Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power
One-dimensional (1D) kinematic, force, and EMG trajectories are often analyzed using zero-dimensional (0D) metrics like local extrema. Recently whole-trajectory 1D methods have emerged in the literature as alternatives. Since 0D and 1D methods can yield qualitatively different results, the two approaches may appear to be theoretically distinct. The purposes of this paper were (a) to clarify that 0D and 1D approaches are actually just special cases of a more general region-of-interest (ROI) analysis framework, and (b) to demonstrate how ROIs can augment statistical power. We first simulated millions of smooth, random 1D datasets to validate theoretical predictions of the 0D, 1D and ROI approaches and to emphasize how ROIs provide a continuous bridge between 0D and 1D results. We then analyzed a variety of public datasets to demonstrate potential effects of ROIs on biomechanical conclusions. Results showed, first, that a priori ROI particulars can qualitatively affect the biomechanical conclusions that emerge from analyses and, second, that ROIs derived from exploratory/pilot analyses can detect smaller biomechanical effects than are detectable using full 1D methods. We recommend regarding ROIs, like data filtering particulars and Type I error rate, as parameters which can affect hypothesis testing results, and thus as sensitivity analysis tools to ensure arbitrary decisions do not influence scientific interpretations. Last, we describe open-source Python and MATLAB implementations of 1D ROI analysis for arbitrary experimental designs ranging from one-sample t tests to MANOVA.
Pataky et al. (2016) Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power. PeerJ 4:e2652 https://doi.org/10.7717/peerj.2652
The Ecology of Stress: linking life-history traits with physiological control mechanisms in free-living guanacos
Background Providing the context for the evolution of life-history traits, habitat features constrain successful ecological and physiological strategies. In vertebrates, a key response to life’s challenges is the activation of the Stress (HPA) and Gonadal (HPG) axes. Much of the interest in stress ecology is motivated by the desire to understand the physiological mechanisms in which the environment affects fitness. As reported in the literature, several intrinsic and extrinsic factors affect variability in hormone levels. In both social and non-social animals, the frequency and type of interaction with conspecifics, as well as the status in social species, can affect HPA axis activity, resulting in changes in the reproductive success of animals. We predicted that a social environment can affect both guanaco axes by increasing the secretion of testosterone (T) and Glucocorticoid (GCs) in response to individual social interactions and the energetic demands of breeding. Assuming that prolonged elevated levels of GCs over time can be harmful to individuals, it is predicted that the HPA axis suppresses the HPG axis and causes T levels to decrease, as GCs increase. Methods All of the data for individuals were collected by non-invasive methods (fecal samples) to address hormonal activities. This is a novel approach in physiological ecology because feces are easily obtained through non-invasive sampling in animal populations. Results As expected, there was a marked adrenal (p-value = .3.4e−12) and gonadal (p-value = 0.002656) response due to seasonal variation in Lama guanicoe. No significant differences were found in fecal GCs metabolites between males/females*season for the entire study period (p-value = 0.2839). Despite the seasonal activity variation in the hormonal profiles, our results show a positive correlation (p-value = 1.952e−11, COR = 0.50) between the adrenal and gonadal system. The marked endocrine (r2 = 0.806) and gonad (r2 = 0.7231) response due to seasonal variation in male guanaco individuals highlights the individual’s energetic demands according to life-history strategies. This is a remarkable result because no inhibition was found between the axes as theory suggests. Finally, the dataset was used to build a reactive scope model for guanacos. Discussion Guanacos cope with the trade-off between sociability and reproductive benefits and costs, by regulating their GCs and T levels on a seasonal basis, suggesting an adaptive role of both axes to different habitat pressures. The results presented here highlight the functional role of stress and gonad axes on a critical phase of a male mammal’s life—the mating period—when all of the resources are at the disposal of the male and must be used to maximize the chances for reproductive success.
