title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1957 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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 title: Demographic rates of northern royal albatross at Taiaroa Head, New Zealand link: https://peerj.com/articles/906 last-modified: 2015-04-28 description: Demographic rates, such as annual survival rate, are generally difficult to estimate for long-lived seabirds, because of the length of time required for this kind of study and the remoteness of colonies. However, a small colony of northern royal albatross (Diomedea sanfordi) established itself on the mainland of New Zealand at Taiaroa Head, making possible regular banding and monitoring of its individuals since the first chick fledged, in 1938. Data on the presence/absence of birds, as well as on breeding outcomes, were available for the period from 1989–90 to 2011–12, and included 2128 annual resightings of 355 banded individuals of known age. The main goal of the present study was to estimate the annual survival rate of juveniles, pre-breeders, and adults at Taiaroa Head. These rates were estimated simultaneously in a single Bayesian multi-state capture-recapture model. Several models were fitted to the data, with different levels of complexity. From the most parsimonious model, the overall annual adult survival rate was estimated as 0.950 (95% CI [0.941–0.959]). In this model, adult survival declined with age, from 0.976 (95% CI [0.963–0.988]) at 6 years, the minimum age at first breeding, to 0.915 (95% CI [0.879–0.946]) at 40 years. Mean annual survival of pre-breeders was 0.966 (95% CI [0.950–0.980]), and 0.933 (95% CI [0.908–0.966]) for juveniles. There was no discernible difference in survival between males and females, and there was no apparent trend in survival over time. Estimates of other demographic rates were also obtained during the estimation process. The mean age at first return of juveniles to the colony was estimated as 4.8 years (95% CI [4.6–5.1]), and the mean age at first breeding as 8.9 years (95% CI [8.5–9.3]). Because all the birds of the colony were banded, it was possible to estimate the total population size. The number of northern royal albatross present annually at the Taiaroa Head colony has doubled since 1989–90, and the current total population size was estimated to be over 200 individuals. The ratio of the total population size to the number of annual breeding pairs varied from 5 to 12 among years, with an overall mean of 7.65 (95% CI [7.56–7.78]), and this high variability highlights the need for a sufficient number of surveys of seabird breeding populations before reliable conclusions on population trends can be made. Although long-term data allowed estimates of demographic rates of northern royal albatross at Taiaroa Head, the location of the colony and the ongoing management by staff mean that the population dynamics may differ from those of the main population on the Chatham Islands. creator: Yvan Richard creator: Lyndon Perriman creator: Chris Lalas creator: Edward R. Abraham uri: https://doi.org/10.7717/peerj.906 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Richard et al. title: Tunable translational control using site-specific unnatural amino acid incorporation in Escherichia coli link: https://peerj.com/articles/904 last-modified: 2015-04-28 description: Translation of target gene transcripts in Escherichia coli harboring UAG amber stop codons can be switched on by the amber-codon-specific incorporation of an exogenously supplied unnatural amino acid, 3-iodo-L-tyrosine. Here, we report that this translational switch can control the translational efficiency at any intermediate magnitude by adjustment of the 3-iodo-L-tyrosine concentration in the medium, as a tunable translational controller. The translational efficiency of a target gene reached maximum levels with 10−5 M 3-iodo-L-tyrosine, and intermediate levels were observed with suboptimal concentrations (approximately spanning a 2-log10 concentration range, 10−7–10−5 M). Such intermediate-level expression was also confirmed in individual bacteria. creator: Yusuke Kato uri: https://doi.org/10.7717/peerj.904 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kato title: Organization and distribution of glomeruli in the bowhead whale olfactory bulb link: https://peerj.com/articles/897 last-modified: 2015-04-28 description: Although modern baleen whales (Mysticeti) retain a functional olfactory system that includes olfactory bulbs, cranial nerve I and olfactory receptor