title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1536 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Intolerance of uncertainty and conditioned place preference in opioid addiction link: https://peerj.com/articles/4775 last-modified: 2018-05-21 description: Several personality factors have been implicated in vulnerability to addiction by impacting learning and decision making. One such factor is intolerance of uncertainty (IU), the tendency to perceive uncertain situations negatively and avoid them. Conditioned place preference (CPP), which compares preference for contexts paired with reward, has been used to examine the motivation for both drug and non-drug rewards. However, preference for locations associated with non-drug reward, as well as the potential influence of IU, has not been thoroughly studied in individuals with addiction. In the current study, we examined CPP using a computer-based task in a sample of addicted individuals undergoing opioid maintenance treatment and never-addicted controls. Patients were confirmed to have higher IU than controls. In the CPP task, the two groups did not differ in overall time spent in the previously-rewarded context. However, controls were more likely than patients to immediately return to this context. Contrary to our predictions, IU was not a significant predictor of preference for the previously-rewarded context, although higher IU in controls was associated with a higher number of rewards obtained in the task. No such relationship was found in patients. creator: Milen L. Radell creator: Michael Todd Allen creator: Belinda Favaloro creator: Catherine E. Myers creator: Paul Haber creator: Kirsten Morley creator: Ahmed A. Moustafa uri: https://doi.org/10.7717/peerj.4775 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Radell et al. title: Effects of long-term fertilisation on aggregates and dynamics of soil organic carbon in a semi-arid agro-ecosystem in China link: https://peerj.com/articles/4758 last-modified: 2018-05-21 description: BackgroundLong-term fertilisation has a large influence on soil physical and chemical properties in agro-ecosystems. The effects on the distribution of aggregates, however, are not fully understood. We determined the dynamic change of the distribution of aggregates and soil organic carbon (SOC) content over time in a long-term field experiment established in 1998 on the Loess Plateau of China and illustrated the relationship between them.MethodsWe determined SOC content and the distribution of aggregates in nine fertiliser treatments: manure (M); nitrogen (N); phosphorus (P); M and N; M, N, and P; M and P; N and P; bare land; and an unfertilised control. These parameters were then used for a path analysis and to analyse the fractal dimension (Dv).ResultsThe organic fertiliser increased SOC content. The proportions of 0.1–0.25 mm microaggregates and 0.25–0.5 mm macroaggregates were higher and the proportion of the 0.01–0.05 mm size class of the silt + clay fraction was lower in the treatments receiving organic fertiliser (M, MN, MNP, and MP) than that in the control, indicating that the addition of organic fertiliser promoted aggregation. The distribution of aggregates characterised by their fractal dimension (Dv), however, did not differ among the treatments.DiscussionDv was strongly correlated with the proportion of the <0.002 mm size class of the silt + clay fraction that did not differ significantly among the treatments. The change in the distribution of aggregates was strongly correlated with SOC content, which could produce organic polymer binding agents to increase the proportion of larger particles. Long-term application of organic fertiliser is thus necessary for the improvement and maintenance of soil quality in semi-arid agricultural land when residues are removed. creator: Jiaoyang Zhang creator: Caili Sun creator: Guobin Liu creator: Sha Xue uri: https://doi.org/10.7717/peerj.4758 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Living upside down: patterns of red coral settlement in a cave link: https://peerj.com/articles/4649 last-modified: 2018-05-21 description: BackgroundLarval settlement and intra-specific interactions during the recruitment phase are crucial in determining the distribution and density of sessile marine populations. Marine caves are confined and stable habitats. As such, they provide a natural laboratory to study the settlement and recruitment processes in sessile invertebrates, including the valuable Mediterranean red coral Corallium rubrum. In the present study, the spatial and temporal variability of red coral settlers in an underwater cave was investigated by demographic and genetic approaches.MethodsSixteen PVC tiles were positioned on the walls and ceiling of the Colombara Cave, Ligurian Sea, and recovered after twenty months. A total of 372 individuals of red coral belonging to two different reproductive events were recorded. Basal diameter, height, and number of polyps were measured, and seven microsatellites loci were used to evaluate the genetic relationships among individuals and the genetic structure.ResultsSignificant differences in the colonization rate were observed both between the two temporal cohorts and between ceiling and walls. No genetic structuring was observed between