title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1350
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Hierarchical generalized additive models in ecology: an introduction with mgcv
link: https://peerj.com/articles/6876
last-modified: 2019-05-27
description: In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels. We describe the theoretical connection between HGAMs, HGLMs, and GAMs, explain how to model different assumptions about the degree of intergroup variability in functional response, and show how HGAMs can be readily fitted using existing GAM software, the mgcv package in R. We also discuss computational and statistical issues with fitting these models, and demonstrate how to fit HGAMs on example data. All code and data used to generate this paper are available at: github.com/eric-pedersen/mixed-effect-gams.
creator: Eric J. Pedersen
creator: David L. Miller
creator: Gavin L. Simpson
creator: Noam Ross
uri: https://doi.org/10.7717/peerj.6876
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Pedersen et al.

title: Detection of condition-specific marker genes from RNA-seq data with MGFR
link: https://peerj.com/articles/6970
last-modified: 2019-05-27
description: The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups samples with similar gene expression levels and flags potential markers of a sample type if their highest expression values represent all replicates of this type. We have benchmarked MGFR against other methods and found that its proposed markers accurately characterize the functional identity of different tissues and cell types in standard and single cell RNA-seq datasets. Then, we performed a more detailed analysis for three of these datasets, which profile the transcriptomes of different human tissues, immune and human blastocyst cell types, respectively. MGFR’s predicted markers were compared to gold-standard lists for these datasets and outperformed the other marker detectors. Finally, we suggest novel candidate marker genes for the examined tissues and cell types. MGFR is implemented as a freely available Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.MGFR), which facilitates its use and integration with bioinformatics pipelines.
creator: Khadija El Amrani
creator: Gregorio Alanis-Lobato
creator: Nancy Mah
creator: Andreas Kurtz
creator: Miguel A. Andrade-Navarro
uri: https://doi.org/10.7717/peerj.6970
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 El Amrani et al.

title: Enhanced mechanical, thermal and biocompatible nature of dual component electrospun nanocomposite for bone tissue engineering
link: https://peerj.com/articles/6986
last-modified: 2019-05-27
description: Traditionally, in the Asian continent, oils are a widely accepted choice for alleviating bone-related disorders. The design of scaffolds resembling the extracellular matrix (ECM) is of great significance in bone tissue engineering. In this study, a multicomponent polyurethane (PU), canola oil (CO) and neem oil (NO) scaffold was developed using the electrospinning technique. The fabricated nanofibers were subjected to various physicochemical and biological testing to validate its suitability for bone tissue engineering. Morphological analysis of the multicomponent scaffold showed a reduction in fiber diameter (PU/CO—853 ± 141.27 nm and PU/CO/NO—633 ± 137.54 nm) compared to PU (890 ± 116.911 nm). The existence of CO and NO in PU matrix was confirmed by an infrared spectrum (IR) with the formation of hydrogen bond. PU/CO displayed a mean contact angle of 108.7° ± 0.58 while the PU/CO/NO exhibited hydrophilic nature with an angle of 62.33° ± 2.52. The developed multicomponent also exhibited higher thermal stability and increased mechanical strength compared to the pristine PU. Atomic force microscopy (AFM) analysis depicted lower surface roughness for the nanocomposites (PU/CO—389 nm and PU/CO/NO—323 nm) than the pristine PU (576 nm). Blood compatibility investigation displayed the anticoagulant nature of the composites. Cytocompatibility studies revealed the non-toxic nature of the developed composites with human fibroblast cells (HDF) cells. The newly developed porous PU nanocomposite scaffold comprising CO and NO may serve as a potential candidate for bone tissue engineering.
creator: Guanbao Li
creator: Pinquan Li
creator: Qiuan Chen
creator: Mohan Prasath Mani
creator: Saravana Kumar Jaganathan
uri: https://doi.org/10.7717/peerj.6986
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Li et al.

