The archive solution for distributed workflow management agents of the CMS experiment at LHC

The CMS experiment at the CERN LHC developed the Workflow Management Archive system to persistently store unstructured framework job report documents produced by distributed workflow management agents. In this paper we present its architecture, implementation, deployment, and integration with the CMS and CERN computing infrastructures, such as central HDFS and Hadoop Spark cluster. The system leverages modern technologies such as a document oriented database and the Hadoop eco-system to provide the necessary flexibility to reliably process, store, and aggregate $\mathcal{O}$(1M) documents on a daily basis. We describe the data transformation, the short and long term storage layers, the query language, along with the aggregation pipeline developed to visualize various performance metrics to assist CMS data operators in assessing the performance of the CMS computing system.Comment: This is a pre-print of an article published in Computing and Software for Big Science. The final authenticated version is available online at: https://doi.org/10.1007/s41781-018-0005-

Establishment of Arthrobotrys flagrans as biocontrol agent against the root pathogenic nematode Xiphinema index

Plant-parasitic nematodes cause devastating agricultural damage worldwide. Only a few synthetic nematicides can be used and their application is limited in fields. Therefore, there is a need for sustainable and environment-friendly alternatives. Nematode-trapping fungi (NTF) are natural predators of nematodes. They capture and digest them with their hyphae and are starting to being used as bio-control agents. In this study, we applied the NTF Arthrobotrys flagrans (Duddingtonia flagrans) against the wine pathogenic nematode Xiphinema index. A. flagrans reduced the number of X. index juveniles in pot cultures of Ficus carica, an alternative host plant for X. index, significantly. Sodium-alginate pellets with A. flagrans spores were produced for vineyard soil inoculation under laboratory conditions. The NTF A. conoides, A. musiformis and A. superba were enriched from several soil samples, showing their natural presence. Trap formation is an energy-consuming process and depends upon various biotic and abiotic stimuli. Here, we show that bacteria of the genus Delftia, Bacillus, Pseudomonas, Enterobacter and Serratia induced trap formation in NTF like A. conoides and A. oligospora but not in A. flagrans in the absence of nematodes. The application of NTF along with such bacteria could be a combinatorial way of efficient biocontrol in nematode-infested soil

The STRIPAK component SipC is involved in morphology and cell-fate determination in the nematode-trapping fungus Duddingtonia flagrans

The striatin-interacting phosphatase and kinase (STRIPAK) complex is a highly conserved eukaryotic signaling hub involved in the regulation of many cellular processes. In filamentous fungi, STRIPAK controls multicellular development, hyphal fusion, septation, and pathogenicity. In this study, we analyzed the role of the STRIPAK complex in the nematode-trapping fungus Duddingtonia flagrans which forms three-dimensional, adhesive trapping networks to capture Caenorhabditis elegans. Trap networks consist of several hyphal loops which are morphologically and functionally different from vegetative hyphae. We show that lack of the STRIPAK component SipC (STRIP1/2/HAM-2/PRO22) results in incomplete loop formation and column-like trap structures with elongated compartments. The misshapen or incomplete traps lost their trap identity and continued growth as vegetative hyphae. The same effect was observed in the presence of the actin cytoskeleton drug cytochalasin A. These results could suggest a link between actin and STRIPAK complex functions

Soft but not too soft—How a rigid tube expands without breaking

Fungi grow by apical extension of their hyphae. The continuous growth requires constant delivery of vesicles, which fuse with the membrane and secrete cell wall biosynthesis enzymes. The growth mechanism requires the fungal cytoskeleton and turgor pressure. In a recent study by Fukuda et al. (mBio 12:e03196-20, 2021, https://doi.org/10.1128/mBio.03196-20), hyphal growth was studied in microfluidic devices with channels smaller than the hyphal diameter. The authors discovered that fast-growing fungi like Neurospora crassa enter the channels, but hyphal tips become fragile and rupture frequently, whereas slower-growing fungi like Aspergillus nidulans adapt their hyphal diameter and grow without problems through the channels. This study suggests two different growth mechanisms and a tradeoff between hyphal plasticity and growth speed