cohorts. Overall, high levels of relatedness among individuals were found.ConclusionThe results show that C. rubrumindividuals on tiles are highly related at very small spatial scales, suggesting that nearby recruits are likely to be sibs. Self-recruitment and the synchronous settlement of clouds of larvae could be possible explanations for the observed pattern. creator: Federica Costantini creator: Luca Rugiu creator: Carlo Cerrano creator: Marco Abbiati uri: https://doi.org/10.7717/peerj.4649 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Costantini et al. title: I understand you feel that way, but I feel this way: the benefits of I-language and communicating perspective during conflict link: https://peerj.com/articles/4831 last-modified: 2018-05-18 description: Using hypothetical scenarios, we provided participants with potential opening statements to a conflict discussion that varied on I/you language and communicated perspective. Participants rated the likelihood that the recipient of the statement would react in a defensive manner. Using I-language and communicating perspective were both found to reduce perceptions of hostility. Statements that communicated both self- and other-perspective using I-language (e.g. ‘I understand why you might feel that way, but I feel this way, so I think the situation is unfair’) were rated as the best strategy to open a conflict discussion. Simple acts of initial language use can reduce the chances that conflict discussion will descend into a downward spiral of hostility. creator: Shane L. Rogers creator: Jill Howieson creator: Casey Neame uri: https://doi.org/10.7717/peerj.4831 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rogers et al. title: Fitness consequences of fish circadian behavioural variation in exploited marine environments link: https://peerj.com/articles/4814 last-modified: 2018-05-18 description: The selective properties of fishing that influence behavioural traits have recently gained interest. Recent acoustic tracking experiments have revealed between-individual differences in the circadian behavioural traits of marine free-living fish; these differences are consistent across time and ecological contexts and generate different chronotypes. Here, we hypothesised that the directional selection resulting from fishing influences the wild circadian behavioural variation and affects differently to individuals in the same population differing in certain traits such as awakening time or rest onset time. We developed a spatially explicit social-ecological individual-based model (IBM) to test this hypothesis. The parametrisation of our IBM was fully based on empirical data; which represent a fishery formed by patchily distributed diurnal resident fish that are exploited by a fleet of mobile boats (mostly bottom fisheries). We ran our IBM with and without the observed circadian behavioural variation and estimated selection gradients as a quantitative measure of trait change. Our simulations revealed significant and strong selection gradients against early-riser chronotypes when compared with other behavioural and life-history traits. Significant selection gradients were consistent across a wide range of fishing effort scenarios. Our theoretical findings enhance our understanding of the selective properties of fishing by bridging the gaps among three traditionally separated fields: fisheries science, behavioural ecology and chronobiology. We derive some general predictions from our theoretical findings and outline a list of empirical research needs that are required to further understand the causes and consequences of circadian behavioural variation in marine fish. creator: Martina Martorell-Barceló creator: Andrea Campos-Candela creator: Josep Alós uri: https://doi.org/10.7717/peerj.4814 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Martorell-Barceló et al. title: A quantitative approach to determine the taxonomic identity and ontogeny of the pycnodontiform fish Pycnodus (Neopterygii, Actinopterygii) from the Eocene of Bolca Lagerstätte, Italy link: https://peerj.com/articles/4809 last-modified: 2018-05-18 description: BackgroundThe pycnodontiform fish Pycnodus is one of the representatives of the highly diverse actinopterygian fish fauna from the early Eocene Bolca Lagerstätte, representing one of the youngest and thus last occurrences of this extinct neopterygian clade. This genus has historically been used as a wastebasket taxon in regards to poorly known pycnodontiform fossils. Authors have argued over the specific status of the Bolca Lagerstätte Pycnodus in terms of how many species are contained within the genus with some arguing for multiple species and others suggesting lumping all Bolca specimens together into one species.MethodsHere, we use a quantitative approach performing biometric and geometric morphometric analyses on 52 specimens of Pycnodus in order to determine if the morphological variability within the sample might be related to inter- or intraspecific variation.ResultsThe analyses revealed that the variations of body shape, morphometric and meristic characters cannot be used to distinguish different morphotypes. On the contrary, our results show a remarkable link between shape and size, related to ontogeny.DiscussionDifferences in body