Ovejero Aguilar et al. (2016) The Ecology of Stress: linking life-history traits with physiological control mechanisms in free-living guanacos. PeerJ 4:e2640 https://doi.org/10.7717/peerj.2640
Elevational pattern of bird species richness and its causes along a central Himalaya gradient, China
This study examines the relative importance of six variables: area, the mid-domain effect, temperature, precipitation, productivity, and habitat heterogeneity on elevational patterns of species richness for breeding birds along a central Himalaya gradient in the Gyirong Valley, the longest of five canyons in the Mount Qomolangma National Nature Reserve. We conducted field surveys in each of twelve elevational bands of 300 m between 1,800 and 5,400 m asl four times throughout the entire wet season. A total of 169 breeding bird species were recorded and most of the species (74%) were small-ranged. The species richness patterns of overall, large-ranged and small-ranged birds were all hump-shaped, but with peaks at different elevations. Large-ranged species and small-ranged species contributed equally to the overall richness pattern. Based on the bivariate and multiple regression analyses, area and precipitation were not crucial factors in determining the species richness along this gradient. The mid-domain effect played an important role in shaping the richness pattern of large-ranged species. Temperature was negatively correlated with overall and large-ranged species but positively correlated with small-ranged species. Productivity was a strong explanatory factor among all the bird groups, and habitat heterogeneity played an important role in shaping the elevational richness patterns of overall and small-ranged species. Our results highlight the need to conserve primary forest and intact habitat in this area. Furthermore, we need to increase conservation efforts in this montane biodiversity hotspot in light of increasing anthropogenic activities and land use pressure.
Pan et al. (2016) Elevational pattern of bird species richness and its causes along a central Himalaya gradient, China. PeerJ 4:e2636 https://doi.org/10.7717/peerj.2636
Three-dimensional paleohistology of the scale and median fin spine of Lophosteus superbus (Pander 1856)
Lophosteus superbus is one of only a handful of probable stem-group osteichthyans known from the fossil record. First collected and described in the late 19th century from the upper Silurian Saaremaa Cliff locality in Estonia, it is known from a wealth of disarticulated scales, fin spines, and bone fragments. In this study we provide the first description of the morphology and paleohistology of a fin spine and scale from Lophosteus using virtual thin sections and 3D reconstructions that were segmented using phase-contrast synchrotron X-ray microtomography. These data reveal that both structures have fully or partially buried odontodes, which retain fine morphological details in older generations, including sharp nodes and serrated ridgelets. The vascular architecture of the fin spine tip, which is composed of several layers of longitudinally directed bone vascular canals, is much more complex compared to the bulbous horizontal canals within the scale, but they both have distinctive networks of ascending canals within each individual odontode. Other histological characteristics that can be observed from the data are cell spaces and Sharpey’s fibers that, when combined with the vascularization, could help to provide insights into the growth of the structure. The 3D data of the scales from Lophosteus superbus is similar to comparable data from other fossil osteichthyans, and the morphology of the reconstructed buried odontodes from this species is identical to scale material of Lophosteus ohesaarensis, casting doubt on the validity of that species. The 3D data presented in this paper is the first for fossil fin spines and so comparable data is not yet available. However, the overall morphology and histology seems to be similar to the structure of placoderm dermal plates. The 3D datasets presented here provide show that microtomography is a powerful tool for investigating the three-dimensional microstructure of fossils, which is difficult to study using traditional histological methods. These results also increase the utility of fin spines and scales suggest that these data are a potentially rich source of morphological data that could be used for studying questions relating to early vertebrate growth and evolution.
Jerve et al. (2016) Three-dimensional paleohistology of the scale and median fin spine of Lophosteus superbus (Pander 1856). PeerJ 4:e2521 https://doi.org/10.7717/peerj.2521
Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations
Background Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction). Methods The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. Results SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers. Conclusions The results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.
