title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1807 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Osteology of the Late Triassic aetosaur Scutarx deltatylus (Archosauria: Pseudosuchia) link: https://peerj.com/articles/2411 last-modified: 2016-08-30 description: Aetosaurians are some of the most common fossils collected from the Upper Triassic Chinle Formation of Arizona, especially at the Petrified Forest National Park (PEFO). Aetosaurians collected from lower levels of the park include Desmatosuchus spurensis, Paratypothorax, Adamanasuchus eisenhardtae, Calyptosuchus wellesi, and Scutarx deltatylus. Four partial skeletons collected from the park between 2002 and 2009 represent the holotype and referred specimens of Scutarx deltatylus. These specimens include much of the carapace, as well as the vertebral column, and shoulder and pelvic girdles, and a new naming convention proposed for osteoderms descriptions better differentiates portions of the carapace and ventral armor. A partial skull from the holotype specimen represents the first aetosaur skull recovered and described from Arizona since the 1930s. The key morphological feature distinguishing Scutarx deltatylus is the presence of a prominent, triangular boss located in the posteromedial corner of the dorsal surface of the dorsal paramedian osteoderms. Scutarx deltatylus can be distinguished from closely related forms Calyptosuchus wellesi and Adamanasuchus eisenhardtae not only morphologically, but also stratigraphically. Thus, Scutarx deltatylus is potentially an index taxon for the upper part of the Adamanian biozone. creator: William G. Parker uri: https://doi.org/10.7717/peerj.2411 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Short and long term representation of an unfamiliar tone distribution link: https://peerj.com/articles/2399 last-modified: 2016-08-30 description: We report on a study conducted to extend our knowledge about the process of gaining a mental representation of music. Several studies, inspired by research on the statistical learning of language, have investigated statistical learning of sequential rules underlying tone sequences. Given that the mental representation of music correlates with distributional properties of music, we tested whether participants are able to abstract distributional information contained in tone sequences to form a mental representation. For this purpose, we created an unfamiliar music genre defined by an underlying tone distribution, to which 40 participants were exposed. Our stimuli allowed us to differentiate between sensitivity to the distributional properties contained in test stimuli and long term representation of the distributional properties of the music genre overall. Using a probe tone paradigm and a two-alternative forced choice discrimination task, we show that listeners are able to abstract distributional properties of music through mere exposure into a long term representation of music. This lends support to the idea that statistical learning is involved in the process of gaining musical knowledge. creator: Anja X. Cui creator: Charlette Diercks creator: Nikolaus F. Troje creator: Lola L. Cuddy uri: https://doi.org/10.7717/peerj.2399 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cui et al. title: Epidemiology of Salmonella sp. in California cull dairy cattle: prevalence of fecal shedding and diagnostic accuracy of pooled enriched broth culture of fecal samples link: https://peerj.com/articles/2386 last-modified: 2016-08-30 description: BackgroundThe primary objective of this cross-sectional study was to estimate the crude, seasonal and cull-reason stratified prevalence of Salmonella fecal shedding in cull dairy cattle on seven California dairies. A secondary objective was to estimate and compare the relative sensitivity (Se) and specificity (Sp) for pools of 5 and 10 enriched broth cultures of fecal samples for Salmonella sp. detection.MethodsSeven dairy farms located in the San Joaquin Valley of California were identified and enrolled in the study as a convenience sample. Cull cows were identified for fecal sampling once during each season between 2014 and 2015, specifically during spring, summer, fall, and winter, and 10 cows were randomly selected for fecal sampling at the day of their sale. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous four month’s herd management. Fecal samples were frozen until testing for Salmonella. After overnight enrichment in liquid broth, pools of enrichment broth (EBP) were created for 5 and 10 samples. All individual and pooled broths were cultured on selective media with putative Salmonella colonies confirmed by biochemical testing before being serogrouped and serotyped.ResultsA total of 249 cull cows were enrolled into the study and their fecal samples tested for Salmonella. The survey-weighted period prevalence of fecal shedding of all Salmonella sp. in the cull cow samples across all study herds and the entire study period was 3.42% (N = 249; SE 1.07). The within herd prevalence of Salmonella shed in feces did not differ over the four study seasons (P = 0.074). The Se of culture of EBP of five samples was 62.5% (SE = 17.12), which was not statistically different from the Se of culture of EBP of 10 (37.5%, SE = 17.12, P = 0.48). The Sp of culture of EBP of five samples was 95.24% (SE = 3.29) and for pools of 10 samples was 100.00% (SE = 0). There was no statistical difference between the culture relative specificities of EBP of 5 and 10 (P > 0.99).DiscussionOur study showed a numerically higher prevalence of Salmonella shedding in the summer, although the results were not significant, most likely due to a lack of power from the small sample size. A higher prevalence in summer months may be related to heat stress. To detect Salmonella, investigators may expect a 62.5% sensitivity for culture of EBP of five, relative to individual fecal sample enrichment and culture. In contrast, culture of EBP of 10 samples resulted in a numerically lower Se. Culture of EBP of size 5 or 10 samples, given similar prevalence and limit of detection, can be expected to yield specificities of 95 and 100%, respectively. creator: Omran A. Abu Aboud creator: John M. Adaska creator: Deniece R. Williams creator: Paul V. Rossitto creator: John D. Champagne creator: Terry W. Lehenbauer creator: Robert Atwill creator: Xunde Li creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.2386 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Abu Aboud et al. title: An examination of species limits in the Aulacorhynchus “prasinus” toucanet complex (Aves: Ramphastidae) link: https://peerj.com/articles/2381 last-modified: 2016-08-30 description: The number of species recognized in Aulacorhynchus toucanets has varied tremendously over the past century. Revisors seem to disagree on whether head and bill coloration are useful indicators of species limits, especially in the A. “prasinus” complex. Using morphometrics, I tested the hypothesis that the major color-based subspecific groups of A. “prasinus” sensu lato are simply “cookie-cutter” (i.e., morphologically nearly identical) toucanets with different head and bill colorations. Univariate and multivariate analyses show that they are not simply morphological replicates of different colors: a complex array of morphometric similarities and dissimilarities occur between the major subspecific groups, and these variations differ between the sexes. Latitude and longitude had a small but significant association with female (but not male) PC1 and PC2. Hybridization and intergradation were also considered using plumage and bill characters as a surrogate to infer gene flow. Hybridization as indicated by phenotype appears to be substantial between A. “p.” cyanolaemus and A. “p.” atrogularis and nonexistent between other major groups, although from genetic evidence it is likely rare between A. “p.” albivitta and A. “p.” cyanolaemus. The congruence and complexities of the morphological and color changes occurring among these groups suggest that ecological adaptation (through natural selection) and social selection have co-occurred among these groups and that species limits are involved. Further, hybridization is not evident at key places, despite in many cases (hypothetical) opportunity for gene flow. Consequently, I recommend that this complex be recognized as comprising five biological species: A. wagleri, prasinus, caeruleogularis, albivitta, and atrogularis. Four of these also have valid subspecies within them, and additional work may eventually support elevation of some of these subspecies to full species. Species limits in South America especially need more study. creator: Kevin Winker uri: https://doi.org/10.7717/peerj.2381 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Winker title: A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units link: https://peerj.com/articles/2341 last-modified: 2016-08-30 description: A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions. creator: Matthew A. Jackson creator: Jordana T. Bell creator: Tim D. Spector creator: Claire J. Steves uri: https://doi.org/10.7717/peerj.2341 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jackson et al. title: Genome sequencing-assisted