PlantCV v2: Image analysis software for high-throughput plant phenotyping
Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.
Gehan et al. (2017) PlantCV v2: Image analysis software for high-throughput plant phenotyping. PeerJ 5:e4088 https://doi.org/10.7717/peerj.4088
Examining publication bias—a simulation-based evaluation of statistical tests on publication bias
Background Publication bias is a form of scientific misconduct. It threatens the validity of research results and the credibility of science. Although several tests on publication bias exist, no in-depth evaluations are available that examine which test performs best for different research settings. Methods Four tests on publication bias, Egger’s test (FAT), p-uniform, the test of excess significance (TES), as well as the caliper test, were evaluated in a Monte Carlo simulation. Two different types of publication bias and its degree (0%, 50%, 100%) were simulated. The type of publication bias was defined either as file-drawer, meaning the repeated analysis of new datasets, or p-hacking, meaning the inclusion of covariates in order to obtain a significant result. In addition, the underlying effect (β = 0, 0.5, 1, 1.5), effect heterogeneity, the number of observations in the simulated primary studies (N = 100, 500), and the number of observations for the publication bias tests (K = 100, 1,000) were varied. Results All tests evaluated were able to identify publication bias both in the file-drawer and p-hacking condition. The false positive rates were, with the exception of the 15%- and 20%-caliper test, unbiased. The FAT had the largest statistical power in the file-drawer conditions, whereas under p-hacking the TES was, except under effect heterogeneity, slightly better. The CTs were, however, inferior to the other tests under effect homogeneity and had a decent statistical power only in conditions with 1,000 primary studies. Discussion The FAT is recommended as a test for publication bias in standard meta-analyses with no or only small effect heterogeneity. If two-sided publication bias is suspected as well as under p-hacking the TES is the first alternative to the FAT. The 5%-caliper test is recommended under conditions of effect heterogeneity and a large number of primary studies, which may be found if publication bias is examined in a discipline-wide setting when primary studies cover different research problems.
Schneck (2017) Examining publication bias—a simulation-based evaluation of statistical tests on publication bias. PeerJ 5:e4115 https://doi.org/10.7717/peerj.4115
A tyrannosauroid metatarsus from the Merchantville Formation of Delaware increases the diversity of non-tyrannosaurid tyrannosauroids on Appalachia
During the Late Cretaceous, the continent of North America was divided into two sections: Laramidia in the west and Appalachia in the east. Although the sediments of Appalachia recorded only a sparse fossil record of dinosaurs, the dinosaur faunas of this landmass were different in composition from those of Laramidia. Represented by at least two taxa (Appalachiosaurus montgomeriensis and Dryptosaurus aquilunguis), partial and fragmentary skeletons, and isolated bones, the non-tyrannosaurid tyrannosauroids of the landmass have attracted some attention. Unfortunately, these eastern tyrants are poorly known compared to their western contemporaries. Here, one specimen, the partial metatarsus of a tyrannosauroid from the Campanian Merchantville Formation of Delaware, is described in detail. The specimen can be distinguished from A. montgomeriensis and D. aquilunguis by several morphological features. As such, the specimen represents a potentially previously unrecognized taxon of tyrannosauroid from Appalachia, increasing the diversity of the clade on the landmass. Phylogenetic analysis and the morphology of the bones suggest the Merchantville specimen is a tyrannosauroid of “intermediate” grade, thus supporting the notion that Appalachia was a refugium for relict dinosaur clades.
Brownstein (2017) A tyrannosauroid metatarsus from the Merchantville Formation of Delaware increases the diversity of non-tyrannosaurid tyrannosauroids on Appalachia. PeerJ 5:e4123 https://doi.org/10.7717/peerj.4123
Acute ischemic preconditioning does not influence high-intensity intermittent exercise performance
This study evaluated the acute effect of ischemic preconditioning (IPC) on a high-intensity intermittent exercise performance and physiological indicators in amateur soccer players. Thirteen players (21.5 ± 2 yrs) attended three trials separated by 3–5 days in a counterbalanced randomized cross-over design: IPC (4 × 5-min occlusion 220 mmHg/reperfusion 0 mmHg) in each thigh; SHAM (similar to the IPC protocol but “occlusion” at 20 mmHg) and control (seated during the same time of IPC). After 6-min of each trial (IPC, SHAM or control), the players performed the YoYo Intermittent Endurance Test level 2 (YoYoIE2). The distance covered in the YoYoIE2 (IPC 867 ± 205 m; SHAM 873 ± 212 m; control 921 ± 206 m) was not different among trials (p = 0.10), furthermore, lactate concentration and rate of perceived exertion did not differ (P > 0.05) among protocols. There were also no significant differences in either mean heart rate (HR) or peak HR (p > 0.05) for both IPC and SHAM compared to control. Therefore, we conclude that acute IPC does not influence high-intensity intermittent exercise performance in amateur soccer players and that rate of perceived exertion, heart rate and lactate do not differ between the intervention IPC, SHAM and control.
