title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1731 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Analysis of different vibration patterns to guide blind people link: https://peerj.com/articles/3082 last-modified: 2017-03-23 description: The literature indicates the best vibration positions and frequencies on the human body where tactile information is transmitted. However, there is a lack of knowledge about how to combine tactile stimuli for navigation. The aim of this study is to compare different vibration patterns outputted to blind people and to determine the most intuitive vibration patterns to indicate direction for navigation purposes through a tactile belt. The vibration patterns that stimulate the front side of the waist are preferred for indicating direction. Vibration patterns applied on the back side of the waist could be suitable for sending messages such as stop. creator: Juan V. Durá-Gil creator: Bruno Bazuelo-Ruiz creator: David Moro-Pérez creator: Fernando Mollà-Domenech uri: https://doi.org/10.7717/peerj.3082 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Durá-Gil et al. title: Are floating algal mats a refuge from hypoxia for estuarine invertebrates? link: https://peerj.com/articles/3080 last-modified: 2017-03-23 description: Eutrophic aquatic habitats are characterized by the proliferation of vegetation leading to a large standing biomass that upon decomposition may create hypoxic (low-oxygen) conditions. This is indeed the case in nutrient impacted estuaries of Prince Edward Island, Canada, where macroalgae, from the genus Ulva, form submerged ephemeral mats. Hydrological forces and gases released from photosynthesis and decomposition lead to these mats occasionally floating to the water’s surface, henceforth termed floating mats. Here, we explore the hypothesis that floating mats are refugia during periods of sustained hypoxia/anoxia and examine how the invertebrate community responds to it. Floating mats were not always present, so in the first year (2013) sampling was attempted monthly and limited to when both floating and submerged mats occurred. In the subsequent year sampling was weekly, but at only one estuary due to logistical constraints from increased sampling frequency, and was not limited to when both mat types occurred. Water temperature, salinity, and pH were monitored bi-weekly with dissolved oxygen concentration measured hourly. The floating and submerged assemblages shared many of the same taxa but were statistically distinct communities; submerged mats tended to have a greater proportion of benthic animals and floating mats had more mobile invertebrates and insects. In 2014, sampling happened to occur in the weeks before the onset of anoxia, during 113 consecutive hours of sustained anoxia, and for four weeks after normoxic conditions returned. The invertebrate community on floating mats appeared to be unaffected by anoxia, indicating that these mats may be refugia during times of oxygen stress. Conversely, there was a dramatic decrease in animal abundances that remained depressed on submerged mats for two weeks. Cluster analysis revealed that the submerged mat communities from before the onset of anoxia and four weeks after anoxia were highly similar to each other, indicating recovery. When mobile animals were considered alone, there was an exponential relationship between the percentage of animals on floating mats, relative to the total number on both mat types, and hypoxia. The occupation of floating mats by invertebrates at all times, and their dominance there during hypoxia/anoxia, provides support for the hypothesis that floating mats are refugia. creator: Michael R.S. Coffin creator: Kyle M. Knysh creator: Emma F. Theriault creator: Christina C. Pater creator: Simon C. Courtenay creator: Michael R. van den Heuvel uri: https://doi.org/10.7717/peerj.3080 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Coffin et al. title: Climate change promotes hybridisation between deeply divergent species link: https://peerj.com/articles/3072 last-modified: 2017-03-23 description: Rare hybridisations between deeply divergent animal species have been reported for decades in a wide range of taxa, but have often remained unexplained, mainly considered chance events and reported as anecdotal. Here, we combine field observations with long-term data concerning natural hybridisations, climate, land-use, and field-validated species distribution models for two deeply divergent and naturally sympatric toad species in Europe (Bufo bufo and Bufotes viridis species groups). We show that climate warming and seasonal extreme temperatures are conspiring to set the scene for these maladaptive hybridisations, by differentially affecting life-history traits of both species. Our results identify and provide evidence of an ultimate cause for such events, and reveal that the potential influence of climate change on interspecific hybridisations goes far beyond closely related species. Furthermore, climate projections suggest that the chances for these events will steadily increase in the near future. creator: Daniele Canestrelli creator: Roberta Bisconti creator: Andrea Chiocchio creator: Luigi Maiorano creator: Mauro Zampiglia creator: Giuseppe Nascetti uri: https://doi.org/10.7717/peerj.3072 