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Modern Applied Statistics With S

Nature Communications 4: Article number: 1828 (2013); Published: 7 May 2013; Updated: 11 February 2014. In this Article, the museum catalogue numbers for the paratype and referred specimens of Acrotholus audeti nov. gen. et. sp. were inadvertently exchanged. The paratype reference should have been ROM 2964 and the catalogue number for the referred specimen should have been ROM 2962.

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Correction: Corrigendum: The oldest North American pachycephalosaurid and the hidden diversity of small-bodied ornithischian dinosaurs

It has been reported that the composition of human gut microbiota changes with age; however, few studies have used molecular techniques to investigate the long-term, sequential changes in gut microbiota composition. In this study, we investigated the sequential changes in gut microbiota composition in newborn to centenarian Japanese subjects. Fecal samples from 367 healthy Japanese subjects between the ages of 0 and 104 years were analyzed by high-throughput sequencing of amplicons derived from the V3-V4 region of the 16S rRNA gene. Analysis based on bacterial co-abundance groups (CAGs) defined by Kendall correlations between genera revealed that certain transition types of microbiota were enriched in infants, adults, elderly individuals and both infant and elderly subjects. More positive correlations between the relative abundances of genera were observed in the elderly-associated CAGs compared with the infant- and adult-associated CAGs. Hierarchical Ward’s linkage clustering based on the abundance of genera indicated five clusters, with median (interquartile range) ages of 3 (0–35), 33 (24–45), 42 (32–62), 77 (36–84) and 94 (86–98) years. Subjects were predominantly clustered with their matched age; however, some of them fell into mismatched age clusters. Furthermore, clustering based on the proportion of transporters predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) showed that subjects were divided into two age-related groups, the adult-enriched and infant/elderly-enriched clusters. Notably, all the drug transporters based on Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology groups were found in the infant/elderly-enriched cluster. Our results indicate some patterns and transition points in the compositional changes in gut microbiota with age. In addition, the transporter property prediction results suggest that nutrients in the gut might play an important role in changing the gut microbiota composition with age.

/pdf/age-related-changes-in-gut-microbiota-composition-from-a35vmo6dnh.pdf

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Understanding electrochemical potentials of cathode materials in rechargeable batteries

For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complemen...

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Isolated small theropod teeth are abundant in vertebrate microfossil assemblages, and are frequently used in studies of species diversity in ancient ecosystems. However, determining the taxonomic affinities of these teeth is problematic due to an absence of associated diagnostic skeletal material. Species such as Dromaeosaurus albertensis, Richardoestesia gilmorei, and Saurornitholestes langstoni are known from skeletal remains that have been recovered exclusively from the Dinosaur Park Formation (Campanian). It is therefore likely that teeth from different formations widely disparate in age or geographic position are not referable to these species. Tooth taxa without any associated skeletal material, such as Paronychodon lacustris and Richardoestesia isosceles, have also been identified from multiple localities of disparate ages throughout the Late Cretaceous. To address this problem, a dataset of measurements of 1183 small theropod teeth (the most specimen-rich theropod tooth dataset ever constructed) from North America ranging in age from Santonian through Maastrichtian were analyzed using multivariate statistical methods: canonical variate analysis, pairwise discriminant function analysis, and multivariate analysis of variance. The results indicate that teeth referred to the same taxon from different formations are often quantitatively distinct. In contrast, isolated teeth found in time equivalent formations are not quantitatively distinguishable from each other. These results support the hypothesis that small theropod taxa, like other dinosaurs in the Late Cretaceous, tend to be exclusive to discrete host formations. The methods outlined have great potential for future studies of isolated teeth worldwide, and may be the most useful non-destructive technique known of extracting the most data possible from isolated and fragmentary specimens. The ability to accurately assess species diversity and turnover through time based on isolated teeth will help illuminate patterns of evolution and extinction in these groups and potentially others in greater detail than has previously been thought possible without more complete skeletal material.

