title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1953
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Pre- and postmortem tyrannosaurid bite marks on the remains of Daspletosaurus (Tyrannosaurinae: Theropoda) from Dinosaur Provincial Park, Alberta, Canada
link: https://peerj.com/articles/885
last-modified: 2015-04-09
description: Trace marks on the bones of non-avian dinosaurs may relate to feeding by large carnivores or as a result of combat. Here the cranium and mandible of a specimen of Daspletosaurus are described that show numerous premortem injuries with evidence of healing and these are inferred to relate primarily to intraspecific combat. In addition, postmortem damage to the mandible is indicative of late stage carcass consumption and the taphonomic context suggests that this was scavenging. These postmortem bites were delivered by a large bodied tyrannosaurid theropod and may have been a second Daspletosaurus, and thus this would be an additional record of tyrannosaurid cannibalism.
creator: DWE Hone
creator: DH Tanke
uri: https://doi.org/10.7717/peerj.885
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hone and Tanke

title: Widespread mitovirus sequences in plant genomes
link: https://peerj.com/articles/876
last-modified: 2015-04-09
description: The exploration of the evolution of RNA viruses has been aided recently by the discovery of copies of fragments or complete genomes of non-retroviral RNA viruses (Non-retroviral Endogenous RNA Viral Elements, or NERVEs) in many eukaryotic nuclear genomes. Among the most prominent NERVEs are partial copies of the RNA dependent RNA polymerase (RdRP) of the mitoviruses in plant mitochondrial genomes. Mitoviruses are in the family Narnaviridae, which are the simplest viruses, encoding only a single protein (the RdRP) in their unencapsidated viral plus strand. Narnaviruses are known only in fungi, and the origin of plant mitochondrial mitovirus NERVEs appears to be horizontal transfer from plant pathogenic fungi. At least one mitochondrial mitovirus NERVE, but not its nuclear copy, is expressed.
creator: Jeremy A. Bruenn
creator: Benjamin E. Warner
creator: Pradeep Yerramsetty
uri: https://doi.org/10.7717/peerj.876
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bruenn et al.

title: A field based study of swimbladder adjustment in a physostomous teleost fish
link: https://peerj.com/articles/892
last-modified: 2015-04-09
description: The present study assesses swimbladder dynamics in natural occurring sardine, Sardina pilchardus, populations with the aim to examine whether this is affected by bathymetric positioning and the physiological state of the individuals. To do so, swimbladder size and shape were modeled in relation to catch depth and the size of various visceral compartments such as gonad, liver, fat and stomach. Swimbladder size was shown to be related to depth in a way that individuals with smaller swimbladders occurred at larger depths. Moreover, evidence is provided that the swimbladder in sardine might have a functional relationship both with the reproductive and the feeding state of individuals, since none of the fish with hydrated gonads and/or large stomachs displayed distended swimbladders.
creator: Kostas Ganias
creator: Stella Michou
creator: Cristina Nunes
uri: https://doi.org/10.7717/peerj.892
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ganias et al.

title: Reducing workplace burnout: the relative benefits of cardiovascular and resistance exercise
link: https://peerj.com/articles/891
last-modified: 2015-04-09
description: Objectives. The global burden of burnout cost is in excess of $300 billion annually. Locally, just under half of working Australians experience high levels of occupational burnout. Consequently, burnout interventions are paramount to organisational productivity. Exercise has the potential to provide a multilevel and cost effective burnout intervention. The current study aims to extend the literature by comparing cardiovascular with resistance exercise to assess their relative effectiveness against well-being, perceived stress, and burnout.Design. Participants were 49 (36 females and 13 males) previously inactive volunteers ranging in age from 19 to 68 that completed a four week exercise program of either cardiovascular, resistance, or no exercise (control). Randomised control trial design was employed.Method. Participants were measured against the Subjective Exercise Experience Scale, the Perceived Stress Scale, and the Maslach Burnout Inventory.Results. After four weeks of exercise participants had greater positive well-being and personal accomplishment, and concomitantly less psychological distress, perceived stress, and emotional exhaustion. Cardiovascular exercise was found to increase well-being and decrease psychological distress, perceived stress, and emotional exhaustion. Resistance training was noticeably effective in increasing well-being and personal accomplishment and to reduce perceived stress. The present findings revealed large effect sizes suggesting that exercise may be an effective treatment for burnout. However, given a small sample size further research needs to be conducted.Conclusion. Exercise has potential to be an effective burnout intervention. Different types of exercise may assist employees in different ways. Organisations wishing to proactively reduce burnout can do so by encouraging their employees to access regular exercise programs.
creator: Rachel Judith Bretland
creator: Einar Baldvin Thorsteinsson
uri: https://doi.org/10.7717/peerj.891
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bretland and Thorsteinsson

