title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1232 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Assessing the effect of fish size on species distribution model performance in southern Chilean rivers link: https://peerj.com/articles/7771 last-modified: 2019-12-06 description: Despite its theoretical relationship, the effect of body size on the performance of species distribution models (SDM) has only been assessed in a few studies, and to date, the evidence shows unclear results. In this context, Chilean fishes provide an ideal case to evaluate this relationship due to their short size (fishes between 5 cm and 40 cm) and conservation status, providing evidence for species at the lower end of the worldwide fish size distribution and representing a relevant management tool for species conservation. We assessed the effect of body size on the performance of SDM in nine Chilean river fishes, considering the number of records, performance metrics, and predictor importance. The study was developed in the Bueno and Valdivia basins of southern Chile. We used a neural network modeling algorithm, training models with a cross-validation scheme. The effect of fish size on selected metrics was assessed using linear models and beta regressions. While no relationship between fish size and the number of presences was found, our results indicate that the model specificity increases with fish size. Additionally, the predictive importance of Riparian Vegetation and Within-Channel Structures variables decreases for larger species. Our results suggest that the relationship between the grain of the dataset and the home range of the species could bias SDM, leading in our case, to overprediction of absences. We also suggest that evolutionary adaptation to low slopes among Chilean fishes increases the relevance of riparian vegetation in the SDMs of smaller species. This study provides evidence on how species size may bias SDM, which could potentially be corrected by adjusting the model grain. creator: Daniel Zamorano creator: Fabio A. Labra creator: Marcelo Villarroel creator: Shaw Lacy creator: Luca Mao creator: Marcelo A. Olivares creator: Matías Peredo-Parada uri: https://doi.org/10.7717/peerj.7771 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zamorano et al. title: Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max) link: https://peerj.com/articles/7950 last-modified: 2019-12-06 description: In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean. creator: Yongbin Wang creator: Lei Ling creator: Zhenfeng Jiang creator: Weiwei Tan creator: Zhaojun Liu creator: Licheng Wu creator: Yuanling Zhao creator: Shanyong Xia creator: Jun Ma creator: Guangjin Wang creator: Wenbin Li uri: https://doi.org/10.7717/peerj.7950 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Improving the prediction accuracy of river inflow using two data pre-processing techniques coupled with data-driven model link: https://peerj.com/articles/8043 last-modified: 2019-12-06 description: River inflow prediction plays an important role in water resources management and power-generating systems. But the noises and multi-scale nature of river inflow data adds an extra layer of complexity towards accurate predictive model. To overcome this issue, we proposed a hybrid model, Variational Mode Decomposition (VMD), based on a singular spectrum analysis (SSA) denoising technique. First, SSA his applied to denoise the river inflow data. Second, VMD, a signal processing technique, is employed to decompose the denoised river inflow data into multiple intrinsic mode functions (IMFs), each with a relative frequency scale. Third, Empirical Bayes Threshold (EBT) is applied on non-linear IMF to smooth out. Fourth, predicted models of denoised and decomposed IMFs are established by learning the feature values of the Support Vector Machine (SVM). Finally, the ensemble predicted results are formulated by adding the predicted IMFs. The proposed model is demonstrated using daily river inflow data from four river stations of the Indus River Basin (IRB) system, which is the largest water system in Pakistan. To fully illustrate the superiority of our proposed approach, the SSA-VMD-EBT-SVM hybrid model was compared with SSA-VMD-SVM, VMD-SVM, Empirical Mode Decomposition (EMD) based i.e., EMD-SVM, SSA-EMD-SVM, Ensemble EMD (EEMD) based i.e., EEMD-SVM and SSA-EEMD-SVM. We found that our proposed hybrid SSA-EBT-VMD-SVM model outperformed than others based on following performance measures: the Nash-Sutcliffe Efficiency (NSE), Mean Absolute Percentage Error (MAPE) and Root Mean Square Error (RMSE). Therefore, SSA-VMD-EBT-SVM model can be used for water resources management and power-generating systems using non-linear time series data. creator: Hafiza Mamona Nazir creator: Ijaz Hussain creator: Muhammad Faisal creator: Elsayed Elsherbini Elashkar creator: Alaa Mohamd Shoukry uri: https://doi.org/10.7717/peerj.8043 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nazir et al. title: Dynamic changes in