title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1945
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Phylogeographic structure and northward range expansion in the barnacle Chthamalus fragilis
link: https://peerj.com/articles/926
last-modified: 2015-04-30
description: The barnacle Chthamalus fragilis is found along the US Atlantic seaboard historically from the Chesapeake Bay southward, and in the Gulf of Mexico. It appeared in New England circa 1900 coincident with warming temperatures, and is now a conspicuous member of rocky intertidal communities extending through the northern shore of Cape Cod, Massachusetts. The origin of northern C. fragilis is debated. It may have spread to New England from the northern end of its historic range through larval transport by ocean currents, possibly mediated by the construction of piers, marinas, and other anthropogenic structures that provided new hard substrate habitat. Alternatively, it may have been introduced by fouling on ships originating farther south in its historic distribution. Here we examine mitochondrial cytochrome c oxidase I sequence diversity and the distribution of mitochondrial haplotypes of C. fragilis from 11 localities ranging from Cape Cod, to Tampa Bay, Florida. We found significant genetic structure between northern and southern populations. Phylogenetic analysis revealed three well-supported reciprocally monophyletic haplogroups, including one haplogroup that is restricted to New England and Virginia populations. While the distances between clades do not suggest cryptic speciation, selection and dispersal barriers may be driving the observed structure. Our data are consistent with an expansion of C. fragilis from the northern end of its mid-19th century range into Massachusetts.
creator: Annette F. Govindarajan
creator: Filip Bukša
creator: Katherine Bockrath
creator: John P. Wares
creator: Jesús Pineda
uri: https://doi.org/10.7717/peerj.926
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Govindarajan et al.

title: Temporal changes in nasopharyngeal carriage of Streptococcus pneumoniae serotype 1 genotypes in healthy Gambians before and after the 7-valent pneumococcal conjugate vaccine
link: https://peerj.com/articles/903
last-modified: 2015-04-30
description: Streptococcus pneumoniae serotype 1 is one of the leading causes of invasive pneumococcal disease. However, this invasive serotype is hardly found in nasopharyngeal asymptomatic carriage and therefore large epidemiological studies are needed to assess the dynamics of serotype 1 infection. Within the context of a large cluster randomized trial conducted in rural Gambia to assess the impact of PCV-7 vaccination on nasopharyngeal carriage, we present an ancillary analysis describing the prevalence of nasopharyngeal carriage of pneumococcal serotype 1 and temporal changes of its more frequent genotypes. Nasopharyngeal swabs (NPS) were collected before PCV-7 vaccination (December 2003–May 2004) and up to 30 months after PCV-7 vaccination. The post-vaccination time was divided in three periods to ensure an equal distribution of the number of samples: (1) July 2006–March 2007, (2) April 2007–March 2008 and (3) April 2008–Feb 2009. S. pneumoniae serotype 1 were genotyped by MLST. Serotype 1 was recovered from 87 (0.71%) of 12,319 NPS samples collected. In the pre-vaccination period, prevalence of serotype 1 was 0.47% in both study arms. In the post-vaccination periods, prevalence in the fully vaccinated villages ranged between 0.08% in period 1 and 0.165% in period 2, while prevalence in partly vaccinated villages was between 0.17% in period 3 and 1.34% in period 2. Overall, four different genotypes were obtained, with ST3081 the most prevalent (60.71%), followed by ST618 (29.76%). ST3081 was found only in post-vaccination period 2 and 3, while ST618 had disappeared in post-vaccination period 3. Distribution of these major genotypes was similar in both study arms. Emergence of ST3081 and concomitant disappearance of ST618 may suggest a change in the molecular epidemiology of pneumococcal serotype 1 in this region. This change is not likely to be associated with the introduction of PCV-7 which lacks serotype 1, as it was observed simultaneously in both study arms. Future population-based epidemiological studies will provide further evidence of substantive changes in the pneumococcal serotype 1 epidemiology and the likely mechanisms.
creator: Chinelo Ebruke
creator: Anna Roca
creator: Uzochukwu Egere
creator: Ousainou Darboe
creator: Philip C. Hill
creator: Brian Greenwood
creator: Brendan W. Wren
creator: Richard A. Adegbola
creator: Martin Antonio
uri: https://doi.org/10.7717/peerj.903
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ebruke et al.