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Canestrelli et al. title: Neogene amphibians and reptiles (Caudata, Anura, Gekkota, Lacertilia, and Testudines) from the south of Western Siberia, Russia, and Northeastern Kazakhstan link: https://peerj.com/articles/3025 last-modified: 2017-03-23 description: BackgroundThe present-day amphibian and reptile fauna of Western Siberia are the least diverse of the Palaearctic Realm, as a consequence of the unfavourable climatic conditions that predominate in this region. The origin and emergence of these herpetofaunal groups are poorly understood. Aside from the better-explored European Neogene localities yielding amphibian and reptile fossil remains, the Neogene herpetofauna of Western Asia is understudied. The few available data need critical reviews and new interpretations, taking into account the more recent records of the European herpetofauna. The comparison of this previous data with that of European fossil records would provide data on palaeobiogeographic affiliations of the region as well as on the origin and emergence of the present-day fauna of Western Siberia. An overview of the earliest occurrences of certain amphibian lineages is still needed. In addition, studies that address such knowledge gaps can be useful for molecular biologists in their calibration of molecular clocks.Methods and ResultsIn this study, we considered critically reviewed available data from amphibian and reptile fauna from over 40 Western Siberian, Russian and Northeastern Kazakhstan localities, ranging from the Middle Miocene to Early Pleistocene. Herein, we provided new interpretations that arose from our assessment of the previously published and new data. More than 50 amphibians and reptile taxa were identified belonging to families Hynobiidae, Cryptobranchidae, Salamandridae, Palaeobatrachidae, Bombinatoridae, Pelobatidae, Hylidae, Bufonidae, Ranidae, Gekkonidae, Lacertidae, and Emydidae. Palaeobiogeographic analyses were performed for these groups and palaeoprecipitation values were estimated for 12 localities, using the bioclimatic analysis of herpetofaunal assemblages.ConclusionThe Neogene assemblage of Western Siberia was found to be dominated by groups of European affinities, such as Palaeobatrachidae, Bombina, Hyla, Bufo bufo, and a small part of this assemblage included Eastern Palaearctic taxa (e.g. Salamandrella, Tylototriton, Bufotes viridis). For several taxa (e.g. Mioproteus, Hyla, Bombina, Rana temporaria), the Western Siberian occurrences represented their most eastern Eurasian records. The most diverse collection of fossil remains was found in the Middle Miocene. Less diversity has been registered towards the Early Pleistocene, potentially due to the progressive cooling of the climate in the Northern Hemisphere. The results of our study showed higher-amplitude changes of precipitation development in Western Siberia from the Early Miocene to the Pliocene, than previously assumed. creator: Davit Vasilyan creator: Vladimir S. Zazhigin creator: Madelaine Böhme uri: https://doi.org/10.7717/peerj.3025 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Vasilyan et al. title: Effects of long-term elevated temperature on covering, sheltering and righting behaviors of the sea urchin Strongylocentrotus intermedius link: https://peerj.com/articles/3122 last-modified: 2017-03-22 description: Increases in ocean temperature due to climate change are predicted to change the behaviors of marine invertebrates. Altered behaviors of keystone ecosystem engineers such as echinoderms will have consequences for the fitness of individuals, which are expected to flow on to the local ecosystem. Relatively few studies have investigated the behavioral responses of echinoderms to long-term elevated temperature. We investigated the effects of exposure to long-term (∼31 weeks) elevated temperature (∼3 °C above the ambient water temperature) on covering, sheltering and righting behaviors of the sea urchin Strongylocentrotus intermedius. Long-term elevated temperature showed different effects on the three behaviors. It significantly decreased covering behavior, including both covering behavior reaction (time to first covering) and ability (number of covered sea urchins and number of shells used for covering). Conversely, exposure to long-term elevated temperature significantly increased sheltering behavior. Righting response in S. intermedius was not significantly different between temperature treatments. The results provide new information into behavioral responses of echinoderms to ocean warming. creator: Lisheng Zhang creator: Lingling Zhang creator: Dongtao Shi creator: Jing Wei creator: Yaqing Chang creator: Chong Zhao uri: https://doi.org/10.7717/peerj.3122 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhang et al. title: Effects of various factors on Doppler flow ultrasonic radial and coccygeal artery systolic blood pressure measurements in privately-owned, conscious dogs link: https://peerj.com/articles/3101 last-modified: 2017-03-22 description: ObjectiveThe purpose of this study was to assess the effects of age, body condition score (BCS) and muscle condition score (MCS) on indirect radial and coccygeal Doppler systolic arterial blood pressure (SAP) measurements in dogs.MethodsSixty-two privately-owned dogs were enrolled