prescription opioids from 2006 to 2017 in Texas link: https://peerj.com/articles/8108 last-modified: 2019-12-06 description: BackgroundThe US is experiencing an epidemic of opioid overdoses which may be at least partially due to an over-reliance on opioid analgesics in the treatment of chronic non-cancer pain and subsequent escalation to heroin or illicit fentanyl. As Texas was reported to be among the lowest in the US for opioid use and misuse, further examination of this state is warranted.Materials and MethodsThis study was conducted to quantify prescription opioid use in Texas. Data was obtained from the publicly available US Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System (ARCOS) which monitors controlled substances transactions from manufacture to commercial distribution. Data for 2006–2017 from Texas for ten prescription opioids including eight primarily used to relieve pain (codeine, fentanyl, hydrocodone, hydromorphone, meperidine, morphine, oxycodone, oxymorphone) and two (buprenorphine and methadone) for the treatment of an Opioid Use Disorder (OUD) were examined.ResultsThe change in morphine mg equivalent (MME) of all opioids (+23.3%) was only slightly greater than the state’s population gains (21.1%). Opioids used to treat an OUD showed pronounced gains (+90.8%) which were four-fold faster than population growth. Analysis of individual agents revealed pronounced elevations in codeine (+387.5%), hydromorphone (+106.7%), and oxycodone (+43.6%) and a reduction in meperidine (−80.3%) in 2017 relative to 2006. Methadone in 2017 accounted for a greater portion (39.5%) of the total MME than hydrocodone, oxycodone, morphine, hydromorphone, oxymorphone, and meperidine, combined. There were differences between urban and rural areas in the changes in hydrocodone and buprenorphine.ConclusionsCollectively, these findings indicate that continued vigilance is needed in Texas to appropriately treat pain and an OUD while minimizing the potential for prescription opioid diversion and misuse. Texas may lead the US in a return to pre-opioid epidemic prescription levels. creator: Ebuwa O. Ighodaro creator: Kenneth L. McCall creator: Daniel Y. Chung creator: Stephanie D. Nichols creator: Brian J. Piper uri: https://doi.org/10.7717/peerj.8108 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ighodaro et al. title: A multiple comparative study of putative endosymbionts in three coexisting apple snail species link: https://peerj.com/articles/8125 last-modified: 2019-12-06 description: We here compare morphological and molecular characters of some putative endosymbiotic elements of the digestive gland of three ampullariid species (Pomacea canaliculata, Pomacea scalaris and Asolene platae) which coexist in Lake Regatas (Palermo, Buenos Aires). The putative endosymbionts were reported in these species and were identified as C and K corpuscles. The three species show tubuloacinar glands, each adenomere was constituted mainly by two distinct cell types (columnar and pyramidal). C and K corpuscles together occupied from one-fourth to one-fifth of the tissue area in the three host species, where C corpuscles were round and greenish-brown, were delimited by a distinct wall, stained positively with Alcian Blue and were associated with columnar cells. K corpuscles were oval, dark-brown multilamellar bodies and were associated with pyramidal cells. Under TEM, C corpuscles occurred within vacuoles of columnar cells and contained many electron-dense clumps and irregular membrane stacks and vesicles spread in an electron-lucent matrix. Sometimes a membrane appeared detached from the inner surface of the wall, suggesting the existence of a plasma membrane. In turn, K corpuscles were contained within vacuoles of pyramidal cells and were made of concentric lamellae, which were in turn made of an electron-dense fibrogranular material. No membranes were seen in them. Interspecifically, C corpuscles vary significantly in width and inner contents. K corpuscles were also variable in length and width. However, both C and K corpuscles in the three studied species hybridised with generalised cyanobacterial/chloroplast probes for 16S rRNA. Also, both corpuscle types (isolated from gland homogenates) were sensitive to lysozyme digestion, which indicates that bacterial peptidoglycans are an integral part of their covers. The reported data confirm and extend previous studies on P. canaliculata in which the endosymbiotic nature of C and K corpuscles were first proposed. We further propose that the endosymbiotic corpuscles are related to the Cyanobacteria/chloroplasts clade. Based on the known distribution of these corpuscles in the major clades of Ampullariidae, we hypothesise they may be universally distributed in this family, and that may constitute an interesting model for studying the co-evolution of endosymbionts and their gastropod hosts. creator: Federico A. Dellagnola creator: Cristian Rodriguez creator: Alfredo Castro-Vazquez creator: Israel A. Vega uri: https://doi.org/10.7717/peerj.8125 