title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1528
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Predicting New Zealand riverine fish reference assemblages
link: https://peerj.com/articles/4890
last-modified: 2018-05-28
description: Biomonitoring is a common method to monitor environmental change in river ecosystems, a key advantage of biomonitoring over snap-shot physicochemical monitoring is that it provides a more stable, long-term insight into change that is also effects-based. In New Zealand, the main biomonitoring method is a macroinvertebrate sensitivity scoring index, with little established methods available for biomonitoring of fish. This study models the contemporary distribution of common freshwater fish and then uses those models to predict freshwater fish assemblages for each river reach under reference conditions. Comparison of current fish assemblages with those predicted in reference conditions (as observed/expected (O/E) ratios) may provide a suitable option for freshwater fish biomonitoring. Most of the fish communities throughout the central North Island and lower reaches show substantial deviation from the modelled reference community. Most of this deviation is explained by nutrient enrichment, followed by downstream barriers (i.e. dams) and loss of riparian vegetation. The presence of modelled introduced species had relatively little impact on the presence of the modelled native fish. The maps of O/E fish assemblage may provide a rapid way to identify potential restoration sites.
creator: Adam D. Canning
uri: https://doi.org/10.7717/peerj.4890
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Canning

title: Expression analysis of vitellogenins in the workers of the red imported fire ant (Solenopsis invicta)
link: https://peerj.com/articles/4875
last-modified: 2018-05-28
description: Vitellogenin has been proposed to regulate division of labor and social organization in social insects. The red imported fire ant (Solenopsis invicta) harbors four distinct, adjacent vitellogenin genes (Vg1, Vg2, Vg3, and Vg4). Contrary to honey bees that have a single Vg ortholog as well as potentially fertile nurses, and to other ant species that lay trophic eggs, S. invicta workers completely lack ovaries or the ability to lay eggs. This provides a unique model to investigate whether Vg duplication in S. invicta was followed by subfunctionalization to acquire non-reproductive functions and whether Vg was co-opted to regulate behavior within the worker caste. To investigate these questions, we compared the expression patterns of S. invicta Vg genes among workers from different morphological subcastes or performing different tasks. RT-qPCRs revealed higher relative expression of Vg1 in major workers compared to both medium and minor workers, and of Vg2 in major workers when compared to minor workers. Relative expression of Vg1 was also higher in carbohydrate foragers when compared to nurses and protein foragers. By contrast, the level of expression of Vg2, Vg3, and Vg4 were not significantly different among the workers performing the specific tasks. Additionally, we analyzed the relationship between the expression of the Vg genes and S-hydroprene, a juvenile hormone analog. No changes in Vg expression were recorded in workers 12 h after application of the analog. Our results suggest that in S. invicta the Vg gene underwent subfunctionalization after duplication to new functions based on the expression bias observed in these data. This may suggest an alternative and still unknown function for Vg in the workers that needs to be investigated further.
creator: Chloe Hawkings
creator: Cecilia Tamborindeguy
uri: https://doi.org/10.7717/peerj.4875
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Hawkings and Tamborindeguy

title: Redescription and affinities of Hulsanpes perlei (Dinosauria, Theropoda) from the Upper Cretaceous of Mongolia
link: https://peerj.com/articles/4868
last-modified: 2018-05-28
description: Hulsanpes perlei is an enigmatic theropod dinosaur from the Baruungoyot Formation (?mid- to upper Campanian, Upper Cretaceous) of Mongolia. It was discovered in 1970, during the third Polish-Mongolian paleontological expedition to the Nemegt Basin. The taxon is known based on a partial braincase and an incomplete right hindlimb. However, the braincase fragment has never been described nor illustrated. We redescribe all elements that form the holotype of Hulsanpes and discuss the affinities of this taxon. The braincase fragment is interpreted as belonging to the inner ear region, and includes the floccular recess and part of the labyrinth. Hulsanpes perlei is confirmed as a valid taxon, diagnosed by a unique combination of metatarsal characters, including two autapomorphies. Historically, it represents the oldest record of the recently-established clade Halszkaraptorinae. Our findings identify subcursorial adaptations for Hulsanpes, shared with Mahakala, and differentiating them from Halszkaraptor. As such, appendicular disparity in the potentially sympatric halszkaraptorines suggest a reduced ecological overlap among these taxa, which may explain the co-occurrence of multiple species of this clade during the latest Cretaceous in what is now the Nemegt Basin.
creator: Andrea Cau
creator: Daniel Madzia
uri: https://doi.org/10.7717/peerj.4868
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Cau and Madzia

