title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1636
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Unanticipated discovery of two rare gastropod molluscs from recently located hydrothermally influenced areas in the Okinawa Trough
link: https://peerj.com/articles/4121
last-modified: 2017-12-01
description: BackgroundThe deep-sea hydrothermal vent is one of the most ‘extreme’ environments in the marine realm. Few species are capable of inhabiting such ecosystems, despite extremely high productivity there supported by microbial chemosynthesis, leading to high biomass and low species richness. Although gastropod molluscs are one of the main constituents of megafaunal communities at vent ecosystems, most species belong to several typical families (e.g., Provannidae, Peltospiridae, Lepetodrilidae) specialised and adapted to life at vents.MethodsDuring recent surveys of Okinawa Trough hydrothermal vent systems, two snails atypical of vent ecosystems were unexpectedly found in newly discovered hydrothermally influenced areas. Shell and radular characteristics were used to identify the gastropods morphologically.ResultsOne species was a vetigastropod, the calliostomatid Tristichotrochus ikukoae (Sakurai, 1994); and the other was a caenogastropod, the muricid Abyssotrophon soyoae (Okutani, 1959). Both gastropods were previously only known from regular non-chemosynthetic deep-sea and very rare—only two definitive published records exist for T. ikukoae and three for A. soyoae. The radula formula of Tristichotrochus ikukoae is accurately reported for the first time and based on that it is returned to genus Otukaia. For both species, barcode sequences of the cytochrome c oxidase I (COI) gene were obtained and deposited for future references.DiscussionThese new records represent the second record of calliostomatids from vents (third from chemosynthetic ecosystems) and the third record of muricids from vents (tenth from chemosynthetic ecosystems), and extend the distribution of both species to the southwest. Neither family has been recorded at chemosynthetic ecosystems in the western Pacific. Both were from weakly diffuse flow areas not subject to high temperature venting but were nevertheless associated with typical vent-reliant taxa such as Lamellibrachia tubeworms and Bathymodiolus mussels. These new records show that these species are capable of tolerating environmental stress associated with weak hydrothermally influenced areas, despite not being vent endemic species, adding to the list of known vent/non-vent species intersections. This signifies that such weakly influenced areas may provide key habitats for them, and that such areas may play a role in the evolution of biological adaptations to ‘extreme’ chemosynthetic ecosystems.
creator: Chong Chen
creator: Hiromi Kayama Watanabe
creator: Junichi Miyazaki
creator: Shinsuke Kawagucci
uri: https://doi.org/10.7717/peerj.4121
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Chen et al.

title: Effects of shinbuto and ninjinto on prostaglandin E2 production in lipopolysaccharide-treated human gingival fibroblasts
link: https://peerj.com/articles/4120
last-modified: 2017-12-01
description: Previously, we revealed that several kampo medicines used for patients with excess and/or medium patterns (kakkonto (TJ-1), shosaikoto (TJ-9), hangeshashinto (TJ-14), and orento (TJ-120)) reduced prostaglandin (PG)E2 levels using LPS-treated human gingival fibroblasts (HGFs). Recently, we examined other kampo medicines used for patients with the deficiency pattern [bakumondoto (TJ-29), shinbuto (TJ-30), ninjinto (TJ-32), and hochuekkito (TJ-41)] and the herbs comprising shinbuto and ninjinto using the same experimental model. Shinbuto and ninjinto concentration-dependently reduced LPS-induced PGE2 production by HGFs, whereas hochuekkito weakly reduced and bakumondoto did not reduce PGE2 production. Shinbuto and ninjinto did not alter cyclooxygenase (COX) activity or the expression of molecules involved in the arachidonic acid cascade. Therefore, we next examined which herbs compromising shinbuto and ninjinto reduce LPS-induced PGE2 production. Among these herbs, shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) strongly and concentration-dependently decreased LPS-induced PGE2 production. However, both shokyo and kankyo increased the expression of cytosolic phospholipase (cPL)A2 but did not affect annexin1 or COX-2 expression. These results suggest that shokyo and kankyo suppress cPLA2 activity. We demonstrated that kampo medicines suppress inflammatory responses in patients with the deficiency pattern, and in those with excess or medium patterns. Moreover, kampo medicines that contain shokyo or kankyo are considered to be effective for the treatment of inflammatory diseases.
creator: Toshiaki Ara
creator: Norio Sogawa
uri: https://doi.org/10.7717/peerj.4120
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Ara and Sogawa