genes, their olfactory capabilities have been reduced to a great degree. This reduction likely occurred as a selective response to their fully aquatic lifestyle. The glomeruli that occur in the olfactory bulb can be divided into two non-overlapping domains, a dorsal domain and a ventral domain. Recent molecular studies revealed that all modern whales have lost olfactory receptor genes and marker genes that are specific to the dorsal domain. Here we show that olfactory bulbs of bowhead whales (Balaena mysticetus) lack glomeruli on the dorsal side, consistent with the molecular data. In addition, we estimate that there are more than 4,000 glomeruli elsewhere in the bowhead whale olfactory bulb, which is surprising given that bowhead whales possess only 80 intact olfactory receptor genes. Olfactory sensory neurons that express the same olfactory receptors in rodents generally project to two specific glomeruli in an olfactory bulb, implying an approximate 1:2 ratio of the number of olfactory receptors to the number of glomeruli. Here we show that this ratio does not apply to bowhead whales, reiterating the conceptual limits of using rodents as model organisms for understanding the initial coding of odor information among mammals. creator: Takushi Kishida creator: JGM Thewissen creator: Sharon Usip creator: Robert S. Suydam creator: John C. George uri: https://doi.org/10.7717/peerj.897 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kishida et al. title: Tiludronate concentrations and cytologic findings in synovial fluid after intravenous regional limb perfusion with tiludronate in horses link: https://peerj.com/articles/889 last-modified: 2015-04-28 description: Anecdotal accounts of tiludronate administration via intravenous regional limb perfusion (IVRLP) exist despite a lack of information regarding safety for synovial structures in the perfused area. The objective of this study was to determine whether tiludronate concentrations in synovial structures after IVRLP with low dose (0.5 mg, LDT) or high dose (50 mg, HDT) tiludronate remain below a value demonstrated in vitro to be safe for articular cartilage (<19,000 ng/ml), and to determine effects of tiludronate on synovial fluid cytology variables compared to saline perfused control limbs. Using a randomized controlled experimental study design, horses received IVRLP with LDT (n = 6) or HDT (n = 6) in one forelimb and IVRLP with saline in the contralateral limb. Synovial fluid cytology variables and tiludronate concentrations were evaluated in navicular bursae (NB), and distal interphalangeal (DIP) and metacarpophalangeal (MCP) joints one week before and 30–45 min after IVRLP, and in DIP and MCP joints 24 h after IVRLP. Data were analyzed with 2-way rmANOVA (p < 0.05). Highest measured synovial fluid tiludronate concentrations occurred 30–45 min post-perfusion. Mean tiludronate concentrations were lower in LDT limbs (MCP = 39.6 ± 14.3 ng/ml, DIP = 118.1 ± 66.6 ng/ml, NB = 82.1 ± 30.2 ng/ml) than in HDT limbs (MCP = 3,745.1 ± 1,536.6 ng/ml, DIP = 16,274.0 ± 5,460.2 ng/ml, NB = 6,049.3 ± 1,931.7 ng/ml). Tiludronate concentration was >19,000 ng/ml in DIP joints of two HDT limbs. Tiludronate was measurable only in synovial fluid from HDT limbs 24 h post-perfusion. There were no differences in synovial fluid cytology variables between control and treated limbs.Conclusions. In some horses, IVRLP with HDT may result in synovial fluid concentrations of tiludronate that may have adverse effects on articular cartilage, based on in vitro data. IVRLP with LDT is unlikely to promote articular cartilage degradation. Further studies to determine a safe and effective dose for IVRLP with tiludronate are needed. creator: Barbara G. Hunter creator: Katja F. Duesterdieck-Zellmer creator: Maureen K. Larson uri: https://doi.org/10.7717/peerj.889 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hunter et al. title: DCEMRI.jl: a fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis link: https://peerj.com/articles/909 last-modified: 2015-04-23 description: We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10–20× speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 × 192 breast image, we achieved run times of <1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N1.9), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise. creator: David S. Smith creator: Xia Li creator: Lori R. Arlinghaus creator: Thomas E. Yankeelov creator: E. Brian Welch uri: https://doi.org/10.7717/peerj.909 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Smith et al.