dataesr/scientific-paragraphs-categorization huggingface dataset:
This paper shows an application of a vertex-based Compatible Discrete Operator (CDO) scheme to simulate the Richards equation on meshes using polyhedral cells. Second order spatial accuracy is reached for a verification test case using two meshes made of different types of polyhedral cells. A second validation test case dealing with a variably saturated soil inside a vertical column has been simulated, with three advected passive pollutants being released. Results are in good agreement with the reference for both types of mesh. MPI scalability has also been assessed at scale up to 98,304 cores of a Cray X30 for a 1. 7 B cell mesh for the simulation of the aforementioned case, and nearly linear speed-up is observed. Finally the implementation of hybrid MPI-OpenMP has been tested on 2 types of Intel Xeon Phi Knights Landing co-processors, showing that the best configuration for the code is obtained when all the physical cores are filled by MPI tasks and the 4 hyperthreads by OpenMP threads.
Parallel mesh joining on-the-fly  [4]  is a very efficient tool to speed-up the mesh generation of complex geometries. This feature exists in Code Saturne  [5]  as an in-house algorithm. A side effect of this flexibility is the addition of polyhedral cells at the interface between the two meshes to join if this interface is non-conforming. This yields a need to consider numerical schemes robust with respect to polyhedral meshes. Research on discretisation schemes for polyhedral/distorted meshes (see Figure  1 ) has been worked on for many years  [6, 7, 8] , but has gained more and more attention in the last years  [3]. Several methods have been recently revived or developed to be able to fulfil the following requirements, i. e. robustness, flexibility and accuracy. Besides the Compatible Discrete Operator (CDO) schemes  [9, 10, 11, 12, 13] , Figure  1 : Examples of meshes used in the FVCA6 benchmark  [3].
The implementation of CDO schemes is carried out in the Code Saturne solver  [5, 20] , primarily developed by EDF, and open-source since 2007. The software uses the Finite Volume discretisation to simulate multi-physics CFD on meshes handling any type of cells. But as always for all the FV two-point discretisation methods, accuracy and robustness require good mesh quality. The FV version of the code relies on MPI to handle communications and OpenMP directives are added to speed-up the simulations. The code has been tested using over 3 million threads on MIRA (full machine) at Argonne (US DOE machine) for a 105 billion cell mesh and over 1. 8 million threads on JUQUEEN (full machine) at Jülich (GE) for a 7 billion cell mesh, showing in both cases good strong scalability. The ambition of this work and its novelty is to retain this level of parallelisation with the newly implemented CDO schemes, and to develop an hybrid MPI-OpenMP software showing good performance at scale, when keeping spacial second order accuracy for polyhedral cell meshes.
Base parallelisation approach Although the CDO type schemes represent new developments in Code Saturne, we seek to leverage the code parallelisation used for the base 2-point flux FV schemes, so as both to allow future simultaneous use of different schemes for incremental coupling of specific physical models, and mostly to benefit from the significant efforts already invested in this area. The base Finite Volume scheme is cell-centered, and uses classical MPI-based parallelism with cellbased partitioning and ghost cells. Interior faces and vertices on rank boundaries are duplicated, and shared-memory (OpenMP) parallelism may be used inside each domain. Global (partition-independent) numbering and a "block" distribution based on global number ranges is used for parallel checkpoint/restart and post-processing I/O as well as global mesh modifications.
An optimised partitioning based on a graph bisection (PT-SCOTCH or ParMETIS) or space-filling-curve (Morton or Hilbert) approach is used for most compute operations. Data can be swapped from one distribution scheme to the other, so that except for initial mesh import to a native low-level format, all operations are distributed. This first level of parallelism is naturally based on MPI, and includes some aspects specific to Code Saturne: • Base halo contains cells with face-adjacency for main scheme (see Figure  3 ), optional extended halo with vertex-adjacency for least-squares gradient reconstruction; • Halos also used for true implicit periodicity handling, subdivided by transformation to allow rotating vectors when synchronising; • A second (reduction-based) global numbering is also used for optional external linear algebra libraries such as PETSc or HYPRE.
A loop-based OpenMP approach is also used for a second layer of parallelism. On a small number of MPI ranks, this does not usually provide high performance (as the code is mostly memory-bound, with low computational intensity in most operations, and some less compute-intensive parts are not threaded) but with OpenMP's usually lower overheads, Hybrid MPI-OpenMP performance becomes competitive when using small cell counts per thread, and for a given number of total threads, memory consumption is usually reduced using several OpenMP threads per MPI ranks, possibly allowing runs on a higher number of threads when available memory per thread is limited.
