title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1944 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Options for modulating intra-specific competition in colonial pinnipeds: the case of harbour seals (Phoca vitulina) in the Wadden Sea link: https://peerj.com/articles/957 last-modified: 2015-06-09 description: Colonial pinnipeds may be subject to substantial consumptive competition because they are large, slow-moving central place foragers. We examined possible mechanisms for reducing this competition by examining the diving behaviour of harbour seals (Phoca vitulina) after equipping 34 seals (11 females, 23 males) foraging from three locations; Rømø, Denmark and Lorenzenplate and Helgoland, Germany, in the Wadden Sea area with time-depth recorders. Analysis of 319,021 dives revealed little between-colony variation but appreciable inter-sex differences, with males diving deeper than females, but for shorter periods. Males also had higher vertical descent rates. This result suggests that males may have higher overall swim speeds, which would increase higher oxygen consumption, and may explain the shorter dive durations compared to females. Intersex variation in swim speed alone is predicted to lead to fundamental differences in the time use of three-dimensional space, which may help reduce consumptive competition in harbour seals and other colonial pinnipeds. creator: Rory P. Wilson creator: Nikolai Liebsch creator: Agustina Gómez-Laich creator: William P. Kay creator: Andrew Bone creator: Victoria J. Hobson creator: Ursula Siebert uri: https://doi.org/10.7717/peerj.957 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wilson et al. title: Properties evaluation of silorane, low-shrinkage, non-flowable and flowable resin-based composites in dentistry link: https://peerj.com/articles/864 last-modified: 2015-06-09 description: Purpose. This study tested the null hypothesis that different classes of direct restorative dental materials: silorane-based resin, low-shrinkage and conventional (non-flowable and flowable) resin-based composite (RBC) do not differ from each other with regard to polymerization shrinkage, depth of cure or microhardness.Methods. 140 RBC samples were fabricated and tested by one calibrated operator. Polymerization shrinkage was measured using a gas pycnometer both before and immediately after curing with 36 J/cm2 light energy density. Depth of cure was determined, using a penetrometer and the Knoop microhardness was tested from the top surface to a depth of 5 mm.Results. Considering polymerization shrinkage, the authors found significant differences (p < 0.05) between different materials: non-flowable RBCs showed lower values compared to flowable RBCs, with the silorane-based resin presenting the smallest shrinkage. The low shrinkage flowable composite performed similarly to non-flowable with significant statistical differences compared to the two other flowable RBCs. Regarding to depth of cure, low-shrinkage flowable RBC, were most effective compared to other groups. Microhardness was generally higher for the non-flowable vs. flowable RBCs (p < 0.05). However, the values for low-shrinkage flowable did not differ significantly from those of non-flowable, but were significantly higher than those of the other flowable RBCs.Clinical Significance. RBCs have undergone many modifications as they have evolved and represent the most relevant restorative materials in today’s dental practice. This study of low-shrinkage RBCs, conventional RBCs (non-flowable and flowable) and silorane-based composite—by in vitro evaluation of volumetric shrinkage, depth of cure and microhardness—reveals that although filler content is an important determinant of polymerization shrinkage, it is not the only variable that affects properties of materials that were tested in this study. creator: Rodrigo R. Maia creator: Rodrigo S. Reis creator: André F.V. Moro creator: Cesar R. Perez creator: Bárbara M. Pessôa creator: Katia R.H.C. Dias uri: https://doi.org/10.7717/peerj.864 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Maia et al. title: Seven new microendemic species of Brachycephalus (Anura: Brachycephalidae) from southern Brazil link: https://peerj.com/articles/1011 last-modified: 2015-06-04 description: Brachycephalus (Anura: Brachycephalidae) is a remarkable genus of miniaturized frogs of the Brazilian Atlantic Rainforest. Many of its species are highly endemic to cloud forests, being found only on one or a few mountaintops. Such level of microendemism might be caused by their climatic tolerance to a narrow set of environmental conditions found only in montane regions. This restriction severely limits the chance of discovery of new species, given the difficulty of exploring these inaccessible habitats. Following extensive fieldwork in montane areas of the southern portion of the Atlantic Rainforest, in this study we describe seven new species of Brachycephalus from the states of Paraná and Santa Catarina, southern Brazil. These species can be distinguished from one another based on coloration and the level of rugosity of the skin in different parts of their body. These discoveries increase considerably the number of described species of Brachycephalus in southern Brazil. creator: Luiz F. Ribeiro creator: Marcos R. Bornschein creator: Ricardo Belmonte-Lopes creator: Carina R. Firkowski creator: Sergio A.A. Morato creator: Marcio R. Pie uri: https://doi.org/10.7717/peerj.1011 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ribeiro et al. title: Assessment of water pollution in the Brazilian Pampa biome by means of stress biomarkers in tadpoles of the leaf frog Phyllomedusa iheringii (Anura: Hylidae) link: https://peerj.com/articles/1016 last-modified: 