title: Indirect effects of overfishing on Caribbean reefs: sponges overgrow reef-building corals
link: https://peerj.com/articles/901
last-modified: 2015-04-28
description: Consumer-mediated indirect effects at the community level are difficult to demonstrate empirically. Here, we show an explicit indirect effect of overfishing on competition between sponges and reef-building corals from surveys of 69 sites across the Caribbean. Leveraging the large-scale, long-term removal of sponge predators, we selected overfished sites where intensive methods, primarily fish-trapping, have been employed for decades or more, and compared them to sites in remote or marine protected areas (MPAs) with variable levels of enforcement. Sponge-eating fishes (angelfishes and parrotfishes) were counted at each site, and the benthos surveyed, with coral colonies scored for interaction with sponges. Overfished sites had >3 fold more overgrowth of corals by sponges, and mean coral contact with sponges was 25.6%, compared with 12.0% at less-fished sites. Greater contact with corals by sponges at overfished sites was mostly by sponge species palatable to sponge predators. Palatable species have faster rates of growth or reproduction than defended sponge species, which instead make metabolically expensive chemical defenses. These results validate the top-down conceptual model of sponge community ecology for Caribbean reefs, as well as provide an unambiguous justification for MPAs to protect threatened reef-building corals.An unanticipated outcome of the benthic survey component of this study was that overfished sites had lower mean macroalgal cover (23.1% vs. 38.1% for less-fished sites), a result that is contrary to prevailing assumptions about seaweed control by herbivorous fishes. Because we did not quantify herbivores for this study, we interpret this result with caution, but suggest that additional large-scale studies comparing intensively overfished and MPA sites are warranted to examine the relative impacts of herbivorous fishes and urchins on Caribbean reefs.
creator: Tse-Lynn Loh
creator: Steven E. McMurray
creator: Timothy P. Henkel
creator: Jan Vicente
creator: Joseph R. Pawlik
uri: https://doi.org/10.7717/peerj.901
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Loh et al.

title: Inductive heating kills cells that contribute to plaque: a proof-of-concept
link: https://peerj.com/articles/929
last-modified: 2015-04-28
description: Inducing cell death by heating targeted particles shows promise in cancer treatment. Here, we aim to demonstrate the feasibility of extending the use of this technique to treat and remove vascular deposits and thrombosis. We used induction heating of macrophages, which are key contributors to atherosclerosis and have demonstrated clear feasibility for heating and destroying these cells using ferromagnetic and pure iron particles. Specifically, iron particles achieved maximum temperatures of 51 ± 0.5 °C and spherical particles achieved a maximum temperature of 43.9 ± 0.2 °C (N = 6) after 30 min of inductive heating. Two days of subsequent observation demonstrated that inductive heating led to a significant reduction in cell number. Prior to induction heating, cell density was 105,000 ± 20,820 cells/ml (N = 3). This number was reduced to 6,666 ± 4,410 cells/ml for the spherical particles and 16,666 ± 9,280 cells/ml for the iron particles 24 h after inductive heating. Though cell density increased on the second day following inductive heating, the growth was minimal. Cells grew to 26,667 ± 6,670 cells/ml and 30,000 ± 15,280 cells/ml respectively. Compared to cell cultures with iron and spherical particles that were not subjected to induction heating, we observed a 97% reduction in cell count for the spherical particles and a 91% reduction for the iron particles after the first 24 h. After 48 h we observed a 95% reduction in cell growth for both spherical and iron particles. Induction heating of microparticles was thus highly effective in reducing the macrophage population and preventing their growth. These results demonstrate the feasibility of targeting cells involved in atherosclerosis and warrant further research into potential clinical applications.
creator: Angelo Gaitas
creator: Gwangseong Kim
uri: https://doi.org/10.7717/peerj.929
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gaitas and Kim