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dellagnola et al. title: Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality link: https://peerj.com/articles/8155 last-modified: 2019-12-06 description: Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence. creator: Aozora Kakuda creator: Hideyuki Doi creator: Rio Souma creator: Mariko Nagano creator: Toshifumi Minamoto creator: Izumi Katano uri: https://doi.org/10.7717/peerj.8155 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kakuda et al. title: According, against, and above dietary norms: a key to understanding the relationship between personality style and taste preferences link: https://peerj.com/articles/8198 last-modified: 2019-12-06 description: BackgroundUnderstanding individual food preferences is critical for creating tailored strategies that promote healthy individual eating behaviors. Individual sensory liking appears to be an essential determinant of dietary intake. Taste preferences influence satisfaction and satiety, and may consequently influence weight status and psychological adjustment. The purpose of this study was to identify the association between taste preferences (sweet, salty, sweet & fatty, salty & fatty) and personality features.MethodsThe Millon Clinical Multiaxial Inventory-III (MCMI-III) was used for the assessment of personality traits and PrefQuest (PQ) was used for measuring recalled food preferences. A total of 137 participants were included in the study. The relationship between compulsive and antisocial features and taste preferences was assessed by hierarchical multiple linear regression, while controlling for age, gender, BMI, marital status, and educational level.ResultsThe antisocial personality traits were a negative explanatory variable for sweet & fatty taste preference, R2 = .15, t(132) =  − 2.40, p = .018, 95% [−.57, −.06] and salty & fatty taste preference, R2 = .16, t(133) =  − 2.38, p = .019, 95% [−.07, −.01], while controlling for anthropological factors. In addition, men showed a higher preference than women for sweet & fatty food, such as chocolate or desserts, rsp = .19, p = .021, and for the salty & fatty food, rsp = .30, p < .001. BMI was not found to moderate the relationship between personality and taste preference. No significant association was found between compulsive personality traits and food preference, as assessed by sensory liking.ConclusionsThe findings can bring a much better understanding of the relationship between the compulsive or antisocial personality and taste preferences. In addition, it may help build psychotherapeutic and nutritional strategies that promote healthy eating behaviors, tailored to a particular personality style. creator: Ligiana Mihaela Petre creator: Bianca Nicoleta Vatasescu uri: https://doi.org/10.7717/peerj.8198 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Petre and Vatasescu title: In vitro histomorphometric comparison of dental pulp tissue in different teeth link: https://peerj.com/articles/8212 last-modified: 2019-12-06 description: BackgroundDental pulp (DP) represents an accessible and valuable source promising of stem cells for clinical application. However, there are some disadvantages associated with the isolation of dental pulp stem cells (DPSCs), which include the size and weight of the pulp tissue needed to yield sufficient cells for culturing in vitro. Therefore, the objective of this study was to compare in vitro histomorphometry of DP from permanent (premolars, third molar), supernumerary and deciduous teeth of patients between 5 and 25 years old with regards to weight, length, width and the cell density in the four regions of the DP in order to obtain quantitative parameters in a tissue that represents a valuable source of stem cells.MethodsDPs were obtained from 10 central incisors deciduous, 20 permanent teeth (10 premolars, 10 third molars) and 10 supernumeraries (six mesiodents and four inferior premolar shapes). The pulps were carefully removed, and the entire tissue was weighed. The pulp length and the width were measured with a digital Vernier caliper. The cellular density analysis was performed according to the four regions of the DP (coronal, cervical, medial and apical) in histological slides using photography and the ImageJ® program for quantification.ResultsThe Pearson correlation test revealed that DP weight among different types of teeth is correlated with age in male patients. A significant positive correlation was noted between length and width of the DP with age in both genders. The mean DP weight for supernumerary and third molar teeth was greater than deciduous and premolar teeth. Finally, the histological analysis showed that the coronal and apical portions of DP in supernumerary and premolar teeth have the highest cell density.ConclusionsThe DP of supernumerary teeth has quantitatively the best morphometric parameters and cell density comparable with the quality of DP obtained from deciduous teeth. creator: Marytere Guerrero-Jiménez