/pdf/multivariate-analyses-of-small-theropod-dinosaur-teeth-and-3qry998l7y.pdf

Multivariate analyses of small theropod dinosaur teeth and implications for paleoecological turnover through time.

Taphonomic biases dictate how organisms are represented in the fossil record, but their effect on studies of vertebrate diversity dynamics is poorly studied. In contrast to the high diversity and abundance of small-bodied animals in extant ecosystems, small-bodied dinosaurs are less common than their large-bodied counterparts, but it is unclear whether this reflects unique properties of dinosaurian ecosystems or relates to taphonomic biases. A new, fully domed pachycephalosaurid dinosaur, Acrotholus audeti, from the Santonian of Alberta predates incompletely domed taxa, and provides important new information on pachycephalosaur evolution and the completeness of the ornithischian fossil record. Here we provide the first empirical evidence that the diversity of small-bodied ornithischian dinosaurs is strongly underestimated based on ghost lineages and the high proportion of robust and diagnostic frontoparietal domes compared with other pachycephalosaur fossils. This suggests preservational biases have a confounding role in attempts to decipher vertebrate palaeoecology and diversity dynamics through the Mesozoic.

/pdf/the-oldest-north-american-pachycephalosaurid-and-the-hidden-qvq3nq28dv.pdf

The oldest North American pachycephalosaurid and the hidden diversity of small-bodied ornithischian dinosaurs

The faunal assemblage from the early Maastrichtian portion of the Horseshoe Canyon Formation is described on the basis of four new vertebrate microfossil localities and remains from the Albertosaur...

Faunal assemblages from the upper Horseshoe Canyon Formation, an early Maastrichtian cool-climate assemblage from Alberta, with special reference to the Albertosaurus sarcophagus bonebedThis article is one of a series of papers published in this Special Issue on the theme Albertosaurus.

Dromaeosaurids from the Maastrichtian of North America have a poor fossil record and are known largely from isolated teeth, which have typically been referred to taxa based on more complete material from earlier Campanian strata An almost complete maxilla with well-preserved dentition and an associated dentary from the Hell Creek Formation of Montana are used to establish a new dromaeosaurid taxon in the latest Maastrichtian, immediately prior to the end-Cretaceous extinction event Acheroraptor temertyorum gen et sp nov is differentiated from other dromaeosaurids on the basis of a hypertrophied postantral wall that projects posteriorly into the antorbital fenestra, a maxillary fenestra positioned low in the antorbital fossa and directly posterior to the promaxillary fenestra, and distinctive dentition with marked apicobasal ridges The new material allows a dromaeosaurid from the Maastrichtian of North America to be placed within a phylogenetic framework for the first time Phylogenetic analysis suggests Acheroraptor is a velociraptorine that is more closely related to Asian dromaeosaurids, including Tsaagan and Velociraptor, than it is to Dromaeosaurus, Saurornitholestes, or any other taxon from North America As part of the Lancian Tyrannosaurus–Triceratops fauna, A temertyorum is the latest occurring dromaeosaurid Its relationships and occurrence suggest a complex historical biogeographic scenario that involved multiple, bi-directional faunal interchanges between Asia and North America during the Late Cretaceous

Derek W. Larson

Papers

Correction: Corrigendum: The oldest North American pachycephalosaurid and the hidden diversity of small-bodied ornithischian dinosaurs

Multivariate analyses of small theropod dinosaur teeth and implications for paleoecological turnover through time.

The oldest North American pachycephalosaurid and the hidden diversity of small-bodied ornithischian dinosaurs

Faunal assemblages from the upper Horseshoe Canyon Formation, an early Maastrichtian cool-climate assemblage from Alberta, with special reference to the Albertosaurus sarcophagus bonebedThis article is one of a series of papers published in this Special Issue on the theme Albertosaurus.

A new dromaeosaurid (Dinosauria: Theropoda) with Asian affinities from the latest Cretaceous of North America