2015-06-04 description: The Brazilian Pampa biome is currently under constant threat due to increase of agriculture and improper management of urban effluents. Studies with a focus on the assessment of impacts caused by human activities in this biome are scarce. In the present study, we measured stress-related biomarkers in tadpoles of the leaf frog Phyllomedusa iheringii, an endemic species to the Pampa biome, and tested its suitability as a bioindicator for the assessment of potential aquatic contamination in selected ponds (S1 and S2) nearby agricultural areas in comparison to a reference site. A significant decrease in acetylcholinesterase activity was observed in S2 when compared to S1 and reference. The levels of total-hydroperoxides were increased in S2 site. In parallel, increased activity of the antioxidant enzymes catalase, superoxide dismutase and glutathione S-transferase were observed in S2 when compared to S1 and reference. Further studies are necessary in order to correlate the changes observed here with different chemical stressors in water, as well as to elucidate mechanisms of toxicity induced by pesticides in amphibian species endemic to the Pampa biome. Nevertheless, our study validates Phyllomedusa iheringii as a valuable bioindicator in environmental studies. creator: TG Santos creator: R Melo creator: DG Costa-Silva creator: MEM Nunes creator: NR Rodrigues creator: JL Franco uri: https://doi.org/10.7717/peerj.1016 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Santos et al. title: Cryopreservation of lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt link: https://peerj.com/articles/1003 last-modified: 2015-06-04 description: This study has established a successful protocol to cryopreserve lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt. Three cryosolutions were tested based on Mounib’s medium; the original medium including reduced l-glutathione (GSH), the basic sucrose and potassium bicarbonate medium without GSH, or with hen’s egg yolk (EY). Dimethyl sulphoxide (DMSO) was used as the cryoprotectant along with all three diluents in a 1–2 dilution. Cryopreservation was performed with the mentioned cryosolutions at two freezing rates. Motility percentages of spermatozoa were evaluated using ImageJ with a computer assisted sperm analyzer (CASA) plug-in. Findings revealed that spermatozoa cryopreserved in Mounib’s medium without GSH had a post-thaw motility score of 6.4 percentage points (pp) higher than those in the original Mounib’s medium, and an addition of EY to the modified Mounib’s medium lowered the post-thaw motility score by 19.3 pp. The difference in motility between both freezing rates was 13.0 pp, and samples cryopreserved on a 4.8 cm high tray resulted in a better post-thaw motility score. On average, cryopreserved milt had a 24.1 pp lower post-thaw motility score than fresh milt. There was no significant difference in fertilisation success between cryopreserved and fresh milt. Cryopreservation of lumpfish milt has, to our knowledge, never been successfully carried out before. The established protocol will be a main contributing factor in a stable production of lumpfish juveniles in future. creator: Gunnvør Norðberg creator: Asa Johannesen creator: Regin Arge uri: https://doi.org/10.7717/peerj.1003 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Norðberg et al. title: Soundscape manipulation enhances larval recruitment of a reef-building mollusk link: https://peerj.com/articles/999 last-modified: 2015-06-04 description: Marine seafloor ecosystems, and efforts to restore them, depend critically on the influx and settlement of larvae following their pelagic dispersal period. Larval dispersal and settlement patterns are driven by a combination of physical oceanography and behavioral responses of larvae to a suite of sensory cues both in the water column and at settlement sites. There is growing evidence that the biological and physical sounds associated with adult habitats (i.e., the “soundscape”) influence larval settlement and habitat selection; however, the significance of acoustic cues is rarely tested. Here we show in a field experiment that the free-swimming larvae of an estuarine invertebrate, the eastern oyster, respond to the addition of replayed habitat-related sounds. Oyster larval recruitment was significantly higher on larval collectors exposed to oyster reef sounds compared to no-sound controls. These results provide the first field evidence that soundscape cues may attract the larval settlers of a reef-building estuarine invertebrate. creator: Ashlee Lillis creator: DelWayne R. Bohnenstiehl creator: David B. Eggleston uri: https://doi.org/10.7717/peerj.999 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lillis et al. title: Population structure of three Psammodromus species in the Iberian Peninsula link: https://peerj.com/articles/994 last-modified: 2015-06-04 description: The knowledge of a species’ population structure is essential for the development of adequate conservation actions as well as for the understanding of its evolution. The population structure is unknown in all species of the Genus Psammodromus, including the Western Sand Racer (Psammodromus occidentalis; a recently described species), the Edward’s Sand Racer (P. edwardsianus) and the Spanish Sand Racer (P. hispanicus). In this article, the genetic variability and population structure of Psammodromus edwardsianus, P. hispanicus, and P. occidentalis were studied in the Iberian Peninsula covering their natural geographic distribution. Mitochondrial DNA showed genetically different units in all species with higher genetic variability in their southern populations (latitudinal variation). Genetic differentiation was different among