creator: Geovanny I. Nic-Can creator: Nelly Castro-Linares creator: Fernando Javier Aguilar-Ayala creator: Michel Canul-Chan creator: Rafael A. Rojas-Herrera creator: Ricardo Peñaloza-Cuevas creator: Beatriz A. Rodas-Junco uri: https://doi.org/10.7717/peerj.8212 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guerrero-Jiménez et al. title: VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs link: https://peerj.com/articles/8213 last-modified: 2019-12-06 description: In the past decades a number of software programs have been developed to infer phylogenetic relationships between populations. However, most of these programs typically use alignments of sequences from genes to build phylogeny. Recently, many standalone or web applications have been developed to handle large-scale whole genome data, but they are either computationally intensive, dependent on third party software or required significant time and resource of a web server. In the post-genomic era, researchers are able to obtain bioinformatically processed high-quality publication-ready whole genome data for many individuals in a population from next generation sequencing companies due to the reduction in the cost of sequencing and analysis. Such genotype data is typically presented in the Variant Call Format (VCF) and there is no simple software available that directly uses this data format to construct the phylogeny of populations in a short time. To address this limitation, we have developed a user-friendly software, VCF2PopTree that uses genome-wide SNPs to construct and display phylogenetic trees in seconds to minutes. For example, it reads a VCF file containing 4 million SNPs and draws a tree in less than 30 seconds. VCF2PopTree accepts genotype data from a local machine, constructs a tree using UPGMA and Neighbour-Joining algorithms and displays it on a web-browser. It also produces pairwise-diversity matrix in MEGA and PHYLIP file formats as well as trees in the Newick format which could be directly used by other popular phylogenetic software programs. The software including the source code, a test VCF file and a documentation are available at: https://github.com/sansubs/vcf2pop. creator: Sankar Subramanian creator: Umayal Ramasamy creator: David Chen uri: https://doi.org/10.7717/peerj.8213 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Subramanian et al. title: Critical multi-stranded approach for determining the ecological values of diatoms in unique aquatic ecosystems of anthropogenic origin link: https://peerj.com/articles/8117 last-modified: 2019-12-05 description: BackgroundThe ecological state of surface waters is typically assessed by a multi-aspect approach based on a determination of its chemical and physical parameters, by hydromorphology and the use of indicator organisms such as benthic diatoms. By assigning ecological indicator values, it is possible to create diatom indices which serve as the basic tool in assessing the ecological status of surface waters. These ecological indicator values are set according to classification systems, such as the Van Dam, Mertens & Sinkeldam (1994) system, which classifies species of diatoms according to seven different ecological factors. However, recent studies on the autecology of diatoms have shown the need to verify and establish new ecological indicator values. To this end, aquatic ecosystems are good environments to observe the range of tolerance of benthic diatoms to environmental conditions due to their unique physical and chemical parameters. The aim of the present study was to propose the establishment of new, or altered, ecological indicator values, according to the Van Dam, Mertens & Sinkeldam (1994) classification, of species of diatoms characteristic of three post-mining aquatic ecosystems.MethodsIn total, 36 species were identified that were characteristic of three waterbodies: a salt aquatic complex (water outflow, a drainage ditch and a pond), mined iron ore reservoirs and a mined lignite reservoir. Their ecological indicator values were specified using OMNIDIA software, and the environmental conditions prevailing in the studied ecosystems were determined. Of the 36 characteristic species, 16 lacking at least one assigned ecological indicator value were analyzed further. The analysis identified three groups of selected characteristic species which showed a correlation, or lack of such, to the tested physical and chemical parameters.ResultsBased on this multistage study of the autecology of characteristic diatoms, comprising an analysis of environmental conditions, literature analysis and reference ecological indicator values of other species, it is proposed that 32 ecological indicator values be established or adjusted for 16 species, and that Planothidium frequentissimum be excluded from water quality assessments. creator: Rafał M. Olszyński creator: Ewelina Szczepocka creator: Joanna Żelazna-Wieczorek uri: https://doi.org/10.7717/peerj.8117 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Olszyński et al.