title: New anatomical information of the wukongopterid Kunpengopterus sinensis Wang et al., 2010 based on a new specimen
link: https://peerj.com/articles/4102
last-modified: 2017-12-01
description: The Wukongopteridae compose a non-pterodactyloid clade of pterosaurs that are the most abundant flying reptiles in the deposits of the Middle-Late Jurassic Yanliao Biota. Until now, five species of three genera and two additional unnamed specimens have been described. Here we report on a new material, IVPP V 23674, that can be referred to the wukongopterid Kunpengopterus sinensis due to several features such as a comparably short nasoantorbital fenestra, the dorsally rising posterodorsal margin of the ischium, and the very short first pedal phalanx of digit V relative to metatarsal IV. IVPP V 23674 provides the first view of a wukongopterid palate, which differs from all other pterosaurs by having a very large postpalatine fenestra and laterally compressed choanae, indicating that the evolution of the pterosaur palate was more complex than previously thought. Sesamoid bones at the dorsal side of manual unguals are present and are reported for the first time in a wukongopterid suggesting an arboreal life-style for these pterosaurs.
creator: Xin Cheng
creator: Shunxing Jiang
creator: Xiaolin Wang
creator: Alexander W.A. Kellner
uri: https://doi.org/10.7717/peerj.4102
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Cheng et al.

title: PlantCV v2: Image analysis software for high-throughput plant phenotyping
link: https://peerj.com/articles/4088
last-modified: 2017-12-01
description: 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.
creator: Malia A. Gehan
creator: Noah Fahlgren
creator: Arash Abbasi
creator: Jeffrey C. Berry
creator: Steven T. Callen
creator: Leonardo Chavez
creator: Andrew N. Doust
creator: Max J. Feldman
creator: Kerrigan B. Gilbert
creator: John G. Hodge
creator: J. Steen Hoyer
creator: Andy Lin
creator: Suxing Liu
creator: César Lizárraga
creator: Argelia Lorence
creator: Michael Miller
creator: Eric Platon
creator: Monica Tessman
creator: Tony Sax
uri: https://doi.org/10.7717/peerj.4088
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Gehan et al.

title: Examining publication bias—a simulation-based evaluation of statistical tests on publication bias
link: https://peerj.com/articles/4115
last-modified: 2017-11-30
description: BackgroundPublication 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.MethodsFour 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.ResultsAll 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.DiscussionThe 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.
creator: Andreas Schneck
uri: https://doi.org/10.7717/peerj.4115
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Schneck

title: A tyrannosauroid metatarsus from the Merchantville Formation of Delaware increases the diversity of non-tyrannosaurid tyrannosauroids on Appalachia
link: https://peerj.com/articles/4123
last-modified: 2017-11-30
description: 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.
creator: Chase D. Brownstein
uri: https://doi.org/10.7717/peerj.4123
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Brownstein

title: Acute ischemic preconditioning does not influence high-intensity intermittent exercise performance
link: https://peerj.com/articles/4118
last-modified: 2017-11-30
description: 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.
creator: Isabela Coelho Marocolo
creator: Gustavo Ribeiro da Mota
creator: André Monteiro Londe
creator: Stephen D. Patterson
creator: Octávio Barbosa Neto
creator: Moacir Marocolo
uri: https://doi.org/10.7717/peerj.4118
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Marocolo et al.

title: Ability to predict repetitions to momentary failure is not perfectly accurate, though improves with resistance training experience
link: https://peerj.com/articles/4105
last-modified: 2017-11-30
description: ‘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.
creator: James Steele
creator: Andreas Endres
creator: James Fisher
creator: Paulo Gentil
creator: Jürgen Giessing
uri: https://doi.org/10.7717/peerj.4105
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Steele et al.

title: Diagnosis value of aberrantly expressed microRNA profiles in lung squamous cell carcinoma: a study based on the Cancer Genome Atlas
link: https://peerj.com/articles/4101
last-modified: 2017-11-30
description: BackgroundLung 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 ResultsThe 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.ConclusionThis study indicates that this novel microRNA expression signature may be a useful biomarker of the diagnosis for LUSC patients, based on bioinformatics analysis.
creator: Sheng Yang
creator: Jing Sui
creator: Geyu Liang
uri: https://doi.org/10.7717/peerj.4101
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Yang et al.

title: Ordinary kriging vs inverse distance weighting: spatial interpolation of the sessile community of Madagascar reef, Gulf of Mexico
link: https://peerj.com/articles/4078
last-modified: 2017-11-30
description: 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.
creator: Salvador Zarco-Perello
creator: Nuno Simões
uri: https://doi.org/10.7717/peerj.4078
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Zarco-Perello and Simões