All the simulations run on both machines are carried out in cache mode, with 10 (resp. 24) of the 12 (resp. 48) for ARCHER (resp. for FRIOUL). In this case all 16 GB on-chip MCDRAM memory is automatically used to cache accesses to system DDR memory. The mesh corresponds to the PrG-based mesh used in Section 6. 2. Figures  12  and 13  show the  evolution of the time to solution as a function of the number of threads, using either the KNL nodes with 64 physical cores or the KNL nodes with 68 physical cores. For both architectures, using 64 (resp. 68) MPI tasks and not taking advantage of hyperthreading is the worst case scenario. Conversely, using 4 OpenMP threads combined with 64 (resp. 68) MPI tasks per node shows the best performance on both architectures. Figure  14  presents a comparison of the performance of the code using 64 (resp.
68) MPI tasks and 4 OpenMP threads. The better timings are observed on the 68 cores per node machine, where more MPI tasks are dealt with at a higher frequency. Finally, Figures 15 and 16 plot the evolution as a function of the number of threads, of all the operations required for the code to reach solution, for both architectures and using 64 (resp. 68) MPI tasks and 4 OpenMP threads. All the operations scale well, apart some specially-dedicated post-processing, and also the matrix assembly stage which curve tails off, when increasing the number of threads. However this time to assemble the matrices is very small compare to the time to solve the equations. parallelise CDO schemes has demonstrated good performance at scale either on a traditionnal CPU architecture or on a modern KNL architecture using an hybrid MPI-OpenMP approach.
RESULTS Overall evolutionary conservation of the Smc5/6 complex in primates. To trace the evolutionary history of the Smc5/6 complex, we compared the sequences of its six subunits in primates (Fig. 1 ). As a comparison, we also analyzed the evolutionary history of the other primate SMC genes. These include the Smc1 and Smc3 genes, which encode the core cohesin subunits, and the Smc2 and Smc4 genes, encoding the condensin core subunits. The sequences of these genes were retrieved from publicly available data sets (Table  1 ; see also supplemental data set 1 at https://figshare. com/ articles/DatasetS1_Host_gene_alignments_used_in_the_study_fasta_format_and _phylogenetic_analyses_newick_format_Nsmce1-4_Smc1-6/6194813). To perform more FIG 1  Smc6  is the least conserved subunit of the Smc5/6 complex in primates.
(A) Architecture of the Smc5/6 complex. The complex is made of two core subunits (Smc5 and Smc6) and four non-SMC elements (Nsmce1 to Nsmce4). (B) Phylogenetic analysis of primate Smc6 genes. Sequences were aligned with MUSCLE and phylogeny was performed with PhyML and an HKYϩIϩG model with an approximate likelihood ratio test (aLRT) as statistical support (**, aLRT Ͼ 0. 8). Newly sequenced genes (arrow) are indicated. The newly sequenced Smc6 gene from Chlorocebus pygerythrus (vervet African green monkey [AGM] Vero cells) is not represented because the nucleotide sequence is identical to the retrieved Chlorocebus sabaeus (Sabaeus AGM) sequence of Smc6. Alignments and phylogenies of the 10 analyzed SMC genes are available in supplemental data set 1 at https://figshare. com/articles/DatasetS1_Host_gene_alignments_used_in_the_study_fasta_format_and_phylogenetic _analyses_newick_format_Nsmce1-4_Smc1-6/6194813.
com/articles/DatasetS1_Host _gene_alignments_used_in_the_study_fasta_format_and_phylogenetic_analyses _newick_format_Nsmce1-4_Smc1-6/6194813). Smc6 was the least conserved SMC protein, with 97. 4% pairwise identity in simian primates. Using the Genetic Algorithm for Recombination Detection (GARD) on the complete set of genes  (28) , evidence of recombination (GARD, P Ͻ 0. 05) was found only for Nsmce3, and therefore subsequent phylogenetic and selection analyses were performed on both the whole Nsmce3 gene and the two identified Nsmce3 gene fragments (from bp 1 to 246 and bp 247 to 912). Phylogenetic analysis of the 10 genes showed that the gene trees derived from nucleotide alignments were largely in accordance with the accepted species tree from Perelman and colleagues (27) (Fig. 1B ; see also supplemental data set 1 at https://figshare.
