title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1627 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles link: https://peerj.com/articles/4375 last-modified: 2018-02-13 description: Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice. creator: Heather Piwowar creator: Jason Priem creator: Vincent Larivière creator: Juan Pablo Alperin creator: Lisa Matthias creator: Bree Norlander creator: Ashley Farley creator: Jevin West creator: Stefanie Haustein uri: https://doi.org/10.7717/peerj.4375 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Piwowar et al. title: Under the armor: X-ray computed tomographic reconstruction of the internal skeleton of Coahomasuchus chathamensis (Archosauria: Aetosauria) from the Upper Triassic of North Carolina, USA, and a phylogenetic analysis of Aetosauria link: https://peerj.com/articles/4368 last-modified: 2018-02-13 description: Aetosauria is a clade of heavily armored, quadrupedal omnivorous to herbivorous archosaurs known from the Late Triassic across what was the supercontinent of Pangea. Their abundance in many deposits relative to the paucity of other Triassic herbivores indicates that they were key components of Late Triassic ecosystems. However, their evolutionary relationships remain contentious due, in large part, to their extensive dermal armor, which often obstructs observation of internal skeletal anatomy and limits access to potentially informative characters. In an attempt to address this problem we reanalyzed the holotype of a recently described species of Coahomasuchus, C. chathamensis, from the Sanford sub-basin of North Carolina using computed tomography (CT). CT scans of the holotype specimen clarify preservation of the skeleton, revealing several articulated vertebrae and ribs, an isolated vertebra, left ulna, left scapula, and the right humerus, though none of the material resulted in updated phylogenetic scorings. Reexamination of aetosaur materials from the holotype locality also indicates that several isolated osteoderms and elements of the appendicular skeleton are newly referable. Based on these results, we update the Coahomasuchus chathamensis hypodigm and conduct a revised phylogenetic analysis with improved character scorings for Coahomasuchus and several other aetosaurs. Our study recovers Coahomasuchus in a polytomy with Aetosaurus and the Typothoracinae, in contrast with a recent analysis that recovered Coahomasuchus as a wild-card taxon. creator: Devin K. Hoffman creator: Andrew B. Heckert creator: Lindsay E. Zanno uri: https://doi.org/10.7717/peerj.4368 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hoffman et al. title: Frequency and developmental timing of linear enamel hypoplasia defects in Early Archaic Texan hunter-gatherers link: https://peerj.com/articles/4367 last-modified: 2018-02-13 description: Digital photographs taken under controlled conditions were used to examine the incidence of linear enamel hypoplasia defects (LEHs) in burials from the Buckeye Knoll archaeological site (41VT98 Victoria county, Texas), which spans the Early to Late Archaic Period (ca. 2,500–6,500 BP uncorrected radiocarbon). The majority (68 of 74 burials) date to the Texas Early Archaic, including one extremely early burial dated to 8,500 BP. The photogrammetric data collection method also results in an archive for Buckeye Knoll, a significant rare Archaic period collection that has been repatriated and reinterred. We analyzed the incidence and developmental timing of LEHs in permanent canines. Fifty-nine percent of permanent canines (n = 54) had at least one defect. There were no significant differences in LEH frequency between the maxillary and mandibular canines (U = 640.5, n1 = 37, n2 = 43, p = .110). The sample studied (n = 92 permanent canines) had an overall mean of 0.93 LEH defect per tooth, with a median of one defect, and a mode of zero defects. Average age at first insult was 3.92 (median = 4.00, range = 2.5–5.4) and the mean age of all insults per individual was 4.18 years old (range = 2.5–5.67). Age at first insult is consistent with onset of weaning stress—the weaning age range for hunter-gatherer societies is 1–4.5. Having an earlier age of first insult was associated with having more LEHs (n = 54, rho = −0.381, p = 0.005). creator: J. Colette Berbesque creator: Kara C. Hoover uri: https://doi.org/10.7717/peerj.4367 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Berbesque and Hoover title: A six-year grazing exclusion changed plant species diversity of a Stipa breviflora