between June and July 2016. The BCS and MCS were determined by two investigators. Blood pressure was measured per published guidelines and using headphones, and the order of measurement site was randomized. Dogs were positioned in right lateral recumbency for radial measurements and sternal recumbency or standing for coccygeal measurements. Associations between SAP and other variables were assessed by correlation coefficients and analysis of covariance.ResultsRadial and coccygeal SAP measurements were moderately correlated (r = 0.45, P < 0.01). Radial SAP measurements were higher than coccygeal SAP measurements (mean difference 9 mmHg, P < 0.01), but discordance occurred in both directions. No difference was observed between the first measurement taken, the average of measurements 2–6, or the average of all 6 measurements for either the radial (128, 129, and 129 mmHg; P = 0.36) or coccygeal (121, 122, and 122 mmHg; P = 0.82) site. Associations were not found between SAP measurements for either site and age, weight, BCS, MCS, anxiety score, or cuff size. Heart rate decreased significantly from the start of acclimation to the end of the first data collection series regardless of site (P < 0.01).Conclusions and Clinical RelevanceInitial measurement site can be based on patient and operator preference given lack of associations with patient variables, but the same site should be used for serial SAP measurements given discordant results between sites. creator: Allison P. Mooney creator: Dianne I. Mawby creator: Joshua M. Price creator: Jacqueline C. Whittemore uri: https://doi.org/10.7717/peerj.3101 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mooney et al. title: Curvature reduces bending strains in the quokka femur link: https://peerj.com/articles/3100 last-modified: 2017-03-22 description: This study explores how curvature in the quokka femur may help to reduce bending strain during locomotion. The quokka is a small wallaby, but the curvature of the femur and the muscles active during stance phase are similar to most quadrupedal mammals. Our hypothesis is that the action of hip extensor and ankle plantarflexor muscles during stance phase place cranial bending strains that act to reduce the caudal curvature of the femur. Knee extensors and biarticular muscles that span the femur longitudinally create caudal bending strains in the caudally curved (concave caudal side) bone. These opposing strains can balance each other and result in less strain on the bone. We test this idea by comparing the performance of a normally curved finite element model of the quokka femur to a digitally straightened version of the same bone. The normally curved model is indeed less strained than the straightened version. To further examine the relationship between curvature and the strains in the femoral models, we also tested an extra-curved and a reverse-curved version with the same loads. There appears to be a linear relationship between the curvature and the strains experienced by the models. These results demonstrate that longitudinal curvature in bones may be a manipulable mechanism whereby bone can induce a strain gradient to oppose strains induced by habitual loading. creator: Kyle McCabe creator: Keith Henderson creator: Jess Pantinople creator: Hazel L. Richards creator: Nick Milne uri: https://doi.org/10.7717/peerj.3100 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 McCabe et al. title: Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding link: https://peerj.com/articles/3006 last-modified: 2017-03-22 description: DNA metabarcoding, the PCR-based profiling of natural communities, is becoming the method of choice for biodiversity monitoring because it circumvents some of the limitations inherent to traditional ecological surveys. However, potential sources of bias that can affect the reproducibility of this method remain to be quantified. The interpretation of differences in patterns of sequence abundance and the ecological relevance of rare sequences remain particularly uncertain. Here we used one artificial mock community to explore the significance of abundance patterns and disentangle the effects of two potential biases on data reproducibility: indexed PCR primers and random sampling during Illumina MiSeq sequencing. We amplified a short fragment of the mitochondrial Cytochrome c Oxidase Subunit I (COI) for a single mock sample containing equimolar amounts of total genomic DNA from 34 marine invertebrates belonging to six phyla. We used seven indexed broad-range primers and sequenced the resulting library on two consecutive Illumina MiSeq runs. The total number of Operational Taxonomic Units (OTUs) was ∼4 times higher than expected based on the composition of the mock sample. Moreover, the total number of reads for the 34 components of the mock sample differed by up to three orders of magnitude. However, 79 out of 86 of the unexpected OTUs were represented by <10 sequences that did not appear consistently across replicates. Our data suggest that random sampling of rare OTUs (e.g., small associated fauna such as parasites) accounted for most of variation in OTU presence–absence, whereas biases associated with indexed PCRs accounted for a larger amount of variation in relative abundance patterns. These results suggest that random sampling