com/articles/DatasetS1_Host_gene_alignments_used_in_the _study_fasta_format_and_phylogenetic_analyses_newick_format_Nsmce1-4 _Smc1-6/6194813). To assess whether the Smc5/6 complex and the Smc1 to Smc4 genes have experienced diversifying selection during primate evolution, we performed four types of positive selection analyses. First, we used the BUSTED method, which tests whether a gene has experienced positive selection on at least one site or one branch during evolution  (29). Of the six Smc5/6 complex subunits and the four SMC genes from the cohesin and condensin complexes, only one, Smc6, showed gene-wide evidence of episodic positive selection (BUSTED, P Ͻ 0. 05 [Fig. 1C] ). These findings were confirmed using the PARRIS method, which also detects evidence of positive selection using a codon alignment  (30) , although the level of significance was not reached for the Smc6 gene (P ϭ 0.
19 [Fig. 1C] ). Third, we ran the Codeml program from the PAML package  (31)  on our codon alignments to compare two models: one that allows positive selection at certain sites (M8, alternative hypothesis) and one that disallows positive selection (M7, null hypothesis). We then performed a likelihood ratio test (LRT) to examine which of the two models better fits our data. Overall, there was no convergence for 7 of the 10 genes because they were too conserved (see Materials and Methods for details), and no evidence of significant positive selection was found for the remaining genes (Fig. 1C ). Finally, we used the Bioϩϩ package from Guéguen et al. (32) , which has two main advantages over PAML, to similarly test for evidence of positive selection (M7 versus M8 as implemented in Bioϩϩ). First, the DNA substitution models use nonstationary matrices, which allow nucleotide composition to change over time and therefore improve the fitting to real data  (33).
These "genetic innovations" would be missed in typical methods screening for positive selection. We found some indels in genes encoding several Smc5/6 complex subunits (see supplemental data set 1 at https://figshare. com/articles/DatasetS1_Host _gene_alignments_used_in_the_study_fasta_format_and_phylogenetic_analyses _newick_format_Nsmce1-4_Smc1-6/6194813). In particular, we found a 5-amino-acid (aa) indel in the N-terminal region of Smc6 (Fig. 2C ). The five New World monkey species, including the two for which sequences were determined in this study, display a TASFT motif at this position. However, this 5-aa motif was not present in any of the retrieved Catarrhini species sequences (n ϭ 13) (Fig. 2C , Hominoid and Old World Monk. ). To decipher if this 5-aa indel was specific to simian primates, we extended our analysis to mammals.
Divergent mammalian HBx proteins efficiently rescue replication of a human HBx-deficient hepatitis B virus in primary human hepatocytes. We finally tested FIG  4  Evolutionary analyses of divergent mammalian HBV X proteins. (A) Phylogenetic analysis of the X proteins from hepadnaviruses that naturally infect mammals. The viral X proteins tested in our in vitro functional assays (Fig. 5 to 7 ) are indicated by an asterisk. Phylogenetic analysis of orthohepadnaviral X proteins was performed using a 161-amino-acid alignment obtained with MUSCLE (see supplemental data set 2 at https://figshare. com/articles/DatasetS2 _Orthohepadnaviral_HBx_amino_acid_alignment_interleaved_phylip_format_/6194825) and the tree was built with PhyML and a JTTϩIϩG model with 1,000 bootstrap replicates. Bootstrap values (Ͼ800/1,000) are indicated at the nodes.
GAPDH served as a loading control. (C) Effect of mammalian X proteins on transiently transfected reporter gene activity. HepG2 cells were transfected with a luciferase reporter construct and the next day transduced with lentiviral vectors expressing the indicated proteins as described above. At days 5 to 7, the luciferase activity was measured; the fold increase of relative light units (RLU) versus the GFP control condition (set at 1) is shown. The means from three independent experiments are shown, along with SDs. *, P value ϭ 0. 1. P values correspond to the Wilcoxon Mann-Whitney test against the null hypothesis of no difference in the luciferase activity between the GFP control and GFP-X conditions. Of note, the same six X proteins unfused to GFP (i. e. , in their native forms) also retained this activity (data not shown).
