Neogene amphibians and reptiles (Caudata, Anura, Gekkota, Lacertilia, and Testudines) from the south of Western Siberia, Russia, and Northeastern Kazakhstan
Background The 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 Results In 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. Conclusion The 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.
Vasilyan et al. (2017) Neogene amphibians and reptiles (Caudata, Anura, Gekkota, Lacertilia, and Testudines) from the south of Western Siberia, Russia, and Northeastern Kazakhstan. PeerJ 5:e3025 https://doi.org/10.7717/peerj.3025
Effects of long-term elevated temperature on covering, sheltering and righting behaviors of the sea urchin Strongylocentrotus intermedius
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.
Zhang et al. (2017) Effects of long-term elevated temperature on covering, sheltering and righting behaviors of the sea urchin Strongylocentrotus intermedius. PeerJ 5:e3122 https://doi.org/10.7717/peerj.3122
Effects of various factors on Doppler flow ultrasonic radial and coccygeal artery systolic blood pressure measurements in privately-owned, conscious dogs
Objective The 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. Methods Sixty-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. Results Radial 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 Relevance Initial 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.
Mooney et al. (2017) Effects of various factors on Doppler flow ultrasonic radial and coccygeal artery systolic blood pressure measurements in privately-owned, conscious dogs. PeerJ 5:e3101 https://doi.org/10.7717/peerj.3101
Curvature reduces bending strains in the quokka femur
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.
McCabe et al. (2017) Curvature reduces bending strains in the quokka femur. PeerJ 5:e3100 https://doi.org/10.7717/peerj.3100
Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding
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.
Leray et al. (2017) Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ 5:e3006 https://doi.org/10.7717/peerj.3006
A cross sectional survey on health-related quality of life of elementary school students using the Korean version of the EQ-5D-Y
Background and Objective The 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. Methods Elementary 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. Results A 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. Discussion This 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.
Kim et al. (2017) A cross sectional survey on health-related quality of life of elementary school students using the Korean version of the EQ-5D-Y. PeerJ 5:e3115 https://doi.org/10.7717/peerj.3115
Grape seed proanthocyanidin extract protects lymphocytes against histone-induced apoptosis
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.
Chang et al. (2017) Grape seed proanthocyanidin extract protects lymphocytes against histone-induced apoptosis. PeerJ 5:e3108 https://doi.org/10.7717/peerj.3108
Exploring differential health effects of work stress: a latent class cluster approach
Background While evidence highlights the detrimental health consequences of adverse working conditions, effect sizes vary by the stressor examined. In this study, we aimed to explore the differential effects various constellations of job demands have on prevalent symptom clusters. Methods We analysed self-reported data from a nationwide Austrian survey (N = 16,466), based on a cross-sectional design. By means of latent class analysis, a set of items was used to assess the burden from several job demands as well as the frequency of occurrence of mental and physical symptoms in order to identify stress profiles and symptom clusters, respectively. Results Analysis revealed four subgroups that each demonstrated a typological response pattern regarding job demands and health symptoms, respectively. The revealed stress profiles were found to be strongly related to the symptom clusters, while the effects differed considerably depending on the types of demands experienced. Conclusion The current study presents an alternative method of examining the stress-health link by using a combined person- and variable-centred approach. The findings suggest a hierarchy in stress exposure with the most pronounced health consequences found for a synchronous burden from physical, psychosocial and organizational demands.
Mayerl et al. (2017) Exploring differential health effects of work stress: a latent class cluster approach. PeerJ 5:e3106 https://doi.org/10.7717/peerj.3106
Evolution of the patellar sesamoid bone in mammals
The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that bony patellae most likely evolved between four and six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals and up to three times in therian mammals. Furthermore, an ossified patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition) and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a bony patella is present it plays an important role in hindlimb function, especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats—from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds—remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.
Samuels et al. (2017) Evolution of the patellar sesamoid bone in mammals. PeerJ 5:e3103 https://doi.org/10.7717/peerj.3103
Insect herbivores increase mortality and reduce tree seedling growth of some species in temperate forest canopy gaps
Insect herbivores help maintain forest diversity through selective predation on seedlings of vulnerable tree species. Although the role of natural enemies has been well-studied in tropical systems, relatively few studies have experimentally manipulated insect abundance in temperate forests and tracked impacts over multiple years. We conducted a three-year experiment (2012–2014) deterring insect herbivores from seedlings in new treefall gaps in deciduous hardwood forests in Maryland. During this study, we tracked recruitment of all tree seedlings, as well as survivorship and growth of 889 individual seedlings from five tree species: Acer rubrum, Fagus grandifolia, Fraxinus spp., Liriodendron tulipifera, and Liquidambar styraciflua. Insect herbivores had little effect on recruitment of any tree species, although there was a weak indication that recruitment of A. rubrum was higher in the presence of herbivores. Insect herbivores reduced survivorship of L. tulipifera, but had no significant effects on A. rubrum, Fraxinus spp., F. grandifolia, or L. styraciflua. Additionally, insects reduced growth rates of early pioneer species A. rubrum, L. tulipifera, and L. styraciflua, but had little effect on more shade-tolerant species F. grandifolia and Fraxinus spp. Overall, by negatively impacting growth and survivorship of early pioneer species, forest insects may play an important but relatively cryptic role in forest gap dynamics, with potentially interesting impacts on the overall maintenance of diversity.
Lemoine et al. (2017) Insect herbivores increase mortality and reduce tree seedling growth of some species in temperate forest canopy gaps. PeerJ 5:e3102 https://doi.org/10.7717/peerj.3102