Marocolo et al. (2017) Acute ischemic preconditioning does not influence high-intensity intermittent exercise performance. PeerJ 5:e4118 https://doi.org/10.7717/peerj.4118
Ability to predict repetitions to momentary failure is not perfectly accurate, though improves with resistance training experience
‘Repetitions in Reserve’ (RIR) scales in resistance training (RT) are used to control effort but assume people accurately predict performance a priori (i.e. the number of possible repetitions to momentary failure (MF)). This study examined the ability of trainees with different experience levels to predict number of repetitions to MF. One hundred and forty-one participants underwent a full body RT session involving single sets to MF and were asked to predict the number of repetitions they could complete before reaching MF on each exercise. Participants underpredicted the number of repetitions they could perform to MF (Standard error of measurements [95% confidence intervals] for combined sample ranged between 2.64 [2.36–2.99] and 3.38 [3.02–3.83]). There was a tendency towards improved accuracy with greater experience. Ability to predict repetitions to MF is not perfectly accurate among most trainees though may improve with experience. Thus, RIR should be used cautiously in prescription of RT. Trainers and trainees should be aware of this as it may have implications for the attainment of training goals, particularly muscular hypertrophy.
Steele et al. (2017) Ability to predict repetitions to momentary failure is not perfectly accurate, though improves with resistance training experience. PeerJ 5:e4105 https://doi.org/10.7717/peerj.4105
Diagnosis value of aberrantly expressed microRNA profiles in lung squamous cell carcinoma: a study based on the Cancer Genome Atlas
Background Lung cancer is considered as one of the most frequent and deadly cancers with high mortality all around the world. It is critical to find new biomarkers for early diagnosis of lung cancer, especially lung squamous cell carcinoma (LUSC). The Cancer Genome Atlas (TCGA) is a database which provides both cancer and clinical information. This study is a comprehensive analysis of a novel diagnostic biomarker for LUSC, based on TCGA. Methods and Results The present study investigated LUSC-specific key microRNAs (miRNAs) from large-scale samples in TCGA. According to exclusion criteria and inclusion criteria, the expression profiles of miRNAs with related clinical information of 332 LUSC patients were obtained. Most aberrantly expressed miRNAs were identified between tumor and normal samples. Forty-two LUSC-specific intersection miRNAs (fold change >2, p < 0.05) were obtained by an integrative computational method, among them six miRNAs were found to be aberrantly expressed concerning characteristics of patients (gender, lymphatic metastasis, patient outcome assessment) through Student t-test. Five miRNAs correlated with overall survival (log-rank p < 0.05) were obtained through the univariate Cox proportional hazards regression model and Mantel–Haenszel test. Then, five miRNAs were randomly selected to validate the expression in 47 LUSC patient tissues using quantitative real-time polymerase chain reaction. The results showed that the test findings were consistent with the TCGA findings. Also, the diagnostic value of the specific key miRNAs was determined by areas under receiver operating characteristic curves. Finally, 577 interaction mRNAs as the targets of 42 LUSC-specific intersection miRNAs were selected for further bioinformatics analysis. Conclusion This study indicates that this novel microRNA expression signature may be a useful biomarker of the diagnosis for LUSC patients, based on bioinformatics analysis.
Yang et al. (2017) Diagnosis value of aberrantly expressed microRNA profiles in lung squamous cell carcinoma: a study based on the Cancer Genome Atlas. PeerJ 5:e4101 https://doi.org/10.7717/peerj.4101
Ordinary kriging vs inverse distance weighting: spatial interpolation of the sessile community of Madagascar reef, Gulf of Mexico
Information about the distribution and abundance of the habitat-forming sessile organisms in marine ecosystems is of great importance for conservation and natural resource managers. Spatial interpolation methodologies can be useful to generate this information from in situ sampling points, especially in circumstances where remote sensing methodologies cannot be applied due to small-scale spatial variability of the natural communities and low light penetration in the water column. Interpolation methods are widely used in environmental sciences; however, published studies using these methodologies in coral reef science are scarce. We compared the accuracy of the two most commonly used interpolation methods in all disciplines, inverse distance weighting (IDW) and ordinary kriging (OK), to predict the distribution and abundance of hard corals, octocorals, macroalgae, sponges and zoantharians and identify hotspots of these habitat-forming organisms using data sampled at three different spatial scales (5, 10 and 20 m) in Madagascar reef, Gulf of Mexico. The deeper sandy environments of the leeward and windward regions of Madagascar reef were dominated by macroalgae and seconded by octocorals. However, the shallow rocky environments of the reef crest had the highest richness of habitat-forming groups of organisms; here, we registered high abundances of octocorals and macroalgae, with sponges, Millepora alcicornis and zoantharians dominating in some patches, creating high levels of habitat heterogeneity. IDW and OK generated similar maps of distribution for all the taxa; however, cross-validation tests showed that IDW outperformed OK in the prediction of their abundances. When the sampling distance was at 20 m, both interpolation techniques performed poorly, but as the sampling was done at shorter distances prediction accuracies increased, especially for IDW. OK had higher mean prediction errors and failed to correctly interpolate the highest abundance values measured in situ, except for macroalgae, whereas IDW had lower mean prediction errors and high correlations between predicted and measured values in all cases when sampling was every 5 m. The accurate spatial interpolations created using IDW allowed us to see the spatial variability of each taxa at a biological and spatial resolution that remote sensing would not have been able to produce. Our study sets the basis for further research projects and conservation management in Madagascar reef and encourages similar studies in the region and other parts of the world where remote sensing technologies are not suitable for use.