Bilska et al. (2016) Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations. PeerJ 4:e2504 https://doi.org/10.7717/peerj.2504
Performance, usability and comparison of two versions of a new macular vision test: the handheld Radial Shape Discrimination test
Background Central vision, critical for everyday tasks such as reading and driving, is impacted by age-related changes in the eye and by diseases such as age-related macular degeneration. The detection of changes in macular function is therefore important. The Radial Shape Discrimination (RSD) test measures the threshold at which distortions in a radial frequency pattern can be detected and there is evidence that it is more sensitive to macular pathology than visual acuity (VA). It also provides a more quantitative measure of macular function than the commonly available Amsler grid. Recently, handheld versions of the test (hRSD) in which stimuli are presented on mobile devices (e.g., Apple iPod Touch, iPhone) have been developed. We investigated the characteristics of the hRSD test in healthy participants. Methods Data were collected using both three-alternative forced choice (3AFC) and 4AFC versions of the hRSD test, presented on an Apple iPod Touch. For the 3AFC version, data from a single test session were available for 186 (72 male; mean ± SD age 42 ± 17y; range 16–90y) healthy participants. Test-retest data were available for subgroups of participants (intra-session: N = 74; tests approximately 2 months apart: N = 30; tests 39 months apart: N = 15). The 3AFC and 4AFC versions were directly compared in 106 participants who also completed a usability questionnaire. Distance and near VA and Pelli Robson Contrast Sensitivity (CS) data were collected and undilated fundoscopy performed on the majority of participants. Results Mean (±SD) 3AFC hRSD threshold was −0.77 ± 0.14 logMAR, and was statistically significantly correlated with age (Pearson r = 0.35; p < 0.001). The linear regression of hRSD threshold on age had a slope of +0.0026 compared to +0.0051 for near VA (which also correlated with age: r = 0.51; p < 0.001). There were no statistically significant differences in hRSD thresholds for any of the test-retest subgroups. We also observed no statistically significant difference between 3AFC (−0.82 ± 0.11 logMAR) and 4AFC (−0.80 ± 0.12 logMAR) hRSD thresholds (t = 1.85, p = 0.067) and participants reported excellent test usability with no strong preference expressed between the 3AFC and 4AFC versions of the test. Discussion The 3AFC hRSD thresholds we report are consistent with a number of previous studies, as is its greater stability in ageing compared to VA. We have also shown that in the absence of pathology, thresholds are stable over short and long timescales. The 4AFC thresholds we have reported provide a baseline for future investigations, and we have confirmed that 3AFC and 4AFC thresholds are similar, providing a basis of comparisons between studies using the different versions. As the hRSD test is easy to use and relatively inexpensive, clinical studies are now required to establish its ability to detect and monitor macular pathologies.
Ku et al. (2016) Performance, usability and comparison of two versions of a new macular vision test: the handheld Radial Shape Discrimination test. PeerJ 4:e2650 https://doi.org/10.7717/peerj.2650
The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland
Background Ferox Trout are large, long-lived piscivorous Brown Trout (Salmo trutta). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However, despite their recreational and theoretical importance, little is known about the typical abundance of Ferox Trout. Methods To rectify this situation a 16 year angling-based mark-recapture study was conducted on Loch Rannoch, which at 19 km2 is one of the largest lakes in the United Kingdom. Results A hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual differences in catchability are negligible the population of Ferox Trout in Loch Rannoch in 2009 was approximately 71 fish. The results also suggest that a single, often unaccompanied, highly-experienced angler was able to catch roughly 8% of the available fish on an annual basis. Discussion It is recommended that anglers adopt a precautionary approach and release all trout with a fork length ≥400 mm caught by trolling in Loch Rannoch. There is an urgent need to assess the status of Ferox Trout in other lakes.