desert steppe community, northern China link: https://peerj.com/articles/4359 last-modified: 2018-02-13 description: Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe community in Northern China, we established six plots to examine spatial patterns of plant species diversity under grazed and fenced conditions, respectively. We addressed three aspects of species diversity: (1) The logistic, exponential and power models were used to describe the species-area curve (SAR). Species richness, abundance and Shannon diversity values change differently with increasing sampling areas inside and outside of the fence. The best fitted model for SAR was the logistic model. Excluding grazers had a significant impact on the shape of SAR. (2) Variograms was applied to examine the spatial characteristics of plant species diversity. We found strong spatial autocorrelations in the diversity variables both inside and outside the fence. After grazing exclusion, the spatial heterogeneity decreased in species richness, increased in abundance and did not change in Shannon diversity. (3) We used variance partitioning to determine the relative contributions of spatial and environmental factors to plant species diversity patterns. Environmental factors explained the largest proportion of variation in species diversity, while spatial factors contributed little. Our results suggest that grazing enclosures decreased species diversity patterns and the spatial pattern of the S. breviflora desert steppe community was predictable. creator: Xing Wang creator: Xinguo Yang creator: Lei Wang creator: Lin Chen creator: Naiping Song creator: Junlong Gu creator: Yi Xue uri: https://doi.org/10.7717/peerj.4359 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: A new slider turtle (Testudines: Emydidae: Deirochelyinae: Trachemys) from the late Hemphillian (late Miocene/early Pliocene) of eastern Tennessee and the evolution of the deirochelyines link: https://peerj.com/articles/4338 last-modified: 2018-02-13 description: Trachemys (Testudines: Emydidae) represents one of the most well-known turtle genera today. The evolution of Trachemys, while being heavily documented with fossil representatives, is not well understood. Numerous fossils from the late Hemphillian Gray Fossil Site (GFS) in northeastern Tennessee help to elucidate its evolution. The fossil Trachemys at the GFS represent a new species. The new taxon, Trachemys haugrudi, is described, and currently represents the most thoroughly described fossil emydid species known. A phylogenetic analysis, including 31 species, focusing on the subfamily Deirochelyinae is performed that includes the new fossil species, along with numerous other modern and fossil deirochelyine species, representing the first phylogenetic analysis published that includes several fossil deirochelyines. The phylogenetic analysis, utilizing morphological evidence, provides monophyletic clades of all modern deirochelyines, including Chrysemys, Deirochelys, Pseudemys, Malaclemys, Graptemys, and Trachemys. A strict consensus tree finds the recently described fossil species Graptemys kerneri to be part of a clade of Graptemys + Malaclemys. Three fossil taxa, including one previously referred to Pseudemys (Pseudemys caelata) and two to Deirochelys (Deirochelys carri and Deirochelys floridana) are found to form a clade with modern Deirochelys reticularia reticularia, with D. floridana sister to the other members of the clade. Chrysemys is found to be part of a basal polytomy with Deirochelys in relation to other deirochelyine taxa. Two fossil taxa previously referred to Chrysemys (Chrysemys timida and Chrysemys williamsi) form a paraphyly with the modern Chrysemys picta picta and Deirochelys, and may be referable to distinct genera. Additionally, fossil taxa previously attributed to Trachemys (Trachemys hillii, Trachemys idahoensis, Trachemys inflata, and Trachemys platymarginata) and T. haugrudi are found to form a clade separate from clades of northern and southern Trachemys species, potentially suggesting a distinct lineage of Trachemys with no modern survivors. Hypotheses of phylogenetic relationships mostly agree between the present study and previous ones, although the inclusion of fossil taxa provides further clues to the evolution of parts of the Deirochelyinae. The inclusion of more fossil taxa and characters may help resolve the placement of some taxa, and further elucidate the evolution of these New World turtles. creator: Steven E. Jasinski uri: https://doi.org/10.7717/peerj.4338 