shape of small (juvenile) and large (adult) individuals is probably related to different microhabitats occupation on the Bolca reef with juveniles sheltering within crevices on the reef and adults being more powerful swimmers that swim above the coral. Taxonomically, we suggest that the Bolca Pycnodus should be referred to strictly as Pycnodus apodus as this was the name given to the holotype. Additionally, an overview of species assigned to Pycnodus is given. creator: John Joseph Cawley creator: Giuseppe Marramà creator: Giorgio Carnevale creator: Jürgen Kriwet uri: https://doi.org/10.7717/peerj.4809 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cawley et al. title: Helicobacter pylori genetic diversification in the Mongolian gerbil model link: https://peerj.com/articles/4803 last-modified: 2018-05-18 description: Helicobacter pylori requires genetic agility to infect new hosts and establish long-term colonization of changing gastric environments. In this study, we analyzed H. pylori genetic adaptation in the Mongolian gerbil model. This model is of particular interest because H. pylori-infected gerbils develop a high level of gastric inflammation and often develop gastric adenocarcinoma or gastric ulceration. We analyzed the whole genome sequences of H. pylori strains cultured from experimentally infected gerbils, in comparison to the genome sequence of the input strain. The mean annualized single nucleotide polymorphism (SNP) rate per site was 1.5e−5, which is similar to the rates detected previously in H. pylori-infected humans. Many of the mutations occurred within or upstream of genes associated with iron-related functions (fur, tonB1, fecA2, fecA3, and frpB3) or encoding outer membrane proteins (alpA, oipA, fecA2, fecA3, frpB3 and cagY). Most of the SNPs within coding regions (86%) were non-synonymous mutations. Several deletion or insertion mutations led to disruption of open reading frames, suggesting that the corresponding gene products are not required or are deleterious during chronic H. pylori colonization of the gerbil stomach. Five variants (three SNPs and two deletions) were detected in isolates from multiple animals, which suggests that these mutations conferred a selective advantage. One of the mutations (FurR88H) detected in isolates from multiple animals was previously shown to confer increased resistance to oxidative stress, and we now show that this SNP also confers a survival advantage when H. pylori is co-cultured with neutrophils. Collectively, these analyses allow the identification of mutations that are positively selected during H. pylori colonization of the gerbil model. creator: Amber C. Beckett creator: John T. Loh creator: Abha Chopra creator: Shay Leary creator: Aung Soe Lin creator: Wyatt J. McDonnell creator: Beverly R.E.A. Dixon creator: Jennifer M. Noto creator: Dawn A. Israel creator: Richard M. Peek Jr creator: Simon Mallal creator: Holly M. Scott Algood creator: Timothy L. Cover uri: https://doi.org/10.7717/peerj.4803 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Beckett et al. title: Association of epilepsy and asthma: a population-based retrospective cohort study link: https://peerj.com/articles/4792 last-modified: 2018-05-18 description: BackgroundEpidemiologic data supporting the epilepsy–asthma association are insufficient. Therefore, we examined this association in this study.MethodsBy using claims data from the National Health Insurance Research Database (Taiwan), we executed a retrospective cohort analysis. Analysis 1 entailed comparing 150,827 patients diagnosed as having incident asthma during 1996–2013 with disease-free controls who were selected randomly during the same period, frequency matched in terms of age and sex. Similarly, analysis 2 entailed comparing 25,274 patients newly diagnosed as having epilepsy with sex- and age-matched controls who were selected randomly. At the end of 2013, we evaluated in analysis 1 the epilepsy incidence and risk and evaluated in analysis 2 the asthma incidence and risk. We applied Kaplan–Meier analysis to derive plots of the proportion of asthma-free seizures.ResultsIn analysis 1, the asthma group exhibited a higher epilepsy incidence than did the control group (3.05 versus 2.26 per 1,000 person-years; adjusted hazard ratio: 1.39, 95% CI [1.33–1.45]). We also noted a greater risk of subsequent epilepsy in women and girls. In analysis 2, we determined that the asthma incidence between the control and epilepsy groups did not differ significantly; however, some age subgroups including children and individuals in their 30s had an increased risk. A negative association was found in adolescents. The Kaplan–Meier analysis revealed epilepsy to be positively associated with subsequent onset of asthma within seven years of epilepsy diagnosis.DiscussionAsthma may be associated with high epilepsy risk, and epilepsy may be associated with high asthma risk among children and individuals in their 30s. Nevertheless, people with epilepsy in other age subgroups should be aware of the possibility of developing asthma within seven years of epilepsy diagnosis. creator: Kuo-Liang Chiang creator: Fang-Chuan Kuo creator: Jen-Yu Lee creator: Chin-Yin Huang uri: https://doi.org/10.7717/peerj.4792 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chiang