title: Effectiveness of nasal irrigation devices: a Thai multicentre survey
link: https://peerj.com/articles/7000
last-modified: 2019-05-27
description: BackgroundNasal irrigation is widely used as an adjunctive treatment for nasal diseases. There is little evidence regarding the efficacy of the devices used in this procedure. The objective of this survey was to evaluate the effectiveness of nasal irrigation devices based on the experiences of patients and physicians.MethodsWe conducted a multicentre survey study between November 2017 and October 2018. Physician and patient questionnaires were developed based on the available literature and expert opinion. The physician questionnaire was submitted to the Otolaryngology residents and staff of each centre and their network. The physicians were also asked to distribute the patient questionnaire to their patients.ResultsInformation regarding 331 devices used by the patients was collected. The mean age of the patients was 45.46 ± 17.19 years (from 5 to 81). Roughly half were male, and half were female (48.6%: 51.4%). Among the high-pressure devices, we found that the high-pressure large-volume nasal irrigation devices yielded significantly higher symptom scores in seven of 12 domains (p < 0.05). Among the large-volume devices, we found that the large-volume high-pressure nasal irrigation devices received significantly higher symptom scores in 4 of 12 domains (p < 0.05). However, a higher proportion of patients using the large-volume high-pressure devices had retained fluid in the sinuses compared to those using large-volume low-pressure devices (p < 0.001).ConclusionsThis survey supports the regular use of nasal irrigation, particularly with large-volume high-pressure devices, as an effective treatment for nasal disease. It may be effective at clearing nasal secretion, improve nasal congestion, decrease post-nasal drip, improve sinus pain or headache, improve taste and smell, and improve sleep quality. It could be used by patients with good compliance and minimal side effects.
creator: Patorn Piromchai
creator: Charoiboon Puvatanond
creator: Virat Kirtsreesakul
creator: Saisawat Chaiyasate
creator: Sanguansak Thanaviratananich
uri: https://doi.org/10.7717/peerj.7000
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Piromchai et al.

title: On the presence of Dipturus nidarosiensis (Storm, 1881) in the Central Mediterranean area
link: https://peerj.com/articles/7009
last-modified: 2019-05-27
description: The Norwegian skate Dipturus nidarosiensis (Storm, 1881) has only recently been recorded in the western Mediterranean Sea along the coast of southern Sardinia, off Algeria and the Alboran Sea. The present study confirmed the presence of the species in the Central Mediterranean Sea by identifying morphometric, morphological features and molecular markers. Biological sampling was conducted from 2010 to 2016 on eight specimens collected through commercial landings, offshore observer programmes and scientific surveys in Adriatic and Ionian waters at depths between 320 and 720 m. The total lengths of the specimens (juveniles and adults) ranged from 268 to 1,422 mm, and their body weights ranged from 44.5 to 12,540.0 g. They showed morphometric features that corresponded to those of Norwegian skates in the Northeast Atlantic and the Western Mediterranean. In previous analyses, molecular data were obtained by mitochondrial COI sequences. The haplotype network showed the occurrence of a common haplotype (Hap_1) shared by the individuals from areas in the North Atlantic, Sardinian, Algerian and Spanish Mediterranean Sea areas but not South Africa. The occurrence of individuals in different stages of life (i.e., juveniles, sub-adults and adults) and sexual development (immature and mature) suggested the presence of a species with a permanent reproductive allocation in the deep waters of the Mediterranean, which was exposed to a low level of fishing exploitation. Indeed, the deep depth distribution of the species could be the reason for the absence of information about this species in onshore or offshore fishery data collection programmes and scientific surveys.
creator: Pierluigi Carbonara
creator: Rita Cannas
creator: Marilena Donnaloia
creator: Riccardo Melis
creator: Cristina Porcu
creator: Maria Teresa Spedicato
creator: Walter Zupa
creator: Maria Cristina Follesa
uri: https://doi.org/10.7717/peerj.7009
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Carbonara et al.