title: Models for the directed evolution of bacterial allelopathy: bacteriophage lysins
link: https://peerj.com/articles/879
last-modified: 2015-04-09
description: Microbes produce a variety of compounds that are used to kill or suppress other species. Traditional antibiotics have their origins in these natural products, as do many types of compounds being pursued today in the quest for new antibacterial drugs. When a potential toxin can be encoded by and exported from a species that is not harmed, the opportunity exists to use directed evolution to improve the toxin’s ability to kill other species—allelopathy. In contrast to the typical application of directed evolution, this case requires the co-culture of at least two species or strains, a host that is unharmed by the toxin plus the intended target of the toxin. We develop mathematical and computational models of this directed evolution process. Two contexts are considered, one with the toxin encoded on a plasmid and the other with the toxin encoded in a phage. The plasmid system appears to be more promising than the phage system. Crucial to both designs is the ability to co-culture two species/strains (host and target) such that the host is greatly outgrown by the target species except when the target species is killed. The results suggest that, if these initial conditions can be satisfied, directed evolution is feasible for the plasmid-based system. Screening with a plasmid-based system may also enable rapid improvement of a toxin.
creator: James J. Bull
creator: Cameron Crandall
creator: Anna Rodriguez
creator: Stephen M. Krone
uri: https://doi.org/10.7717/peerj.879
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bull et al.

title: Models of knot and stem development in black spruce trees indicate a shift in allocation priority to branches when growth is limited
link: https://peerj.com/articles/873
last-modified: 2015-04-09
description: The branch autonomy principle, which states that the growth of individual branches can be predicted from their morphology and position in the forest canopy irrespective of the characteristics of the tree, has been used to simplify models of branch growth in trees. However, observed changes in allocation priority within trees towards branches growing in light-favoured conditions, referred to as ‘Milton’s Law of resource availability and allocation,’ have raised questions about the applicability of the branch autonomy principle. We present models linking knot ontogeny to the secondary growth of the main stem in black spruce (Picea mariana (Mill.) B.S.P.), which were used to assess the patterns of assimilate allocation over time, both within and between trees. Data describing the annual radial growth of 445 stem rings and the three-dimensional shape of 5,377 knots were extracted from optical scans and X-ray computed tomography images taken along the stems of 10 trees. Total knot to stem area increment ratios (KSR) were calculated for each year of growth, and statistical models were developed to describe the annual development of knot diameter and curvature as a function of stem radial increment, total tree height, stem diameter, and the position of knots along an annual growth unit. KSR varied as a function of tree age and of the height to diameter ratio of the stem, a variable indicative of the competitive status of the tree. Simulations of the development of an individual knot showed that an increase in the stem radial growth rate was associated with an increase in the initial growth of the knot, but also with a shorter lifespan. Our results provide support for ‘Milton’s Law,’ since they indicate that allocation priority is given to locations where the potential return is the highest. The developed models provided realistic simulations of knot morphology within trees, which could be integrated into a functional-structural model of tree growth and above-ground resource partitioning.
creator: Emmanuel Duchateau
creator: David Auty
creator: Frédéric Mothe
creator: Fleur Longuetaud
creator: Chhun Huor Ung
creator: Alexis Achim
uri: https://doi.org/10.7717/peerj.873
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Duchateau et al.

title: Relationship between cold pressor pain-sensitivity and sleep quality in opioid-dependent males on methadone treatment
link: https://peerj.com/articles/839
last-modified: 2015-04-09
description: Aim. Poor sleep quality due to pain has been reported among opioid-dependent male patients on methadone maintenance therapy (MMT) but objective pain data are lacking. This study aimed to investigate the rate of pain-sensitivity using cold pressor test (CPT) and the relationship between pain-sensitivity and sleep quality in this population.Methods. A total of 168 male participants were included into the study. Objective pain-tolerance was evaluated at 0 h and at 24 h after the first CPT. Malay version of the Pittsburgh Sleep Quality Index (PSQI) and the subjective opiate withdrawal scale (SOWS) questionnaires were administered to evaluate the quality of sleep and withdrawal symptoms, respectively.Results. The mean age of study participants was 37.22 (SD 6.20) years old. Mean daily methadone dose was 76.64 (SD 37.63) mg/day, mean global PSQI score was 5.47 (SD 2.74) and mean averaged SOWS score was 5.43 (SD 6.91). The averaged pain-tolerance time ranged from 7 to 300 s with a mean time of 32.16 (SE 2.72) s, slightly below the cut-off score of 37.53 s. More specifically, 78.6% (n = 132) of participants were identified as pain-sensitive (averaged pain-tolerance time ≤37.53 s), and 36 (21.4%) participants were pain-tolerant (averaged pain-tolerance time >37.53 s). The pain-sensitive group reported poorer sleep quality with mean (SD) PSQI of 5.78 (2.80) compared with the pain-tolerant group with mean (SD) PSQI of 4.31 (2.18) (p = 0.005). With analysis of covariance, pain-sensitive group was found to have higher global PSQI scores (adjusted mean 5.76, 95% CI 5.29; 6.22) than pain-tolerant participants (adjusted mean 4.42, 95% CI 3.52; 5.32) (p = 0.010).Conclusions. Majority of opioid-dependent male patients on methadone treatment are pain-sensitive with CPT. Poor sleep quality is associated with cold pressor pain-sensitivity. Pain and sleep complaints in this male population should not be overlooked.
creator: Zalina Zahari
creator: Chee Siong Lee
creator: Soo Choon Tan
creator: Nasir Mohamad
creator: Yeong Yeh Lee
creator: Rusli Ismail
uri: https://doi.org/10.7717/peerj.839
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zahari et al.