during sequencing leads to the low reproducibility of rare OTUs. We suggest that the strategy for handling rare OTUs should depend on the objectives of the study. Systematic removal of rare OTUs may avoid inflating diversity based on common β descriptors but will exclude positive records of taxa that are functionally important. Our results further reinforce the need for technical replicates (parallel PCR and sequencing from the same sample) in metabarcoding experimental designs. Data reproducibility should be determined empirically as it will depend upon the sequencing depth, the type of sample, the sequence analysis pipeline, and the number of replicates. Moreover, estimating relative biomasses or abundances based on read counts remains elusive at the OTU level. creator: Matthieu Leray creator: Nancy Knowlton uri: https://doi.org/10.7717/peerj.3006 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Leray and Knowlton title: A cross sectional survey on health-related quality of life of elementary school students using the Korean version of the EQ-5D-Y link: https://peerj.com/articles/3115 last-modified: 2017-03-21 description: Background and ObjectiveThe Korean version of the EQ-5D-Y was launched in 2015 by the EuroQol group. Currently, there is no HRQOL data obtained by using the EQ-5D-Y in Korea. This study aimed to measure health-related quality of life of Korean elementary school students using the EQ-5D-Y.MethodsElementary school students were recruited from 11 primary schools in Gyungbuk, South Korea. The EQ-5D-Y was self-administered in the sample population. Demographic characteristics were collected from the subjects’ parents or guardians. The percentage of respondents reporting problems and VAS scores were calculated. Feasibility of the EQ-5D-Y was assessed by analysing the proportion of missing responses. The percentage of reported problems on the dimensions and VAS score between groups were compared by demographic factors.ResultsA total of 2,494 questionnaires were collected. There were 24 (0.96%) missing responses on the EQ-5D-Y and 187 (7.5%) missing VAS score responses. The proportion of reported problems ranged from 2.3% on the mobility dimension to 9.8% on the “having pain or discomfort” dimension. There was no significant difference in the proportion of problems by age group in male participants. However, in females, the older group reported significantly more problems on the “having pain or discomfort” and “feeling worried, sad, or unhappy” dimensions compared to the younger group. Students living with parents with the lowest educational level reported significantly more problems on the “looking after myself” and “doing usual activities” dimensions than did those living with parents with higher levels of education.DiscussionThis study showed the distribution of health-related quality of life and explored the feasibility of the EQ-5D-Y for measuring health-related quality of life in Korean elementary school students. Further studies are required to examine other psychometric properties of the Korean EQ-5D-Y. creator: Sang-Kyu Kim creator: Min-Woo Jo creator: Seon-Ha Kim uri: https://doi.org/10.7717/peerj.3115 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kim et al. title: Grape seed proanthocyanidin extract protects lymphocytes against histone-induced apoptosis link: https://peerj.com/articles/3108 last-modified: 2017-03-21 description: Apoptosis of lymphocytes is associated with immunosuppression and poor prognosis in sepsis. Our previous report showed that histones, nuclear proteins released from damaged or dying cells in sepsis, can mediate lymphocyte apoptosis via mitochondria damage. Grape seed proanthocyanidin extract (GSPE), a natural substance with protective properties against oxidative stress, plays a vital role in cell and mitochondria protection. We thus hypothesized that GSPE may play a protective role in histone-induced lymphocyte apoptosis through its anti-oxidative properties. In this study, we investigated the protective efficacy of GSPE on lymphocyte apoptosis induced by extracellular histones, a main contributor of death in sepsis. Human blood lymphocytes were treated with 50 μg/ml histones, 2 μg/ml GSPE, or a combination of both. A total of 100 μM N-acetylcysteine (NAC), a reactive oxygen species (ROS) inhibitor, was used as a positive control for GSPE. Apoptosis, intracellular ROS levels, mitochondrial membrane potential, Bcl-2 expression, and caspase-3 cleavage were measured. Our data clearly indicate that GSPE significantly inhibited lymphocyte apoptosis, generation of ROS, the loss of mitochondrial membrane potential, the decrease in Bcl-2 expression, and caspase-3 activation induced by extracellular histones. In conclusion, we show that GSPE has a protective effect on lymphocyte apoptosis induced by extracellular histones. This study suggests GSPE as a potential therapeutic agent that could help reduce lymphocyte apoptosis, and thus the state of immunosuppression was observed in septic patients. creator: Ping Chang creator: Bing Mo creator: David M. Cauvi creator: Ying Yu creator: Zhenhui Guo creator: Jian Zhou creator: Qiong Huang creator: Qitao Yan creator: Guiming Chen creator: Zhanguo Liu uri: https://doi.org/10.7717/peerj.3108 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Chang et al.