et al. title: Diagnostic accuracy of Onen’s Alternative Grading System combined with Doppler evaluation of ureteral jets as an alternative in the diagnosis of obstructive hydronephrosis in children link: https://peerj.com/articles/4791 last-modified: 2018-05-18 description: IntroductionUreteropelvic junction obstruction (UPJO) is a common congenital anomaly leading to varying degrees of hydronephrosis (HN), ranging from no apparent effect on the renal function to atrophy. Evaluation of these children is based on Diuretic Renal Scintigraphy (DRS) and Ultrasonography (US). Recent studies have suggested that new parameters of conventional and color Doppler ultrasonography (CDUS) may be useful in discriminating which kidneys are obstructed. The present study aims to assess the diagnostic accuracy of such parameters in the diagnosis of obstruction in children with UPJO.MethodsWe evaluated 44 patients (33 boys) with a mean age of 6.53 ± 4.39 years diagnosed with unilateral high-grade hydronephrosis (SFU grades 3 and 4). All underwent DRS and index tests (conventional US and CDUS to evaluate ureteral jets frequency) within a maximum interval of two weeks. Hydronephrotic units were reclassified according to the alternative grading system (AGS) proposed by Onen et al. Obstruction in the DRS was defined as a differential renal function <40% on the affected side and/or features indicating poor drainage function like T1/2 >20 minutes after the administration of furosemide, and a plateau or ascending pattern of the excretion curve.ResultsNineteen hydronephrotic units (43.1%) were obstructed. Some degree of cortical atrophy—grades 3 (segmental) or 4 (diffuse)—was present in those obstructed units. AGS grades had 100% sensitivity, 76% of specificity and 86.4% of accuracy. The absence of ureteral jets had a sensitivity of 73.68%, a specificity of 100% with an accuracy of 88.6%. When we analyzed the two aspects together and considered obstructed the renal units classified as AGS grade 3 or 4 with no jets, sensitivity increased to 78.9%, accuracy to 92%, remaining with a maximum specificity of 100%. These features combined would allow us to avoid performing DRS in 61% of our patients, leaving more invasive tests to inconclusive cases.ConclusionsAlthough DRS remains the mainstay to distinguishing obstructive from non-obstructive kidneys, grade of hydronephrosis and frequency of ureteral jets, independently or in combination may be a reliable alternative in the mostly cases.This alternative approach has high accuracy, it is less invasive, easily reproducible and may play a role in the diagnosis of obstruction in pediatric population. creator: Jose de Bessa Jr creator: Cicilia M. Rodrigues creator: Maria Cristina Chammas creator: Eduardo P. Miranda creator: Cristiano M. Gomes creator: Paulo R. Moscardi creator: Marcia C. Bessa creator: Carlos A. Molina creator: Ricardo B. Tiraboschi creator: Jose M. Netto creator: Francisco T. Denes uri: https://doi.org/10.7717/peerj.4791 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 De Bessa Jr et al. title: Effects of sandfish (Holothuria scabra) removal on shallow-water sediments in Fiji link: https://peerj.com/articles/4773 last-modified: 2018-05-18 description: Sea cucumbers play an important role in the recycling and remineralization of organic matter (OM) in reef sands through feeding, excretion, and bioturbation processes. Growing demand from Asian markets has driven the overexploitation of these animals globally. The implications of sea cucumber fisheries for shallow coastal ecosystems and their management remain poorly understood. To address this knowledge gap, the current study manipulated densities of Holothuria scabra within enclosures on a reef flat in Fiji, between August 2015 and February 2016, to study the effects of sea cucumber removal on sedimentary function as a biocatalytic filter system. Three treatments were investigated: (i) high density (350 g m−2 wet weight; ca. 15 individuals); (ii) natural density (60 g m−2; ca. 3 individuals); and (iii) exclusion (0 g m−2). Quantity of sediment reworked through ingestion by H. scabra, grain size distribution, O2 penetration depth, and sedimentary oxygen consumption (SOC) were quantified within each treatment. Findings revealed that the natural population of H. scabra at the study site can rework ca. 10,590 kg dry sediment 1,000 m−2 year−1; more than twice the turnover rate recorded for H. atra and Stichopus chloronotus. There was a shift towards finer fraction grains in the high treatment. In the exclusion treatment, the O2 penetration depth decreased by 63% following a 6 °C increase in water temperature over the course of two months, while in the high treatment no such change was observed. SOC rates increased ca. two-fold in the exclusion treatment within the first month, and were consistently higher than in the high treatment. These results suggest that the removal of sea cucumbers can reduce the capacity of sediments to buffer OM pulses, impeding the function and productivity of shallow coastal ecosystems. creator: Steven Lee creator: Amanda K. Ford creator: Sangeeta Mangubhai creator: Christian Wild creator: Sebastian C.A. Ferse uri: https://doi.org/10.7717/peerj.4773 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lee et al.