Is Mathematics the Theory of Instantiated Structural Universals?

This paper rejects metaphysical realism about structural universals as a basis for mathematical realism about numbers, and argues that one construal of structural universals via non-well-founded sets should be resisted by the mathematical realist

Evaluating mapping parameters.

A. The performance on local eQTLs of selected mapping settings on cortex samples (average of the NSD and SD conditions) is measured by the percentage of expressed genes that have a significant local eQTL. The BXD-specific references were used. C. As in A but for liver samples.</p

MOESM1 of Social networks help to infer causality in the tumor microenvironment

Additional file 1: Table S1. xlsx. Networks

MOESM2 of Social networks help to infer causality in the tumor microenvironment

Additional file 2: Table S2. Results influence-based network vs. random networks

Domain architecture of FRD superfamily members.

<p>Models of domain architectures are mapped to the phylogenetic gene trees of bacterial (A) and eukaryotic (B) FRD homologs. Tree branch colors correspond to the color code of the models (see highlight color of model identifiers). The three conserved domains of the ‘eukaryotic structural core’ are colored, and other predicted domains are given in black. Domain forms indicate their function; rounded rectangle = binding of electron donor/hydrogen acceptor: FAD-binding, NADPH-binding (M3), FMN (M4); triangle = electron transfer agent: Ferredoxin/Fer2 (M8), Rieske (M4), DOMON (M10), peroxidase-like domain (M15); circle = regulation of enzyme activity: EF-hands (M14–M16); hexagon = protein-protein interaction: NADPH-oxidase-like domain (M16), SH3 (M17); ellipse = transport of small solutes: MSF (M6).</p

Sankar_et_al_data_file_4

Archive of tables (tab-delimited) of the normalized data used in machine learning for the Ler sections from data file 2, combined with the cell type assignment

Biological functions of eukaryotic FRD superfamily members from published experiments.

<p>Biological functions of eukaryotic FRD superfamily members from published experiments.</p

Phyletic profile and molecular function of the FRD superfamily.

<p>On the left-hand side, phyletic profile for 47 species: gene copy numbers are plotted in accordance with the species phylogeny (left) and gene families: The number of NOX homologs of a species is given in red cells, FRE homologs in blue cells, and preNOX in orange ones. Some cells are merged according to the family hierarchy. The number of predicted homologs is given in the last column of the phyletic profile. On the right-hand side, gene copies are represented by lines which link the corresponding species and protein families; the thickness of these lines indicates the number of gene copies. Colored lines flag experimentally confirmed gene functions: red = ROS-generating NADPH oxidase activity; blue = metalloreductase activity. Black circles mark species that possess p22phox homologs.</p

Sequence conservation logos and the proposed structure of the ferric reductase domain of protein groups from the FRD superfamily.

<p>A. Transmembrane domains TM3 to TM5 - as predicted for human cytochrome b-245 heavy chain (NOX2) - are indicated by gray rectangles. The cladogram indicates the phylogenetic relationship of the analyzed homologous groups. In the conservation logos, the height of the stacks indicates sequence conservation; the width of the stacks is proportional to the fraction of amino acids, thus narrowed within gapped regions. B. Proposed structure of ferric reductase domain with conserved amino acid residues corresponding to the annotation in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058126#pone-0058126-g004" target="_blank">figure 4A</a>.</p

Maximum likelihood phylogeny of the FRD superfamily.

<p>A. Phylogram of the NOX family rooted to DUOX genes (outgroup not shown). The tree topology suggests lineage-specific gene duplications in all major taxonomic clades. The NOX1-3 and NOX4 subfamilies possibly diverged before the emergence of metazoans. B. Phylogeny of eukaryotic gene families of the FRE group and the NOX group. According to this model, the DUOX family and NOX family form sister clades, but not the EF-hands containing protein families NOX5 and DUOX. C. Phylogenetic tree of the FRD superfamily. The tree topology proposes that the metazoan STEAP family (red) emerges from the bacterial clade at the base of the YedZ family. The gene AM1_3152 from the cyanobacterium <i>Acaryochloris marina</i> (strain MBIC 11017) (UniProtKB: B0CEP3) was probably obtained from an ancestral gene of the eukaryotic NOX5 family. Explanation: The names of gene families and gene groups are indicated with curly brackets. Branch colors correspond to those of the listed taxonomic groups.</p