title: One-class land-cover classification using MaxEnt: the effect of modelling parameterization on classification accuracy
link: https://peerj.com/articles/7016
last-modified: 2019-05-27
description: Multiple-class land-cover classification approaches can be inefficient when the main goal is to classify only one or a few classes. Under this scenario one-class classification algorithms could be a more efficient alternative. Currently there are several algorithms that can fulfil this task, with MaxEnt being one of the most promising. However, there is scarce information regarding parametrization for performing land-cover classification using MaxEnt. In this study we aimed to understand how MaxEnt parameterization affects the classification accuracy of four different land-covers (i.e., built-up, irrigated grass, evergreen trees and deciduous trees) in the city of Santiago de Chile. We also evaluated if MaxEnt manual parameterization outperforms classification results obtained when using MaxEnt default parameters setting. To accomplish our objectives, we generated a set of 25,344 classification maps (i.e., 6,336 for each assessed land-cover), which are based on all the potential combination of 12 different classes of features restrictions, four regularization multipliers, four different sample sizes, three training/testing proportions, and 11 thresholds for generating the binary maps. Our results showed that with a good parameterization, MaxEnt can effectively classify different land covers with kappa values ranging from 0.68 for deciduous trees to 0.89 for irrigated grass. However, the accuracy of classification results is highly influenced by the type of land-cover being classified. Simpler models produced good classification outcomes for homogenous land-covers, but not for heterogeneous covers, where complex models provided better outcomes. In general, manual parameterization improves the accuracy of classification results, but this improvement will depend on the threshold used to generate the binary map. In fact, threshold selection showed to be the most relevant factor impacting the accuracy of the four land-cover classification. The number of sampling points for training the model also has a positive effect on classification results. However, this effect followed a logarithmic distribution, showing an improvement of kappa values when increasing the sampling from 40 to 60 points, but showing only a marginal effect if more than 60 sampling points are used. In light of these results, we suggest testing different parametrization and thresholds until satisfactory kappa or other accuracy metrics values are achieved. Our results highlight the huge potential that MaxEnt has a as a tool for one-class classification, but a good understanding of the software settings and model parameterization is needed to obtain reliable results.
creator: Ignacio C. Fernández
creator: Narkis S. Morales
uri: https://doi.org/10.7717/peerj.7016
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Fernández and Morales

title: Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic Ocean
link: https://peerj.com/articles/6794
last-modified: 2019-05-24
description: BackgroundIn the ocean, the variability of environmental conditions found along depth gradients exposes populations to contrasting levels of perturbation, which can be reflected in the overall patterns of species genetic diversity. At shallow sites, resource availability may structure large, persistent and well-connected populations with higher levels of diversity. In contrast, the more extreme conditions, such as thermal stress during heat waves, can lead to population bottlenecks and genetic erosion, inverting the natural expectation. Here we examine how genetic diversity varies along depth for a long-lived, important ecosystem-structuring species, the red gorgonian, Paramuricea clavata.MethodsWe used five polymorphic microsatellite markers to infer differences in genetic diversity and differentiation, and to detect bottleneck signs between shallow and deeper populations across the Atlantic Ocean and the Mediterranean Sea. We further explored the potential relationship between depth and environmental gradients (temperature, ocean currents, productivity and slope) on the observed patterns of diversity by means of generalized linear mixed models.ResultsAn overall pattern of higher genetic diversity was found in the deeper sites of the Atlantic Ocean and the Mediterranean Sea. This pattern was largely explained by bottom temperatures, with a linear pattern of decreasing genetic diversity with increasing thermal stress. Genetic differentiation patterns showed higher gene flow within sites (i.e., shallow vs. deeper populations) than between sites. Recent genetic bottlenecks were found in two populations of shallow depths.DiscussionOur results highlight the role of deep refugial populations safeguarding higher and unique genetic diversity for marine structuring species. Theoretical regression modelling demonstrated how thermal stress alone may reduce population sizes and diversity levels of shallow water populations. In fact, the examination of time series on a daily basis showed the upper water masses repeatedly reaching lethal temperatures for P. clavata. Differentiation patterns showed that the deep richer populations are isolated. Gene flow was also inferred across different depths; however, not in sufficient levels to offset the detrimental effects of surface environmental conditions on genetic diversity. The identification of deep isolated areas with high conservation value for the red gorgonian represents an important step in the face of ongoing and future climate changes.
creator: Joanna Pilczynska
creator: Silvia Cocito
creator: Joana Boavida
creator: Ester A. Serrão
creator: Jorge Assis
creator: Eliza Fragkopoulou
creator: Henrique Queiroga
uri: https://doi.org/10.7717/peerj.6794
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Pilczynska et al.