title: Antioxidant status of rats’ blood and liver affected by sodium selenite and selenium nanoparticles
link: https://peerj.com/articles/4862
last-modified: 2018-05-28
description: BackgroundSelenium is an essential element; however, at higher doses, it can be toxic. Therefore, alternative nanotechnological solutions are required to overcome toxicological issues, rather than conventional alternatives. Nanoparticles show new and promising properties that may be able to suppress toxicity while maintaining the positive effects of selenium on an organism. The aim of the experiment was to determine the influence of sodium selenite and selenium nanoparticles (SeNPs) on the antioxidant status of rats.MethodsThe males of the outbreed rat strain Wistar albino were selected as a model organism. Animals were fed different forms of selenium. The control group was given a mixture without selenium addition, whereas other groups were fed a mixture containing sodium selenite, Se-49, and Se-100 SeNPs respectively. The duration of the trial was 30 days.ResultsAnalysis of blood and liver was performed where the concentration of reduced (GSH) and oxidised (GSSG) glutathione, and total selenium content were measured. In the liver, a significant reduction in GSSG was found for all experiment groups. Blood samples showed a significant reduction in GSH and an increase in GSSG.DiscussionThese results show that SeNPs may be an alternative to dietary selenium for animal organisms.
creator: Lenka Urbankova
creator: Pavel Horky
creator: Jiri Skladanka
creator: Magdalena Pribilova
creator: Vendula Smolikova
creator: Pavel Nevrkla
creator: Natalia Cernei
creator: Zuzana Lackova
creator: Josef Hedbavny
creator: Andrea Ridoskova
creator: Vojtech Adam
creator: Pavel Kopel
uri: https://doi.org/10.7717/peerj.4862
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Urbankova et al.

title: Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells
link: https://peerj.com/articles/4860
last-modified: 2018-05-28
description: BackgroundThe Lepidopteran ambidensovirus 1 isolated from Junonia coenia (hereafter JcDV) is an invertebrate parvovirus considered as a viral transduction vector as well as a potential tool for the biological control of insect pests. Previous works showed that JcDV-based circular plasmids experimentally integrate into insect cells genomic DNA.MethodsIn order to approach the natural conditions of infection and possible integration, we generated linear JcDV-gfp based molecules which were transfected into non permissive Spodoptera frugiperda (Sf9) cultured cells. Cells were monitored for the expression of green fluorescent protein (GFP) and DNA was analyzed for integration of transduced viral sequences. Non-structural protein modulation of the VP-gene cassette promoter activity was additionally assayed.ResultsWe show that linear JcDV-derived molecules are capable of long term genomic integration and sustained transgene expression in Sf9 cells. As expected, only the deletion of both inverted terminal repeats (ITR) or the polyadenylation signals of NS and VP genes dramatically impairs the global transduction/expression efficiency. However, all the integrated viral sequences we characterized appear “scrambled” whatever the viral content of the transfected vector. Despite a strong GFP expression, we were unable to recover any full sequence of the original constructs and found rearranged viral and non-viral sequences as well. Cellular flanking sequences were identified as non-coding ones. On the other hand, the kinetics of GFP expression over time led us to investigate the apparent down-regulation by non-structural proteins of the VP-gene cassette promoter.ConclusionAltogether, our results show that JcDV-derived sequences included in linear DNA molecules are able to drive efficiently the integration and expression of a foreign gene into the genome of insect cells, whatever their composition, provided that at least one ITR is present. However, the transfected sequences were extensively rearranged with cellular DNA during or after random integration in the host cell genome. Lastly, the non-structural proteins seem to participate in the regulation of p9 promoter activity rather than to the integration of viral sequences.
creator: Francine Rizk
creator: Sylvain Laverdure
creator: Emmanuelle d’Alençon
creator: Hervé Bossin
creator: Thierry Dupressoir
uri: https://doi.org/10.7717/peerj.4860
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Rizk et al.