title: DNA quantification of basidiomycetous fungi during storage of logging residues
link: https://peerj.com/articles/887
last-modified: 2015-04-07
description: The demand for bioenergy caused an increased use of logging residues, branches and treetops that were previously left on the ground after harvesting. Residues are stored outdoors in piles and it is unclear to what extent fungi transform this material. Our objective was to quantify the amount of wood degrading fungi during storage using quantitative real-time PCR (qPCR) to detect basidiomycetous DNA in logging residues, a novel approach in this field. We found that the qPCR method was accurate in quantifying the fungal DNA during storage. As the moisture content of the piled logging residues decreased during the storage period, the fungal DNA content also decreased. Scots pine residues contained more fungal DNA than residues from Norway spruce. Loose piles had generally more fungal DNA than bundled ones.
creator: Isabella Børja
creator: Gry Alfredsen
creator: Tore Filbakk
creator: Carl Gunnar Fossdal
uri: https://doi.org/10.7717/peerj.887
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Børja et al.

title: Laser photogrammetry improves size and demographic estimates for whale sharks
link: https://peerj.com/articles/886
last-modified: 2015-04-07
description: Whale sharks Rhincodon typus are globally threatened, but a lack of biological and demographic information hampers an accurate assessment of their vulnerability to further decline or capacity to recover. We used laser photogrammetry at two aggregation sites to obtain more accurate size estimates of free-swimming whale sharks compared to visual estimates, allowing improved estimates of biological parameters. Individual whale sharks ranged from 432–917 cm total length (TL) (mean ± SD = 673 ± 118.8 cm, N = 122) in southern Mozambique and from 420–990 cm TL (mean ± SD = 641 ± 133 cm, N = 46) in Tanzania. By combining measurements of stranded individuals with photogrammetry measurements of free-swimming sharks, we calculated length at 50% maturity for males in Mozambique at 916 cm TL. Repeat measurements of individual whale sharks measured over periods from 347–1,068 days yielded implausible growth rates, suggesting that the growth increment over this period was not large enough to be detected using laser photogrammetry, and that the method is best applied to estimating growth rates over longer (decadal) time periods. The sex ratio of both populations was biased towards males (74% in Mozambique, 89% in Tanzania), the majority of which were immature (98% in Mozambique, 94% in Tanzania). The population structure for these two aggregations was similar to most other documented whale shark aggregations around the world. Information on small (<400 cm) whale sharks, mature individuals, and females in this region is lacking, but necessary to inform conservation initiatives for this globally threatened species.
creator: Christoph A. Rohner
creator: Anthony J. Richardson
creator: Clare E.M. Prebble
creator: Andrea D. Marshall
creator: Michael B. Bennett
creator: Scarla J. Weeks
creator: Geremy Cliff
creator: Sabine P. Wintner
creator: Simon J. Pierce
uri: https://doi.org/10.7717/peerj.886
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Rohner et al.

title: Association between virtues and posttraumatic growth: preliminary evidence from a Chinese community sample after earthquakes
link: https://peerj.com/articles/883
last-modified: 2015-04-07
description: Objective. Relationship, vitality, and conscientiousness are three fundamental virtues that have been recently identified as important individual differences to health, well being, and positive development. This cross-sectional study attempted to explore the relationship between the three constructs and post-traumatic growth (PTG) in three directions, including indirect trauma samples without post-traumatic stress disorder (PTSD), direct trauma samples without PTSD, and direct trauma samples with PTSD.Methods. A total of 340 community participants from Sichuan Province, Mainland China involved in the study, most of which experienced Wenchuan and Lushan Earthquake. Participants were required to complete the self-reported questionnaire packages at one time point for obtaining their scores on virtues (Chinese Virtues Questionnaire), PTSD (PTSD Checklist-Specific), and PTG (Post-traumatic Growth Inventory-Chinese).Results. Significant and positive correlations between the three virtues and PTG were identified (r = .39–.56; p < .01). Further regression analysis by stepwise method reveled that: in the indirect trauma samples, vitality explained 32% variance of PTG. In reference to the direct trauma sample without PTSD, both relationship and conscientiousness explained 32% variance of PTG, whereas in the direct trauma sample with PTSD, only conscientiousness accounted for 31% the variance in PTG.Conclusion.This cross-sectional investigation partly revealed the roles of different virtues in trauma context. Findings suggest important implications for strengths-based treatment.
creator: Wenjie Duan
creator: Pengfei Guo
uri: https://doi.org/10.7717/peerj.883
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Duan and Guo