Zarco-Perello et al. (2017) Ordinary kriging vs inverse distance weighting: spatial interpolation of the sessile community of Madagascar reef, Gulf of Mexico. PeerJ 5:e4078 https://doi.org/10.7717/peerj.4078
Hermit crab response to a visual threat is sensitive to looming cues
Prior work in our lab has shown that an expanding image on a computer screen elicits a hiding response in the Caribbean terrestrial hermit crab (Coenobita clypeatus). We conducted two experiments to identify what properties of the expanding stimulus contribute to its effectiveness as a visual threat. First we found that an expanding geometric star evoked a strong hiding response while a contracting or full-sized stationary star did not. A second experiment revealed that the more quickly the stimulus expanded the shorter the latency to hide. These findings suggest that the anti-predator response to looming stimulus relies heavily on visual cues relating to the manner of approach. The simulated visual threat on a computer screen captures key features of a real looming object that elicits hiding behavior in crabs in the wild.
Shragai et al. (2017) Hermit crab response to a visual threat is sensitive to looming cues. PeerJ 5:e4058 https://doi.org/10.7717/peerj.4058
Reference standards to assess physical fitness of children and adolescents of Brazil: an approach to the students of the Lake Itaipú region—Brazil
Background The importance of assessing body fat variables and physical fitness tests plays an important role in monitoring the level of activity and physical fitness of the general population. The objective of this study was to develop reference norms to evaluate the physical fitness aptitudes of children and adolescents based on age and sex from the lake region of Itaipú, Brazil. Methods A descriptive cross-sectional study was carried out with 5,962 students (2,938 males and 3,024 females) with an age range of 6.0 and 17.9 years. Weight (kg), height (cm), and triceps (mm), and sub-scapular skinfolds (mm) were measured. Body Mass Index (BMI kg/m2) was calculated. To evaluate the four physical fitness aptitude dimensions (morphological, muscular strength, flexibility, and cardio-respiratory), the following physical education tests were given to the students: sit-and-reach (cm), push-ups (rep), standing long jump (cm), and 20-m shuttle run (m). Results and Discussion Females showed greater flexibility in the sit-and-reach test and greater body fat than the males. No differences were found in BMI. Percentiles were created for the four components for the physical fitness aptitudes, BMI, and skinfolds by using the LMS method based on age and sex. The proposed reference values may be used for detecting talents and promoting health in children and adolescents.
Hobold et al. (2017) Reference standards to assess physical fitness of children and adolescents of Brazil: an approach to the students of the Lake Itaipú region—Brazil. PeerJ 5:e4032 https://doi.org/10.7717/peerj.4032
Kullback Leibler divergence in complete bacterial and phage genomes
The amino acid content of the proteins encoded by a genome may predict the coding potential of that genome and may reflect lifestyle restrictions of the organism. Here, we calculated the Kullback–Leibler divergence from the mean amino acid content as a metric to compare the amino acid composition for a large set of bacterial and phage genome sequences. Using these data, we demonstrate that (i) there is a significant difference between amino acid utilization in different phylogenetic groups of bacteria and phages; (ii) many of the bacteria with the most skewed amino acid utilization profiles, or the bacteria that host phages with the most skewed profiles, are endosymbionts or parasites; (iii) the skews in the distribution are not restricted to certain metabolic processes but are common across all bacterial genomic subsystems; (iv) amino acid utilization profiles strongly correlate with GC content in bacterial genomes but very weakly correlate with the G+C percent in phage genomes. These findings might be exploited to distinguish coding from non-coding sequences in large data sets, such as metagenomic sequence libraries, to help in prioritizing subsequent analyses.
Akhter et al. (2017) Kullback Leibler divergence in complete bacterial and phage genomes. PeerJ 5:e4026 https://doi.org/10.7717/peerj.4026