title: Tea cultivar classification and biochemical parameter estimation from hyperspectral imagery obtained by UAV
link: https://peerj.com/articles/4858
last-modified: 2018-05-28
description: It is generally feasible to classify different species of vegetation based on remotely sensed images, but identification of different sub-species or even cultivars is uncommon. Tea trees (Camellia sinensis L.) have been proven to show great differences in taste and quality between cultivars. We hypothesize that hyperspectral remote sensing would make it possibly to classify cultivars of plants and even to estimate their taste-related biochemical components. In this study, hyperspectral data of the canopies of tea trees were collected by hyperspectral camera mounted on an unmanned aerial vehicle (UAV). Tea cultivars were classified according to the spectral characteristics of the tea canopies. Furthermore, two major components influencing the taste of tea, tea polyphenols (TP) and amino acids (AA), were predicted. The results showed that the overall accuracy of tea cultivar classification achieved by support vector machine is higher than 95% with proper spectral pre-processing method. The best results to predict the TP and AA were achieved by partial least squares regression with standard normal variant normalized spectra, and the ratio of TP to AA—which is one proven index for tea taste—achieved the highest accuracy (RCV = 0.66, RMSECV = 13.27) followed by AA (RCV = 0.62, RMSECV = 1.16) and TP (RCV = 0.58, RMSECV = 10.01). The results indicated that classification of tea cultivars using the hyperspectral remote sensing from UAV was successful, and there is a potential to map the taste-related chemical components in tea plantations from UAV platform; however, further exploration is needed to increase the accuracy.
creator: Yexin Tu
creator: Meng Bian
creator: Yinkang Wan
creator: Teng Fei
uri: https://doi.org/10.7717/peerj.4858
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Tu et al.

title: Estimation of different data compositions for early-season crop type classification
link: https://peerj.com/articles/4834
last-modified: 2018-05-28
description: Timely and accurate crop type distribution maps are an important inputs for crop yield estimation and production forecasting as multi-temporal images can observe phenological differences among crops. Therefore, time series remote sensing data are essential for crop type mapping, and image composition has commonly been used to improve the quality of the image time series. However, the optimal composition period is unclear as long composition periods (such as compositions lasting half a year) are less informative and short composition periods lead to information redundancy and missing pixels. In this study, we initially acquired daily 30 m Normalized Difference Vegetation Index (NDVI) time series by fusing MODIS, Landsat, Gaofen and Huanjing (HJ) NDVI, and then composited the NDVI time series using four strategies (daily, 8-day, 16-day, and 32-day). We used Random Forest to identify crop types and evaluated the classification performances of the NDVI time series generated from four composition strategies in two studies regions from Xinjiang, China. Results indicated that crop classification performance improved as crop separabilities and classification accuracies increased, and classification uncertainties dropped in the green-up stage of the crops. When using daily NDVI time series, overall accuracies saturated at 113-day and 116-day in Bole and Luntai, and the saturated overall accuracies (OAs) were 86.13% and 91.89%, respectively. Cotton could be identified 40∼60 days and 35∼45 days earlier than the harvest in Bole and Luntai when using daily, 8-day and 16-day composition NDVI time series since both producer’s accuracies (PAs) and user’s accuracies (UAs) were higher than 85%. Among the four compositions, the daily NDVI time series generated the highest classification accuracies. Although the 8-day, 16-day and 32-day compositions had similar saturated overall accuracies (around 85% in Bole and 83% in Luntai), the 8-day and 16-day compositions achieved these accuracies around 155-day in Bole and 133-day in Luntai, which were earlier than the 32-day composition (170-day in both Bole and Luntai). Therefore, when the daily NDVI time series cannot be acquired, the 16-day composition is recommended in this study.
creator: Pengyu Hao
creator: Mingquan Wu
creator: Zheng Niu
creator: Li Wang
creator: Yulin Zhan
uri: https://doi.org/10.7717/peerj.4834
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Hao et al.

title: Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress
link: https://peerj.com/articles/4833
last-modified: 2018-05-28
description: Barley yellow dwarf virus-PAV (BYDV-PAV) is one of the major viruses causing a widespread and serious viral disease affecting cereal crops. To gain a better understanding of plant defence mechanisms of BYDV resistance genes (Bdv2 and RYd2) against BYDV-PAV infection, the differences in agronomical, biochemical and histological changes between susceptible and resistant wheat and barley cultivars were investigated. We found that root growth and total dry matter of susceptible cultivars showed greater reduction than that of resistant ones after infection. BYDV infected leaves in susceptible wheat and barley cultivars showed a significant reduction in photosynthetic pigments, an increase in the concentration of reducing sugar. The protein levels were also low in infected leaves. There was a significant increase in total phenol contents in resistant cultivars, which might reflect a protective mechanism of plants against virus infection. In phloem tissue, sieve elements (SE) and companion cells (CC) were severely damaged in susceptible cultivars after infection. It is suggested that restriction of viral movement in the phloem tissue and increased production of phenolic compounds may play a role in the resistance and defensive mechanisms of both Bdv2 and RYd2 against virus infection.
creator: Shormin Choudhury
creator: Hongliang Hu
creator: Philip Larkin
creator: Holger Meinke
creator: Sergey Shabala
creator: Ibrahim Ahmed
creator: Meixue Zhou
uri: https://doi.org/10.7717/peerj.4833
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Choudhury et al.