identification and the first functional validation of N-acyl-homoserine-lactone synthases from the Sphingomonadaceae family link: https://peerj.com/articles/2332 last-modified: 2016-08-30 description: BackgroundMembers of the genus Novosphingobium have been isolated from a variety of environmental niches. Although genomics analyses have suggested the presence of genes associated with quorum sensing signal production e.g., the N-acyl-homoserine lactone (AHL) synthase (luxI) homologs in various Novosphingobium species, to date, no luxI homologs have been experimentally validated.MethodsIn this study, we report the draft genome of the N-(AHL)-producing bacterium Novosphingobium subterraneum DSM 12447 and validate the functions of predicted luxI homologs from the bacterium through inducible heterologous expression in Agrobacterium tumefaciens strain NTL4. We developed a two-dimensional thin layer chromatography bioassay and used LC-ESI MS/MS analyses to separate, detect and identify the AHL signals produced by the N. subterraneum DSM 12447 strain.ResultsThree predicted luxI homologs were annotated to the locus tags NJ75_2841 (NovINsub1), NJ75_2498 (NovINsub2), and NJ75_4146 (NovINsub3). Inducible heterologous expression of each luxI homologs followed by LC-ESI MS/MS and two-dimensional reverse phase thin layer chromatography bioassays followed by bioluminescent ccd camera imaging indicate that the three LuxI homologs are able to produce a variety of medium-length AHL compounds. New insights into the LuxI phylogeny was also gleemed as inferred by Bayesian inference.DiscussionThis study significantly adds to our current understanding of quorum sensing in the genus Novosphingobium and provide the framework for future characterization of the phylogenetically interesting LuxI homologs from members of the genus Novosphingobium and more generally the family Sphingomonadaceae. creator: Han Ming Gan creator: Lucas K. Dailey creator: Nigel Halliday creator: Paul Williams creator: André O. Hudson creator: Michael A. Savka uri: https://doi.org/10.7717/peerj.2332 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gan et al. title: Minimum information about tolerogenic antigen-presenting cells (MITAP): a first step towards reproducibility and standardisation of cellular therapies link: https://peerj.com/articles/2300 last-modified: 2016-08-30 description: Cellular therapies with tolerogenic antigen-presenting cells (tolAPC) show great promise for the treatment of autoimmune diseases and for the prevention of destructive immune responses after transplantation. The methodologies for generating tolAPC vary greatly between different laboratories, making it difficult to compare data from different studies; thus constituting a major hurdle for the development of standardised tolAPC therapeutic products. Here we describe an initiative by members of the tolAPC field to generate a minimum information model for tolAPC (MITAP), providing a reporting framework that will make differences and similarities between tolAPC products transparent. In this way, MITAP constitutes a first but important step towards the production of standardised and reproducible tolAPC for clinical application. creator: Phillip Lord creator: Rachel Spiering creator: Juan C. Aguillon creator: Amy E. Anderson creator: Silke Appel creator: Daniel Benitez-Ribas creator: Anja ten Brinke creator: Femke Broere creator: Nathalie Cools creator: Maria Cristina Cuturi creator: Julie Diboll creator: Edward K. Geissler creator: Nick Giannoukakis creator: Silvia Gregori creator: S. Marieke van Ham creator: Staci Lattimer creator: Lindsay Marshall creator: Rachel A. Harry creator: James A. Hutchinson creator: John D. Isaacs creator: Irma Joosten creator: Cees van Kooten creator: Ascension Lopez Diaz de Cerio creator: Tatjana Nikolic creator: Haluk Barbaros Oral creator: Ljiljana Sofronic-Milosavljevic creator: Thomas Ritter creator: Paloma Riquelme creator: Angus W. Thomson creator: Massimo Trucco creator: Marta Vives-Pi creator: Eva M. Martinez-Caceres creator: Catharien M.U. Hilkens uri: https://doi.org/10.7717/peerj.2300 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lord et al. title: Microsatellite loci in the tiger shark and cross-species amplification using pyrosequencing technology link: https://peerj.com/articles/2205 last-modified: 2016-08-30 description: The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide. creator: Natália J. Mendes creator: Vanessa P. Cruz creator: Fernando Y. Ashikaga creator: Sâmia M. Camargo creator: Claudio Oliveira creator: Andrew N. Piercy creator: George H. Burgess creator: Rui Coelho creator: Miguel N. Santos creator: Fernando F. Mendonça creator: Fausto Foresti uri: https://doi.org/10.7717/peerj.2205 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mendes et al. title: Depression, anxiety, and stress in partners of Australian combat veterans and military personnel: a comparison with Australian population norms link: https://peerj.com/articles/2373 last-modified: 2016-08-25 description: Partners of Australian combat veterans are at an increased risk of experiencing mental health problems. The present study provides a comparative analysis of the mental health of partners of veterans with that of the Australian normative data. To compare different types of groups of partners, the study samples comprised: (a) partners of Australian combat veterans (Sample 1: n = 282, age M = 60.79, SD = 5.05), (b) a sub-sample of partners of Australian combat veterans from the previous sample (Sample 2: n = 50; M = 60.06, SD = 4.80), (c) partners of Special Air Services Regiment (SASR) personnel (Sample 3: n = 40, age M = 34.39SD = 7.01), and (d) partners of current serving military (non-SASR) personnel (Sample 4: n = 38, age M = 32.37, SD = 6.20). Respondents completed measures assessing their reported levels of depression, anxiety, and stress. Samples 1 and 2 comprised partners of Australian military veterans who reported significantly greater symptoms of depression, anxiety, and stress than the comparative population norms. The sample of SASR personnel partners (Sample 3) reported significantly lower levels of depression and anxiety, whereas the sample with non-SASR personnel partners (Sample 4) reported a significantly greater stress symptomatology than the comparative norms. Number of deployments was found to be associated with depression, anxiety, and stress in partners of non-SASR veterans (Sample 4). Lessons and protective factors can be learnt from groups within the current military as to what may assist partners and families to maintain a better level of psychosocial health. creator: Gail V. MacDonell creator: Navjot Bhullar creator: Einar B. Thorsteinsson uri: https://doi.org/10.7717/peerj.2373 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 MacDonell et al. title: Thermal treatment and leaching of biochar alleviates plant growth inhibition from mobile organic compounds link: https://peerj.com/articles/2385 last-modified: 2016-08-25 description: Recent meta-analyses of plant responses to biochar boast positive average effects of between 10 and 40%. Plant responses, however, vary greatly across systems, and null or negative biochar effects are increasingly reported. The mechanisms responsible for such responses remain unclear. In a glasshouse experiment we tested the effects of three forestry residue wood biochars, applied at five dosages (0, 5, 10, 20, and 50 t/ha) to a temperate forest drystic cambisol as direct surface applications and as complete soil mixes on the herbaceous pioneers Lolium multiflorum and Trifolium repens. Null and negative effects of biochar on growth were found in most cases. One potential cause for null and negative plant responses to biochar is plant exposure to mobile compounds produced during pyrolysis that leach or evolve following additions of biochars to soil. In a second glasshouse experiment we examined the effects of simple leaching and heating techniques to ameliorate potentially phytotoxic effects of volatile and leachable compounds released from biochar. We used Solid Phase Microextraction (SPME)–gas chromatography–mass spectrometry (GC-MS) to qualitatively describe organic compounds in both biochar (through headspace extraction), and in the water leachates (through direct injection). Convection heating and water leaching of biochar prior to application alleviated growth inhibition. Additionally, growth was inhibited when filtrate from water-leached biochar was applied following germination. SPME-GC-MS detected primarily short-chained carboxylic acids and phenolics in both the leachates and solid chars, with relatively high concentrations of several known phytotoxic compounds including acetic acid, butyric acid, 2,4-di-tert-butylphenol and benzoic acid. We speculate that variable plant responses to phytotoxic organic compounds leached from biochars may largely explain negative plant growth responses and also account for strongly species-specific patterns of plant responses to biochar amendments in short-term experiments. creator: Nigel V. Gale creator: Tara E. Sackett creator: Sean C. Thomas uri: https://doi.org/10.7717/peerj.2385 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Gale et al.