title: From Lucy to Kadanuumuu: balanced analyses of Australopithecus afarensis assemblages confirm only moderate skeletal dimorphism
link: https://peerj.com/articles/925
last-modified: 2015-04-28
description: Sexual dimorphism in body size is often used as a correlate of social and reproductive behavior in Australopithecus afarensis. In addition to a number of isolated specimens, the sample for this species includes two small associated skeletons (A.L. 288-1 or “Lucy” and A.L. 128/129) and a geologically contemporaneous death assemblage of several larger individuals (A.L. 333). These have driven both perceptions and quantitative analyses concluding that Au. afarensis was markedly dimorphic. The Template Method enables simultaneous evaluation of multiple skeletal sites, thereby greatly expanding sample size, and reveals that A. afarensis dimorphism was similar to that of modern humans. A new very large partial skeleton (KSD-VP-1/1 or “Kadanuumuu”) can now also be used, like Lucy, as a template specimen. In addition, the recently developed Geometric Mean Method has been used to argue that Au. afarensis was equally or even more dimorphic than gorillas. However, in its previous application Lucy and A.L. 128/129 accounted for 10 of 11 estimates of female size. Here we directly compare the two methods and demonstrate that including multiple measurements from the same partial skeleton that falls at the margin of the species size range dramatically inflates dimorphism estimates. Prevention of the dominance of a single specimen’s contribution to calculations of multiple dimorphism estimates confirms that Au. afarensis was only moderately dimorphic.
creator: Philip L. Reno
creator: C. Owen Lovejoy
uri: https://doi.org/10.7717/peerj.925
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Reno and Lovejoy

title: Plant–insect interactions from Middle Triassic (late Ladinian) of Monte Agnello (Dolomites, N-Italy)—initial pattern and response to abiotic environmental perturbations
link: https://peerj.com/articles/921
last-modified: 2015-04-28
description: The Paleozoic–Mesozoic transition is characterized by the most massive extinction of the Phanerozoic. Nevertheless, an impressive adaptive radiation of herbivorous insects occurred on gymnosperm-dominated floras not earlier than during the Middle to Late Triassic, penecontemporaneous with similar events worldwide, all which exhibit parallel expansions of generalized and mostly specialized insect herbivory on plants, expressed as insect damage on a various plant organs and tissues. The flora from Monte Agnello is distinctive, due to its preservation in subaerially deposited pyroclastic layers with exceptionally preserved details. Thus, the para-autochthonous assemblage provides insights into environmental disturbances, caused by volcanic activity, and how they profoundly affected the structure and composition of herbivory patterns. These diverse Middle Triassic biota supply extensive evidence for insect herbivore colonization, resulting in specific and complex herbivory patterns involving the frequency and diversity of 20 distinctive damage types (DTs). These DT patterns show that external foliage feeders, piercer-and-suckers, leaf miners, gallers, and oviposition culprits were intricately using almost all tissue types from the dominant host plants of voltzialean conifers (e.g., Voltzia), horsetails, ferns (e.g., Neuropteridium, Phlebopteris, Cladophlebis and Thaumatopteris), seed ferns (e.g., Scytophyllum), and cycadophytes (e.g., Bjuvia and Nilssonia).
creator: Torsten Wappler
creator: Evelyn Kustatscher
creator: Elio Dellantonio
uri: https://doi.org/10.7717/peerj.921
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wappler et al.

title: Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR
link: https://peerj.com/articles/919
last-modified: 2015-04-28
description: Alternative splicing enables a single gene to produce multiple mRNA isoforms by varying splice site selection. In animals, alternative splicing of mRNA isoforms between cell types is widespread and supports cellular differentiation. In plants, at least 20% of multi-exon genes are alternatively spliced, but the extent and significance of tissue-specific splicing is less well understood, partly because it is difficult to isolate cells of a single type. Pollen is a useful model system to study tissue-specific splicing in higher plants because pollen grains contain only two cell types and can be collected in large amounts without damaging cells. Previously, we identified pollen-specific splicing patterns by comparing RNA-Seq data from Arabidopsis pollen and leaves. Here, we used semi-quantitative PCR to validate pollen-specific splicing patterns among genes where RNA-Seq data analysis indicated splicing was most different between pollen and leaves. PCR testing confirmed eight of nine alternative splicing patterns, and results from the ninth were inconclusive. In four genes, alternative transcriptional start sites coincided with alternative splicing. This study highlights the value of the low-cost PCR assay as a method of validating RNA-Seq results.
creator: April D. Estrada
creator: Nowlan H. Freese
creator: Ivory C. Blakley
creator: Ann E. Loraine
uri: https://doi.org/10.7717/peerj.919
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Estrada et al.