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Jasinski title: Effects of osmolytes and macromolecular crowders on stable GAAA tetraloops and their preference for a CG closing base pair link: https://peerj.com/articles/4236 last-modified: 2018-02-13 description: Osmolytes and macromolecular crowders have the potential to influence the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in vivo. To further understand the cellular function of RNA we observed the effects of a model osmolyte, polyethylene glycol (PEG) 200, and a model macromolecular crowding agent, PEG 8000, on the GAAA tetraloop motif. GAAA tetraloops are conserved, stable tetraloops, and are critical participants in RNA tertiary structure. They also have a thermodynamic preference for a CG closing base pair. The thermal denaturation of model hairpins containing GAAA loops was monitored using UV-Vis spectroscopy in the presence and absence of PEG 200 or PEG 8000. Both of the cosolutes tested influenced the thermodynamic preference for a CG base pair by destabilizing the loop with a CG closing base pair relative to the loop with a GC closing base pair. This result also extended to a related DNA triloop, which provides further evidence that the interactions between the loop and closing base pair are identical for the d(GCA) triloop and the GAAA tetraloop. Our results suggest that in the presence of model PEG molecules, loops with a GC closing base pair may retain some preferential interactions with the cosolutes that are lost in the presence of the CG closing base pair. These results reveal that relatively small structural changes could influence how neutral cosolutes tune the stability and function of secondary structure motifs in vivo. creator: Kaethe N. Leonard creator: Joshua M. Blose uri: https://doi.org/10.7717/peerj.4236 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Leonard and Blose title: The effect of supragingival glycine air polishing on periodontitis during maintenance therapy: a randomized controlled trial link: https://peerj.com/articles/4371 last-modified: 2018-02-12 description: BackgroundGlycine air polishing has been proved to be safe, comfortable and time-saving. Whether it could substitute ultrasonic scaling to remove dental plaque biofilm during periodontal maintenance remains unclear. The purposes of this study were to evaluate the effect of supragingival glycine air polishing (SGAP) on the subgingival periodontal pathogens during maintenance therapy and to check the association of periodontal pathogens and clinical parameters.MethodsTwenty-three chronic periodontitis patients during their maintenance therapy were enrolled in the 12-week study. According to randomized split-mouth design, the test side was treated with SGAP (65 μm), while the control side was treated with supragingival ultrasonic scaling and polishing (SUSP) with rubber cup. Clinical examination including plaque index (PLI), probing depth (PD), bleeding index (BI) were performed at baseline and 12 weeks post-treatment. Sampling of the subgingival plaque at each investigational site (mesiobuccal site of the mandibular first molar) was performed at baseline and 2, 4, 8, 12 weeks after maintenance treatment. Four periodontal pathogens including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola and Fusobacterium nucleatum were detected by 16S rDNA polymerase chain reaction.ResultsClinical status generally improved after treatment in both groups. PLI in both groups, PD in SGAP group and bleeding on probing (%) in SUSP group significantly decreased after treatment (p < 0.05). There was no significant difference of clinical parameters between two groups before and after treatment. The detection rates of P. gingivalis, T. denticola in both groups, T. forsythia in SUSP group and F. nucleatum in SGAP group decreased after maintenance treatment in both groups, although no significant difference was found, and it rebound to baseline level at 12 weeks after maintenance treatment. There was no significant difference between SGAP group and SUSP group at any time point. T. denticola-positive sites had significantly greater BI than T. denticola-negative sites (p < 0.05).DiscussionSupragingival glycine air polishing had a reliable effect in removing subgingival dental plaque biofilm during maintenance period, and three months may be a proper maintenance interval for pockets not more than 5 mm. creator: Hongye Lu creator: Lu He creator: Yibing Zhao creator: Huanxin Meng uri: https://doi.org/10.7717/peerj.4371 