu and Wy-Pb at low RH (≈15%) the d001 spacing corresponds to a low hydration state characterized by one water layer, whereas for higher studied rates of relative humidity (75%), differences of hydration state can be distinguished for Wy-Na, Wy-Cu and Wy-Pb samples

Alkaline activation of metakaolinite-silica mixtures: role of dissolved silica concentration on the formation of geopolymers

The alkali activation of metakaolinite permits the preparation of new amorphous cementitious materials denoted as “geopolymers”. The formation of these aluminosilicates depends on the thermal activation of kaolinites and the amount of silica in the activating solutions. In this work, the influence of Si:Al ratios on the geopolymer's formation is investigated for short reaction times. Structural and morphological transformations were followed with the XRD, SEM, IR and MAS NMR (Si, Al, Na and H) techniques. For kaolinites (SiAl =1) heated at 550 °C, geopolymers with tectosilicate networks easily formed; however, in kaolinites heated at 800 °C, the formation of geopolymers was delayed as a consequence of silica segregation. The addition of silica (Si:Al= 3) favoured the formation of geopolymers particles surrounded by sodium-silicates with tubular morphology. In this association, kinetic and thermodynamic parameters play an important role. For prolonged alkaline activations, zeolites formed from the geopolymers. The quantitative analysis of the NMR spectra made possible the study of the formation of zeolites from amorphous geopolymers.The authors would like to thank the Tunisian Ministry of Education for two short training grants covering the collaboration established between the Spain and Tunisia groups

Entrepreneurial failure: A synthesis and conceptual framework of its effects

Failure is not the outcome which entrepreneurs strive for when they start their businesses. However, thousands of entrepreneurs fail each year, experiencing painful and damaging consequences in their professional and private lives. Current knowledge on entrepreneurial failure is quite fragmentary. Our study aims at integrating knowledge on the effects of entrepreneurial failure. Departing from a systematic literature review, we develop a multilevel framework of entrepreneurial failure effects which categorises: (1) their manifestations over time; (2) the directness of the link to the failure event; (3) the degree of impact on the failed entrepreneur; and (4) the level of long‐term outcomes generated. Our findings reveal a broad scope of multilevel impacts of entrepreneurial failure