The species identity of all the cell lines used in this study was confirmed by amplification and sequencing of cytochrome b and/or beta-actin (data not shown). Expression plasmids. The lentivirus vectors pWPT expressing GFP, GFP-HBx, and GFP-WHx have been previously described  (60) (61) (62). The X coding regions (synthesized by Genewiz) from hepadnaviruses infecting the New World wooly monkey (Lagothrix) (WMHBx) and three distant bat species, including the roundleaf bat (Hipposideros cf. ruber), the horseshoe bat (Rhinolophus Alcyone), and the tent-making bat (Uroderma bilobatum) (RBHBx, HBHBx, TBHBx, respectively)  (52) , were expressed from the same vector. The X insert was ligated to the pWPT-GFP backbone between the PstI and NotI sites following the T4 DNA (New England BioLabs [NEB]; M0202) ligation protocol.
Host phylogenetic analyses. Sequences of primate or mammalian orthologous genes were retrieved from publicly available databases using UCSC Blat and NCBI BLASTN with the human sequence as the query. After including sequences obtained from de novo sequencing in this study, the sequences of the orthologues were codon aligned using Muscle  (67) , with minor adjustments (alignments are in supplemental data set 1 at https://figshare. com/articles/DatasetS1_Host_gene_alignments_used_in_the _study_fasta_format_and_phylogenetic_analyses_newick_format_Nsmce1-4_Smc1-6/6194813). The names of the sequences have been made uniform: the first three letters of the host genus name followed by the first three letters of the species name (e. g. , papAnu for Papio anubis or macMul for Macaca mulata). When sequences were retrieved using Blat on the primate full-genome assembly, the name of the genome assembly was used (e.
Approval from the local and national ethics committees (French Ministry of Research and Education numbers AC-2013-1871, DC-2013-1870, and DC-2008-235) and written informed consent from patients were obtained. Accession number(s). All the new Smc6 sequences are available at GenBank under accession numbers MF624755 to MF624761. Investissements d'Avenir [ANR-11-IDEX-0007] operated by the French National Research Agency, GrASP, to L. E. ), an ANRS grant (ECTZ19143 to L. E. ), a fellowship from La Ligue Contre le Cancer (to L. G. ), a grant from the Swiss National Science Foundation (310030-149626 to M. S. ), and by the Canton of Geneva. F. A. , L. G. , M. S. , and L. E. conceptualized the study. J. H. , M. S. , and L. E. acquired funding. F. F. , F. A. , L. G. , and L. E. designed the methodology.
com/articles/Dataset_S3_Phylogenetic_analyses_of_Smc5_6_in_mammals_fasta_and _newick_format_/6194840 and supplemental Table 2 at https://figshare. com/articles/Table_S2_Species_used_for_the_phylogeny_of_the_mammalian_Smc6 _and_for_the_experiments_/6194846). (D) Plasticity of the N-terminal region of Smc6 in bats. Truncated amino acid alignment (region from aa 20 to 47) of Smc6 sequences from bats. On the left is a cladogram of the bat Smc6. The amino acid alignment was performed with MUSCLE, and residue color coding is from RasMol (in Geneious [Biomatters]). Dashes indicate gaps.
ACKNOWLEDGMENTS We very sincerely thank  Léa Picard  and  Laurent Guéguen  for the Bioϩϩ analyses and input on evolutionary analyses,  Véronique Barateau  for technical support with the flow cytometry analyses,  Andrea Cimarelli ,  Olivier Hantz , and  Isabelle Chemin  for scientific discussions, and  Loic Peyrot ,  Anaelle Dubois , and  Francoise Berby  for technical assistance. We thank  Maud Michelet ,  Jennifer Molle ,  Loic Peyrot ,  Anaelle Dubois ,  Océane Floriot ,  Laura Dimer ,  Marie-Laure Plissonnier , and  Julie Lucifora  ( CRCL ) for the isolation of primary human hepatocytes and  Michel Rivoire 's,  Jean-Yves Mabrut 's, and  Guillaume Passot 's staff for providing liver resections. We thank  A. R. Lehmann  for providing anti-Smc6 antibody. We thank  Michael Emerman ,  Andrea Cimarelli , and  Oliver Fregoso  for their comments on the manuscript.
We thank all the contributors of publicly available genome sequences. This work was supported by an amfAR  Mathilde Krim Phase II Fellowship  ( 109140-58-RKHF  to L. E. ), a  Fondation pour la Recherche Médicale  ( FRM) Projet Innovant grant  ( ING20160435028  to L. E. ), a  FINOVI "recently settled scientist" grant  (to L. E. ), an  ANR   LabEx ECOFECT grant  ( ANR-11-LABX-0048  of  Université de Lyon , within the program.