The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids

peer reviewedDyrosauridae is a clade of neosuchian crocodyliforms that diversified in terrestrial and aquatic environments across the Cretaceous-Paleogene transition. The postcranial anatomy of dyrosaurids has long been overlooked, obscuring both their disparity and their locomotive adaptations. Here we thoroughly describe of the postcranial remains of an unusually small dyrosaurid, Cerrejonisuchus improcerus, from the middle-late Paleocene Cerrejón Formation of Colombia, and we provide a wealth of new data concerning the postcranial anatomy of the key dyrosaurids: Congosaurus bequaerti and Hyposaurus rogersii. We identify a series of postcranial autapomorphies in Cerrejonisuchus improcerus (an elliptic-shaped odontoid laterally wide, a ulna possessing a double concavity, a fibula bearing a widely flattened proximal end, a pubis showing a large non-triangular distal surface) as well as functionally-important traits such as a relatively long ulna (85% of the humerus' length), short forelimb (83% of hindlimb's length), or thoracic vertebra bearing comparatively large lateral process (with widened parapophysis and diapophysis) along with strongly arched thoracic ribs allowing a more sturdy and cylindrical rib cage. These indicate a more terrestrial lifestyle for Cerrejonisuchus compared to the derived members of the clade. We also built a dataset of 187 traits on 27 taxa, that extensively samples the cranial and postcranial architectures of exemplar crocodyliforms. We analyze these data in via Principal Coordinate Analysis (PCoA) to visualize the postcranial morphospace occupation of Dyrosauridae, Thalattosuchia, and Crocodylia. Our data reveal the existence of a distinctive postcranial anatomy for Dyrosauridae that is markedly distinct from that of crocodylians. As a result, modern crocodylians are probably not good functional analog for extinct crocodyliformes. Postcranial data should also be more widely used in phylogenetic and disparity analyses of Crocodyliformes

Mary Anning’s legacy to French vertebrate palaeontology

peer reviewedThe real nature of marine reptile fossils found in England in between the 1700s to the beginning of the 1900s remained enigmatic, until Mary Anning's incredible fossil discoveries and their subsequent study by eminent English and French scientists. In 1820, Georges Cuvier acquired several ichthyosaur specimens found by Mary Anning, now kept or displayed in the Palaeontology Gallery of the MNHN in Paris. Four years later, Cuvier obtained a plesiosaur specimen from Mary Anning, only the second ever discovered. Cuvier was fascinated by these fossils and their study allowed him to apply his comparative anatomical method and to support his catastrophist theory. We re-examined these important specimens from an historical point of view and herein describe them taxonomically for the first time since Cuvier’s works. The Paris specimens belong to two different ichthyosaur genera (Ichthyosaurus and Leptonectes) and one plesiosaur genus (Plesiosaurus)

LIMITED CONVERGENCE IN THE POSTCRANIUM OF AQUATIC CROCODYLOMORPHA

peer reviewedABSTRACT. Thalattosuchia (Early Jurassic–Early Cretaceous) and Dyrosauridea (Late Cretaceous–Early Eocene) are crocodylomorph archosaurs which diversified in fluvial and marine environments and endured extinction events (i.e. Jurassic–Cretaceous boundary for Thalattosuchia; Cretaceous–Paleogene for Dyrosauridea). Their postcrania remain globally undervalued in anatomical descriptions and diagnoses, shrouding the locomotive adaptations that possibly underpinned their radiations and longevity. We thoroughly surveyed the postcranial morphology of Dyrosauridea and Thalattosuchia, recreated their girdles in three-dimensions using tens of high-precisions 3D scans, and analysed their shape using geometric morphometrics. Dyrosauridea and Thalattosuchia have clearly distinct postcrania, even when found within similar environments, suggesting the existence of clade-specific features limiting the strength of evolutionary convergence. Moreover, the range of postcranial morphologies evolved by dyrosaurids and thalattosuchians is large compared to extant crocodylians, making the latter unsatisfactory functional analogues for every group of extinct crocodylomorphs. Our work reveals the previously unsuspected potential of postcranial anatomy as an abundant source of phylogenetic and taxonomic characters to assess the relationships within Crocodylomorpha. Incorporation of postcranial anatomy therefore appears crucial to fully assess the ecology, disparity, and relationships of crocodylomorphs

Not a jaguar after all? Phylogenetic affinities and morphology of the Pleistocene felid Panthera gombaszoegensis

peer reviewedPanthera gombaszoegensis is a fossil pantherine from the Pleistocene of Eurasia. It has been considered to be the closest ancestor the jaguar (Panthera onca) due to dental similarities, and has even sometimes been considered to be a subspecies of jaguar. However, our knowledge of this taxon is limited by the scarcity of cranial remains, which has made it difficult to properly assess the phylogenetic affinities and possible ecological role of this taxon. Here, we describe a new cranium of P. gombaszoegensis from Belgium, and present a morphometric analysis of the cranium and dentition of extinct and extant pantherines. Whereas the lower dentition of P. gombaszoegensis is similar to that of P. onca, similarities were not recovered in other parts of the skull. Some cranial traits of P. gombaszoegensis resemble those of other pantherines, especially larger species such as the tiger (P. tigris). Some similarities with taxa such as tigers (P. tigris), lions (P. leo), and leopards (P. pardus) in the skull of P. gombaszoegensis, suggesting a diet adapted to a wide prey spectrum. The first ever assessment of the phylogenetic placement of P. gombaszoegensis places this taxon closer to P. tigris than to P. onca, which considerably simplifies the biogeographic history of pantherine