title: Fragility Index, power, strength and robustness of findings in sports medicine and arthroscopic surgery: a secondary analysis of data from a study on use of the Fragility Index in sports surgery
link: https://peerj.com/articles/6813
last-modified: 2019-05-24
description: BackgroundA recent study concluded that most findings reported as significant in sports medicine and arthroscopic surgery are not “robust” when evaluated with the Fragility Index (FI). A secondary analysis of data from a previous study was performed to investigate (1) the correctness of the findings, (2) the association between FI, p-value and post hoc power, (3) median power to detect a medium effect size, and (4) the implementation of sample size analysis in these randomized controlled trials (RCTs).MethodsIn addition to the 48 studies listed in the appendix accompanying the original study by Khan et al. (2017) we did a follow-up literature search and 18 additional studies were found. In total 66 studies were included in the analysis. We calculated post hoc power, p-values and confidence intervals associated with the main outcome variable. Use of a priori power analysis was recorded. The median power to detect small (h > 0.2), medium (h > 0.5), or large effect (h > 0.8) with a baseline proportion of events of 10% and 30% in each study included was calculated. Three simulation data sets were used to validate our findings.ResultsInconsistencies were found in eight studies. A priori power analysis was missing in one-fourth of studies (16/66). The median power to detect a medium effect size with a baseline proportion of events of 10% and 30% was 42% and 43%, respectively. The FI was inherently associated with the achieved p-value and post hoc power.DiscussionA relatively high proportion of studies had inconsistencies. The FI is a surrogate measure for p-value and post hoc power. Based on these studies, the median power in this field of research is suboptimal. There is an urgent need to investigate how well research claims in orthopedics hold in a replicated setting and the validity of research findings.
creator: Aleksi Reito
creator: Lauri Raittio
creator: Olli Helminen
uri: https://doi.org/10.7717/peerj.6813
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Reito et al.

title: Application of the urban exposome framework using drinking water and quality of life indicators: a proof-of-concept study in Limassol, Cyprus
link: https://peerj.com/articles/6851
last-modified: 2019-05-24
description: BackgroundCities face rapid changes leading to increasing inequalities and emerging public health issues that require cost-effective interventions. The urban exposome concept refers to the continuous monitoring of urban environmental and health indicators using the city and smaller intra-city areas as measurement units in an interdisciplinary approach that combines qualitative and quantitative methods from social sciences, to epidemiology and exposure assessment.MethodsIn this proof of concept study, drinking water and quality of life indicators were described as part of the development of the urban exposome of Limassol (Cyprus) and were combined with agnostic environment-wide association analysis. This study was conducted as a two-part project with a qualitative part assessing the perceptions of city stakeholders, and quantitative part using a cross-sectional study design (an urban population study). We mapped the water quality parameters and participants’ opinions on city life (i.e., neighborhood life, health care, and green space access) using quarters (small administrative areas) as the reference unit of the city. In an exploratory, agnostic, environment-wide association study analysis, we used all variables (questionnaire responses and water quality metrics) to describe correlations between them.ResultsOverall, urban drinking-water quality using conventional indicators of chemical (disinfection byproducts-trihalomethanes (THM)) and microbial (coliforms, E. coli, and Enterococci) quality did not raise particular concerns. The general health and chronic health status of the urban participants were significantly (false discovery rate corrected p-value < 0.1) associated with different health conditions such as hypertension and asthma, as well as having financial issues in access to dental care. Additionally, correlations between THM exposures and participant behavioral characteristics (e.g., household cleaning, drinking water habits) were documented.ConclusionThis proof-of-concept study showed the potential of using integrative approaches to develop urban exposomic profiles and identifying within-city differences in environmental and health indicators. The characterization of the urban exposome of Limassol will be expanded via the inclusion of biomonitoring tools and untargeted metabolomics.
creator: Xanthi D. Andrianou
creator: Chava van der Lek
creator: Pantelis Charisiadis
creator: Solomon Ioannou
creator: Kalliopi N. Fotopoulou
creator: Zoe Papapanagiotou
creator: George Botsaris
creator: Carijn Beumer
creator: Konstantinos C. Makris
uri: https://doi.org/10.7717/peerj.6851
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Andrianou et al.

title: We need to talk about reliability: making better use of test-retest studies for study design and interpretation
link: https://peerj.com/articles/6918
last-modified: 2019-05-24
description: Neuroimaging, in addition to many other fields of clinical research, is both time-consuming and expensive, and recruitable patients can be scarce. These constraints limit the possibility of large-sample experimental designs, and often lead to statistically underpowered studies. This problem is exacerbated by the use of outcome measures whose accuracy is sometimes insufficient to answer the scientific questions posed. Reliability is usually assessed in validation studies using healthy participants, however these results are often not easily applicable to clinical studies examining different populations. I present a new method and tools for using summary statistics from previously published test-retest studies to approximate the reliability of outcomes in new samples. In this way, the feasibility of a new study can be assessed during planning stages, and before collecting any new data. An R package called relfeas also accompanies this article for performing these calculations. In summary, these methods and tools will allow researchers to avoid performing costly studies which are, by virtue of their design, unlikely to yield informative conclusions.
creator: Granville J. Matheson
uri: https://doi.org/10.7717/peerj.6918
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Matheson