SlowMo: minimal viable product The SlowMo platform is shown in Figure  2. The wireframed storyboards were iteratively coded alongside user testing to produce this minimal viable product. Multimedia Appendix 4 shows screenshots from the therapy sessions, and Multimedia Appendix 5 contains screenshots from the out-of-session mobile app. SlowMo consists of eight individual, faceto-face sessions, lasting 60 -90 minutes, which are supported by a webapp delivered on a laptop or tablet. When a person starts therapy, a unique user profile is set up which is linked to an identification code. No personally identifiable information is required by the system. The identification code allows the user-entered data to be stored on the webapp, which is then synchronised during sessions to a native, android app for use in daily life.
SlowMo native app: minimal viable product There is an emphasis throughout the intervention on practising skills inside and outside sessions, with the SlowMo native app providing a bridge between the therapy meetings and everyday life. The app works by unlocking new content towards the end of each session, based on the learning topic covered in the webapp. This new content is reviewed in session, and where possible the therapist supports the person to practice the use of the app outside the consulting room. The home screen has two viewing modes, one displaying worries and the other 'feeling safer' thoughts and strategies. When the app is in online mode, the home screens are synchronised from the webapp formulation. Thus, in the first session, the home screens automatically populate from the data inputted to the formulation, which consists of the person's worry bubbles.
From an agile science perspective, SlowMo could be implemented as a module within a broader digital therapy platform, with its intuitive monitoring function used to personalise intervention selection to the individual  [42, 74]. As mentioned, the bubble metaphor and interface is also applicable to a range of other difficulties and settings, and we are currently testing the feasibility of a standalone version of the app, Mo, to support stress management and wellbeing in the general population. In conclusion, this study is the first to demonstrate how an inclusive UCD method (which privileges the involvement of a wider range of service users than in conventional participatory design) can enhance the usability of therapy and augment developments in psychological theory and interventions. We hope that our work may serve as a prototypical example of how design thinking can challenge skeuomorphism in digital health, whereby therapy features made redundant by technology are unnecessarily replicated (e.
Acknowledgements We would like to acknowledge funding from the  Maudsley Charity , the  Helen Hamlyn Trust , and PAG and EK's  NIHR Senior Investigator awards , which supported the development of SlowMo therapy. PAG, EK and RE acknowledge support from the  National Institute for Health Research (NIHR) Biomedical Research Centre  of the  South London and Maudsley NHS Foundation Trust and King's College London. We are grateful to the people with lived experience of psychosis who participated in the project and supported the development of SlowMo.
Interviews were conducted in the interviewee's language of choice; nine were conducted in Mooré (the national language) and nine in French. They were recorded with the consent of the participants and then transcribed. Lastly, we analyzed all the available documents concerning the intervention (n = 8), including the intervention protocol, activity reports, minutes of oversight meetings, and training materials, etc. We constructed a fidelity grid based on the content of the intervention theory. This tool was used to document the presence or absence of programmed activities. All collected data were transferred to QDA Miner qualitative analysis software. We drew on the interview guide and the fidelity analysis grid to develop an analytical framework that guided the organization of the data in QDA Miner.
The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the sequencing data as well as the original sample and the environment where it was obtained from is crucial. To date, there are not any publicly available repositories able to capture environmental metadata pertaining to hydrocarbon-rich environments. As such, contextualization and comparative analysis among sequencing datasets derived from these environments is to a certain degree hindered or cannot be fully evaluated. The metagenomics data management system for hydrocarbon resources (MetaHCRs) enables the capturing of marker gene and whole metagenome sequencing data as well as over 300 contextual attributes associated with samples, organisms, environments and geological properties, among others.
Introduction The amount of data produced from metagenomic studies has dramatically increased with the introduction of massively parallel sequencing technologies  (1). Lower sequencing costs and faster processing times have enabled the identification and characterization of microbial assemblages from a number of diverse environments  (2). Appraisal of these microbial communities using the 16S rRNA marker gene empowers the taxonomic identification of the community members, whereas whole metagenome sequencing can provide further insights into the prospective biochemical processes, which could be taking place. The comparison of metagenomic datasets from samples originating from different environments can facilitate the identification of genes and pathways that are prevalent (or rare) under certain environmental conditions  (3).