Thorne et al. (2016) The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland. PeerJ 4:e2646 https://doi.org/10.7717/peerj.2646
Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature
Background Glyphosate-based herbicides are the most widely used pesticides in agriculture, horticulture, municipalities and private gardens that can potentially contaminate nearby water bodies inhabited by amphibians and algae. Moreover, the development and diversity of these aquatic organisms could also be affected by human-induced climate change that might lead to more periods with extreme temperatures. However, to what extent non-target effects of these herbicides on amphibians or algae are altered by varying temperature is not well known. Methods We studied effects of five concentrations of the glyphosate-based herbicide formulation Roundup PowerFlex (0, 1.5, 3, 4 mg acid equivalent glyphosate L−1 as a one time addition and a pulse treatment of totally 4 mg a.e. glyphosate L−1) on larval development of Common toads (Bufo bufo, L.; Amphibia: Anura) and associated algae communities under two temperature regimes (15 vs. 20 °C). Results Herbicide contamination reduced tail growth (−8%), induced the occurrence of tail deformations (i.e. lacerated or crooked tails) and reduced algae diversity (−6%). Higher water temperature increased tadpole growth (tail and body length (tl/bl) +66%, length-to-width ratio +4%) and decreased algae diversity (−21%). No clear relation between herbicide concentrations and tadpole growth or algae density or diversity was observed. Interactive effects of herbicides and temperature affected growth parameters, tail deformation and tadpole mortality indicating that the herbicide effects are temperature-dependent. Remarkably, herbicide-temperature interactions resulted in deformed tails in 34% of all herbicide treated tadpoles at 15 °C whereas no tail deformations were observed for the herbicide-free control at 15 °C or any tadpole at 20 °C; herbicide-induced mortality was higher at 15 °C but lower at 20 °C. Discussion These herbicide- and temperature-induced changes may have decided effects on ecological interactions in freshwater ecosystems. Although no clear dose-response effect was seen, the presence of glyphosate was decisive for an effect, suggesting that the lowest observed effect concentration (LOEC) in our study was 1.5 mg a.e. glyphosate L−1 water. Overall, our findings also question the relevance of pesticide risk assessments conducted at standard temperatures.
Baier et al. (2016) Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature. PeerJ 4:e2641 https://doi.org/10.7717/peerj.2641
Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model
Myelin is a critical component of the nervous system and a major contributor to contrast in Magnetic Resonance (MR) images. However, the precise contribution of myelination to multiple MR modalities is still under debate. The cuprizone mouse is a well-established model of demyelination that has been used in several MR studies, but these have often imaged only a single slice and analysed a small region of interest in the corpus callosum. We imaged and analyzed the whole brain of the cuprizone mouse ex-vivo using high-resolution quantitative MR methods (multi-component relaxometry, Diffusion Tensor Imaging (DTI) and morphometry) and found changes in multiple regions, including the corpus callosum, cerebellum, thalamus and hippocampus. The presence of inflammation, confirmed with histology, presents difficulties in isolating the sensitivity and specificity of these MR methods to demyelination using this model.
Wood et al. (2016) Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model. PeerJ 4:e2632 https://doi.org/10.7717/peerj.2632
Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss
Hepatocyte growth factor (HGF) is a paracrine hormone that plays an important role in epithelial-mesenchymal transition. HGF secreted by mesenchymal cells affects many properties of epithelial cells, such as proliferation, motility, and morphology. HGF has been reported to promote follicular growth. The purpose of the present study is to investigate the therapeutic role of HGF in hair loss treatment. A recombinant vector containing the human HGF (hHGF) gene (pTARGET-hHGF) was constructed, and the expression of hHGF in vitro was quantitatively and qualitatively evaluated. The effect of hHGF on hair growth was tested in mice, and results demonstrated that pTARGET-hHGF was successfully delivered into fibroblasts in vitro leading to a high expression of hHGF. Local injections of the pTARGET-hHGF recombinant vector into mice resulted in multiple beneficial effects compared to placebo, including faster hair regeneration, improved follicle development, and significantly increased HGF receptor (HGF-R). In conclusion, we have established a nonviral vector of hHGF which could be utilized to manipulate the sheath fibroblasts surrounding hair follicles (HF), thereby stimulating hair regeneration.
Qi et al. (2016) Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss. PeerJ 4:e2624 https://doi.org/10.7717/peerj.2624