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lu et al. title: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip link: https://peerj.com/articles/4364 last-modified: 2018-02-12 description: Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates. creator: Joshua M. Miller creator: Marco Festa-Bianchet creator: David W. Coltman uri: https://doi.org/10.7717/peerj.4364 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Miller et al. title: A bibliometric analysis in gene research of myocardial infarction from 2001 to 2015 link: https://peerj.com/articles/4354 last-modified: 2018-02-12 description: ObjectivesWe aimed to evaluate the global scientific output of gene research of myocardial infarction and explore their hotspots and frontiers from 2001 to 2015, using bibliometric methods.MethodsArticles about the gene research of myocardial infarction between 2001 and 2015 were retrieved from the Web of Science Core Collection (WoSCC). We used the bibliometric method and Citespace V to analyze publication years, journals, countries, institutions, research areas, authors, research hotspots, and trends. We plotted the reference co-citation network, and we used key words to analyze the research hotspots and trends.ResultsWe identified 1,853 publications on gene research of myocardial research from 2001 to 2015, and the annual publication number increased with time. Circulation published the highest number of articles. United States ranked highest in the countries with most publications, and the leading institute was Harvard University. Relevant publications were mainly in the field of Cardiovascular system cardiology. Keywords and references analysis indicated that gene expression, microRNA and young women were the research hotspots, whereas stem cell, chemokine, inflammation and cardiac repair were the frontiers.ConclusionsWe depicted gene research of myocardial infarction overall by bibliometric analysis. Mesenchymal stem cells Therapy, MSCs-derived microRNA and genetic modified MSCs are the latest research frontiers. Related studies may pioneer the future direction of this filed in next few years. Further studies are needed. creator: Huaqiang Zhou creator: Wulin Tan creator: Zeting Qiu creator: Yiyan Song creator: Shaowei Gao uri: https://doi.org/10.7717/peerj.4354 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhou et al. title: An observational study on risk of secondary cancers in chronic myeloid leukemia patients in the TKI era in the United States link: https://peerj.com/articles/4342 last-modified: 2018-02-12 description: IntroductionThe treatment with tyrosine kinase inhibitors (TKIs) has drastically improved the outcome of chronic myeloid leukemia (CML) patients. This study was conducted to examine the risk of secondary cancers (SCs) in the CML patients who were diagnosed and treated in the TKI era in the United States.MethodsThe surveillance epidemiology and end results (SEER) database was used to identify CML patients who were diagnosed and received treatment during January 2002–December 2014. Standardized incidence ratios (SIRs) and absolute excess risks (AER) were calculated.ResultsOverall, 511 SCs (excluding acute leukemia) developed in 9,200 CML patients followed for 38,433 person-years. The risk of developing SCs in the CML patients was 30% higher than the age, sex and race matched standard population (SIR 1.30, 95% CI: 1.2–1.40; p < 0.001). The SIRs for CLL (SIR 3.4, 95% CI: 2–5.5; p < 0.001), thyroid (SIR 2.2, 95% CI: 1.2–3.5; p < 0.001), small intestine (SIR 3.1, 95% CI: 1.1–7; p = 0.004), gingiva (SIR 3.7, 95% CI: 1.2–8.7; p = 0.002), stomach (SIR 2.1, 95% CI: 1.1–3.5; p = 0.005), lung (SIR 1.4, 95% CI: 1.1–1.7; p = 0.006) and prostate (SIR 1.3, 95% CI: 1.02–1.6; p = 0.026) cancer among CML patients were significantly higher than the general population. The risk of SCs was higher irrespective of age and it was highest in the period 2–12 months after the diagnosis of CML. The risk of SCs in women was similar to that of the general population.ConclusionCML patients diagnosed and treated in the TKI era in the United States are at an increased risk of developing a second malignancy. The increased risk of SCs in the early period after CML diagnosis suggests that the risk of SCs may be increased due to the factors other than TKIs treatment. creator: Vivek Kumar creator: Mohit Garg creator: Neha Chaudhary creator: Abhinav Binod Chandra uri: https://doi.org/10.7717/peerj.4342 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kumar et al.