species and contrasted to those of species with similar characteristics. Our results therefore highlight the importance of species-specific studies analysing population structure. creator: Jose L. Horreo creator: Patrick Fitze uri: https://doi.org/10.7717/peerj.994 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Horreo and Fitze title: NxRepair: error correction in de novo sequence assembly using Nextera mate pairs link: https://peerj.com/articles/996 last-modified: 2015-06-02 description: Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available. creator: Rebecca R. Murphy creator: Jared O’Connell creator: Anthony J. Cox creator: Ole Schulz-Trieglaff uri: https://doi.org/10.7717/peerj.996 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Murphy et al. title: Profiling and initial validation of urinary microRNAs as biomarkers in IgA nephropathy link: https://peerj.com/articles/990 last-modified: 2015-06-02 description: Background. MicroRNAs (miRNAs) have been found in virtually all body fluids and used successfully as biomarkers for various diseases. Evidence indicates that miRNAs have important roles in IgA nephropathy (IgAN), a major cause of renal failure. In this study, we looked for differentially expressed miRNAs in IgAN and further evaluated the correlations between candidate miRNAs and the severity of IgAN.Methods. Microarray and RT-qRCR (real-time quantitative polymerase chain reaction) were sequentially used to screen and further verify miRNA expression profiles in urinary sediments of IgAN patients in two independent cohorts. The screening cohort consisted of 32 urine samples from 18 patients with IgAN, 4 patients with MN (membranous nephropathy), 4 patients with MCD (minimal changes disease) and 6 healthy subjects; the validation cohort consisted of 102 IgAN patients, 41 MN patients, 27 MCD patients and 34 healthy subjects. The renal pathological lesions of patients with IgAN were evaluated according to Lee’s grading system and Oxford classification.Results. At the screening phase, significance analysis of microarrays analysis showed that no miRNA was differentially expressed in the IgAN group compared to all control groups. But IgAN grade I–II and III subgroups (according to Lee’s grading system) shared dysregulation of two miRNAs (miR-3613-3p and miR-4668-5p). At the validation phase, RT-qPCR results showed that urinary level of miR-3613-3p was significantly lower in IgAN than that in MN, MCD and healthy controls (0.47, 0.44 and 0.24 folds, respectively, all P < 0.01 by Mann–Whitney U test); urinary level of miR-4668-5p was also significantly lower in IgAN than that in healthy controls (0.49 fold, P < 0.01). Significant correlations were found between urinary levels of miR-3613-3p with 24-hour urinary protein excretion (Spearman r = 0.50, P = 0.034), eGFR (estimated glomerular filtration rate) (r = − 0.48, P = 0.043) and Lee’s grades (r = 0.57, P = 0.014). Similarly, miR-4668-5p was significantly correlated with eGFR (r = − 0.50, P = 0.034) and Lee’s grades (r = 0.57, P = 0.013). For segmental glomerulosclerosis according to Oxford classification, patients scored as S0 had significantly lower levels of urinary miR-3613-3p and miR-4668-5p than those scored as S1 (0.41 and 0.43 folds, respectively, all P < 0.05).Conclusions. The expression profile of miRNAs was significantly altered in urinary sediments from patients with IgAN. Urinary expression of miR-3613-3p was down-regulated in patients with IgAN. Moreover, urinary levels of both miR-3613-3p and miR-4668-5p were correlated with disease severity. Further studies are needed to explore the roles of miR-3613-3p and miR-4668-5p in the pathogenesis and progression of IgA nephropathy. creator: Nannan Wang creator: Ru Bu creator: Zhiyu Duan creator: Xueguang Zhang creator: Pu Chen creator: Zuoxiang Li creator: Jie Wu creator: Guangyan Cai creator: Xiangmei Chen uri: https://doi.org/10.7717/peerj.990 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wang et al. title: The sensitivity of biological finite element models to the resolution of surface geometry: a case study of crocodilian crania link: https://peerj.com/articles/988 last-modified: 2015-06-02 description: The reliability of finite element analysis (FEA) in biomechanical investigations depends upon understanding the influence of model assumptions. In producing finite element models, surface mesh resolution is influenced by the resolution of input geometry, and influences the resolution of the ensuing solid mesh used for numerical analysis. Despite a large number of studies incorporating sensitivity studies of the effects of solid mesh resolution there has not yet been any investigation into the effect of surface mesh resolution upon results in a comparative context. Here we use a dataset of crocodile crania to examine the effects of surface resolution on FEA results in a comparative context. Seven high-resolution surface meshes were each down-sampled to varying degrees while keeping the resulting number of solid elements constant. These models were then subjected to bite and shake load cases using finite element analysis. The results show that incremental decreases in surface resolution can result in fluctuations in strain magnitudes, but that it is possible to obtain stable results using lower resolution surface in a comparative FEA study. As surface mesh resolution links input geometry with the resulting solid mesh, the implication of these results is that low resolution input geometry and solid meshes may provide valid results in a comparative context. creator: Matthew R. McCurry creator: Alistair R. Evans creator: Colin R. McHenry uri: https://doi.org/10.7717/peerj.988 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McCurry et al.