title: An elaborate data set on human gait and the effect of mechanical perturbations
link: https://peerj.com/articles/918
last-modified: 2015-04-28
description: Here we share a rich gait data set collected from fifteen subjects walking at three speeds on an instrumented treadmill. Each trial consists of 120 s of normal walking and 480 s of walking while being longitudinally perturbed during each stance phase with pseudo-random fluctuations in the speed of the treadmill belt. A total of approximately 1.5 h of normal walking (>5000 gait cycles) and 6 h of perturbed walking (>20,000 gait cycles) is included in the data set. We provide full body marker trajectories and ground reaction loads in addition to a presentation of processed data that includes gait events, 2D joint angles, angular rates, and joint torques along with the open source software used for the computations. The protocol is described in detail and supported with additional elaborate meta data for each trial. This data can likely be useful for validating or generating mathematical models that are capable of simulating normal periodic gait and non-periodic, perturbed gaits.
creator: Jason K. Moore
creator: Sandra K. Hnat
creator: Antonie J. van den Bogert
uri: https://doi.org/10.7717/peerj.918
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Moore et al.

title: Physician consultation in young children with recurrent pain—a population-based study
link: https://peerj.com/articles/916
last-modified: 2015-04-28
description: Background. Recurrent pain is a common experience in childhood, but only few children with recurrent pain attend a physician. Previous studies yielded conflicting findings with regard to predictors of health care utilization in children with recurrent pain.Methods. The present study analyzes data from the German Health Interview and Examination Survey for Children and Adolescents (KiGGS) study comprising n = 2,149 children (3–10 years old) with recurrent pain to find robust predictors. We used multiple logistic regressions to investigate age, gender, socio-economic status (SES), migration background, pain intensity, pain frequency, pain-related disability, mental health problems, and health-related quality of life (HRQL) as predictors for visiting a doctor due to pain.Results. Overall, young girls with high pain-related disability, intensity, frequency, and migration background were more likely to attend a physician. Pain-related disability had the largest impact. Socioeconomic status, health-related quality of life and mental health problems were not systematically related to health care utilization. An analysis of the variability of these results indicated that several hundred participants are needed until the results stabilize.Conclusions. Our findings highlight the importance of pain-related disability and frequency in assessing the severity of recurrent pain. Generic predictors and demographic variables are of lesser relevance to children with recurrent pain. On a methodological level, our results show that large-scale studies are need to reliably identify predictors of health care utilization.
creator: G Hirschfeld
creator: J Wager
creator: B Zernikow
uri: https://doi.org/10.7717/peerj.916
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hirschfeld et al.

title: The association between lifetime cigarette smoking and dysphonia in the Korean general population: findings from a national survey
link: https://peerj.com/articles/912
last-modified: 2015-04-28
description: This study aims to investigate the relationship between current smoking and lifetime amount smoked and the incidence of dysphonia using data from a national cross-sectional survey that represents the Korean population. Subjects were 3,600 non-institutionalised civilian adults over the age of 19 (1,501 males and 2,099 females) who completed the laryngeal examination of the 2008 Korea National Health and Nutrition Examination Survey (KNHANES). For lifetime amount smoked, subjects were classified as light smokers (≤26.7 pack years), medium smokers (26.7–40.5 pack years), heavy smokers (40.5–55.5 pack years), and very heavy smokers (55.5–156 pack years) based on pack years (packs smoked per day × years as a smoker). The odds ratio (OR) for the statistical test was presented using hierarchical logistic regression. When adjusted for covariates (age, gender, level of education, income, occupation, alcohol consumption and pain/discomfort during the last two weeks), current smokers had a 1.8 times (OR = 1.77, 95% CI [1.17–2.68]) higher risk for self-reported voice problems than non-smokers. Moreover, current smokers had a 1.6 times (OR = 1.56, 95% CI [1.02–2.38]) higher risk of laryngeal disorder (p < 0.05). In terms of pack years, very heavy smokers were significantly more likely to have laryngeal disorder, while self-reported voice problems were significantly more likely for heavy smokers but not very heavy smokers. The results of this study imply that chronic smoking has a significant relationship with dysphonia. Longitudinal studies are required in future work to verify the causality between lifetime smoking amount and dysphonia.
creator: Haewon Byeon
uri: https://doi.org/10.7717/peerj.912
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Byeon