title: Early and long-term results of minimally invasive mitral valve surgery through a right mini-thoracotomy approach: a retrospective propensity-score matched analysis
link: https://peerj.com/articles/4810
last-modified: 2018-05-28
description: BackgroundMinimally invasive mitral valve surgery (MVS) via right mini-thoracotomy has recently attracted a lot of attention. Minimally invasive MVS shows postoperative results that are comparable to those of conventional MVS through the median sternotomy as per various earlier studies.MethodsBetween 2000 and 2016, a total of 669 isolated mitral valve procedures for isolated mitral valve regurgitation were performed. A propensity score-matched analysis was generated for the elimination of the differences in relevant preoperative risk factors between the cohorts and included 227 patient pairs. Only degenerative mitral valve regurgitation was included. The aim of our study was to examine if the minimally MVS is superior to the conventional approach through sternotomy based on a retrospective propensity-matched analysis. The primary endpoints were early mortality and long-term survival. The secondary endpoints included postoperative complications.ResultsThe in-hospital mortality rate was significantly higher within the conventional sternotomy cohort (3.1%, n = 7 vs 0.4%, n = 1 for the minimally invasive cohort; p = 0.032). The incidence of stroke and exploration for bleeding was comparable. In contrast, the necessity for dialysis was significantly lower in the minimally invasive cohort (p = 0.044). Postoperative pain was not significantly lower in the minimally invasive MVS cohort (p = 0.862). While patients who underwent minimally invasive MVS experienced longer bypass and cross-clamp times, their lengths of stay in the intensive care unit and in the hospital, did not differ from the conventionally operated collective (p = 0.779 and p = 0.516), respectively. The mitral valve repair rate of 81.1% in the minimally invasive cohort was significantly superior to that of the conventional approach, which was 46.3% (p < 0.0001). The one-, five-, and 10-year survival rates were significantly higher in the minimally invasive cohort compared to the conventional approach (96%, 90%, and 84% vs. 89%, 85%, and 70%; log rank p = 0.004).ConclusionDespite prolonged cardiopulmonary bypass and cross-clamping times, the minimally invasive MVS may be considered a safe approach that is equivalent to standard median sternotomy with lower early mortality and superior long-term survival.
creator: Sabreen Mkalaluh
creator: Marcin Szczechowicz
creator: Bashar Dib
creator: Anton Sabashnikov
creator: Gabor Szabo
creator: Matthias Karck
creator: Alexander Weymann
uri: https://doi.org/10.7717/peerj.4810
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Mkalaluh et al.

title: Redescription of Phymolepis  cuifengshanensis (Antiarcha: Yunnanolepididae) using high-resolution computed tomography and new insights into anatomical details of the endocranium in antiarchs
link: https://peerj.com/articles/4808
last-modified: 2018-05-28
description: BackgroundYunnanolepidoids constitute either the most basal consecutive segments or the most primitive clade of antiarchs, a highly diversified jawed vertebrate group from the Silurian and Early Devonian periods. Although the general morphology of yunnanolepidoids is well established, their endocranial features remain largely unclear, thus hindering our further understanding of antiarch evolution, and early gnathostome evolution. Phymolepis cuifengshanensis, a yunnanolepidoid from the Early Devonian of southwestern China, is re-described in detail to reveal the information on endocranial anatomy and additional morphological data of head and trunk shields.MethodsWe scanned the material of P. cuifengshanensis using high-resolution computed tomography and generated virtual restorations to show the internal morphology of its dermal shield. The dorsal aspect of endocranium in P. cuifengshanensis was therefore inferred. The phylogenetic analysis of antiarchs was conducted based on a revised and expanded dataset that incorporates 10 new cranial characters.ResultsThe lateroventral fossa of trunk shield and Chang’s apparatus are three-dimensionally restored in P. cuifengshanensis. The canal that is positioned just anterior to the internal cavity of Chang’s apparatus probably corresponds to the rostrocaudal canal of euantiarchs. The endocranial morphology of P. cuifengshanensis corroborates a general pattern for yunnanolepidoids with additional characters distinguishing them from sinolepids and euantiarchs, such as a developed cranio-spinal process, an elongated endolymphatic duct, and a long occipital portion.DiscussionIn light of new data from Phymolepis and Yunnanolepis, we summarized the morphology on the visceral surface of head shield in antiarchs, and formulated an additional 10 characters for the phylogenetic analysis. These cranial characters exhibit a high degree of morphological disparity between major subgroups of antiarchs, and highlight the endocranial character evolution in antiarchs.
creator: Yajing Wang
creator: Min Zhu
uri: https://doi.org/10.7717/peerj.4808
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Wang and Zhu