title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1321 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Twisted tale of the tiger: the case of inappropriate data and deficient science link: https://peerj.com/articles/7482 last-modified: 2019-08-20 description: Publications in peer-reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer-review process. We review a recent publication by Gopalaswamy et al. (10.1111/2041-210X.12351) that challenges the use of “double sampling” in large-scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large-scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. (10.1111/2041-210X.12351) to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index-Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, the paper of Gopalaswamy et al. could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences. creator: Qamar Qureshi creator: Rajesh Gopal creator: Yadvendradev Jhala uri: https://doi.org/10.7717/peerj.7482 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Qureshi et al. title: Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA link: https://peerj.com/articles/7490 last-modified: 2019-08-20 description: BackgroundThe safety of vaccines is a critical factor in maintaining public trust in national vaccination programs. This study aimed to evaluate the safety profiles of human papillomavirus (HPV) vaccines with regard to the distribution of adverse events (AE) across gender and age, and the correlations across various AEs using the Food and Drug Administration/Centers for Disease Control and Prevention Vaccine Adverse Event Reporting System (VAERS).MethodsFor analyses, 27,348 patients aged between 9 and 25 years old with at least one AE reported in VAERS between the year of 2006 and 2017 were included. AEs were summarized into two levels: the lower level preferred term (PT) and higher level system organ classes (SOCs) based on the structure of Medical Dictionary for Regulatory Activities (MedDRA). A series of statistical analyses were applied on both levels of AEs. Zero-truncated Poisson regression and multivariate logistic regression models were first developed to assess the rate and risk of SOCs across age groups and genders. Pairwise Pearson correlation analyses and hierarchical clustering analyses were then conducted to explore the interrelationships and clustering pattern among AEs.ResultsWe identified 27,337 unique HPV vaccine reports between 2006 and 2017. Disproportional reporting of AEs was observed across age and gender in 21 SOCs (p < 0.05). The correlation analyses found most SOCs demonstrate weak positive correlations except for five pairs which were negatively correlated: skin and subcutaneous tissue disorders + injury poisoning and procedural complications; skin and subcutaneous tissue disorders + nervous system disorders; Skin and subcutaneous tissue disorders + pregnancy, puerperium and perinatal conditions; nervous system disorders + pregnancy, puerperium and perinatal conditions; pregnancy, puerperium and perinatal conditions + general disorders and administration site conditions. Nervous system disorders had the most AEs which contributed to 12,448 (46%) cases. In the further analyses of correlations between PT in nervous system disorders, the three most strongly correlated AEs were psychiatric disorders (r = 0.35), gastrointestinal disorders (r = 0.215), and musculoskeletal and connective tissue disorders (r = 0.261). We observed an inter-SOCs correlation of the PTs among AE pairs by nervous system disorders/psychiatric disorders/gastrointestinal disorders/musculoskeletal and connective tissue disorders.ConclusionsThe analyses revealed a different distribution pattern of AEs across gender and age subgroups in 21 SOC level AEs. Correlation analyses and hierarchical clustering analyses further revealed several correlated patterns across various AEs. However, findings from this study should be interpreted with caution. Further clinical studies are needed to understand the heterogeneity of AEs reporting across subgroups and the biological pathways among the statistically correlated AEs. creator: Yuxi Jia creator: Cong Zhu creator: Jingcheng Du creator: Yang Xiang creator: Yong Chen creator: Wei Wang creator: Cui Tao uri: https://doi.org/10.7717/peerj.7490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jia et al. title: Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland link: https://peerj.com/articles/7506 last-modified: 2019-08-20 description: Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong (Bettongia gaimardi) and that of the exotic European rabbit (Oryctolagus cuniculus). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas. creator: Catherine E. Ross creator: Nicola T. Munro creator: Philip S. Barton creator: Maldwyn J. Evans creator: John Gillen creator: Ben C.T. Macdonald creator: Sue McIntyre creator: Saul A. Cunningham creator: Adrian D. Manning uri: https://doi.org/10.7717/peerj.7506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ross et al. title: Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors link: https://peerj.com/articles/7511 last-modified: 2019-08-20 description: Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions. creator: Ziwei Liang creator: Mengdi Li creator: Zhengyi Liu creator: Jianbo Wang uri: https://doi.org/10.7717/peerj.7511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liang et al. title: Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women link: https://peerj.com/articles/7533 last-modified: 2019-08-20 description: BackgroundMovement velocity has been proposed as an effective tool to prescribe the load during resistance training in young healthy adults. This study aimed to elucidate whether movement velocity could also be used to estimate the relative load (i.e., % of the one-repetition maximum (1RM)) in older women.MethodsA total of 22 older women (age = 68.2 ± 3.6 years, bench press 1RM = 22.3 ± 4.7 kg, leg press 1RM = 114.6 ± 15.9 kg) performed an incremental loading test during the free-weight bench press and the leg press exercises on two separate sessions. The mean velocity (MV) was collected with a linear position transducer.ResultsA strong linear relationship between MV and the relative load was observed for the bench press (%1RM = −130.4 MV + 119.3; r2 = 0.827, standard error of the estimate (SEE) = 6.10%1RM, p < 0.001) and leg press exercises (%1RM = −158.3 MV + 131.4; r2 = 0.913, SEE = 5.63%1RM, p < 0.001). No significant differences were observed between the bench press and leg press exercises for the MV attained against light-medium relative loads (≤70%1RM), while the MV associated with heavy loads (≥80%1RM) was significantly higher for the leg press.ConclusionsThese results suggest that the monitoring of MV could be useful to prescribe the loads during resistance training in older women. However, it should be noted that the MV associated with a given %1RM is significantly lower in older women compared to young healthy individuals. creator: Pablo Jorge Marcos-Pardo creator: Jorge Miguel González-Hernández creator: Amador García-Ramos creator: Abraham López-Vivancos creator: Pedro Jiménez-Reyes uri: https://doi.org/10.7717/peerj.7533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Marcos-Pardo et al. title: Anxiety-like behavior and whole-body cortisol responses to components of energy drinks in zebrafish (Danio rerio) link: https://peerj.com/articles/7546 last-modified: 2019-08-20 description: The current study investigated the independent and combined effects of caffeine and taurine on anxiety-like behavior and neuroendocrine responses in adult zebrafish (Danio rerio). Caffeine (1,3,7-trimethylpurine-2,6-dione), the world’s most commonly used psychoactive drug, acts as an adenosine receptor blocker and a mild central nervous system stimulant. However, excessive use of caffeine is associated with heightened anxiety levels. Taurine (2-aminoethanesulfonic acid), a semi-essential amino acid synthesized within the human brain, has been hypothesized to play a role in regulating anxiolytic behavior. Caffeine and taurine are two common additives in energy drinks and are often found in high concentrations in these beverages. However, few studies have investigated the interaction of these two chemicals with regards to anxiety measures. A suitable vertebrate to examine anxiety-like behavior and physiological stress responses is the zebrafish, which has shown promise due to substantial physiological and genetic homology with humans. Anxiety-like behavior in zebrafish can be determined by analyzing habituation to novelty when fish are placed into a novel tank and scototaxis (light avoidance) behavior in the light-dark test. Stress-related neuroendocrine responses can be measured in zebrafish by analyzing whole-body cortisol levels. The goal of this study was to determine if exposure to caffeine, taurine, or a combination of the two compounds altered anxiety-like behavior and whole-body cortisol levels in zebrafish relative to control. Zebrafish were individually exposed to either caffeine (100 mg/L), taurine (400 mg/L), or both for 15 min. Zebrafish in the control group were handled in the same manner but were only exposed to system tank water. After treatment, fish were transferred to the novel tank test or the light-dark test. Behavior was tracked for the first 6 min in the novel tank and 15 min in the light-tark test. Fifteen min after introduction to the behavioral task, fish were euthanized for the analysis of whole-body cortisol levels. The results demonstrate that caffeine treatment decreased the amount of exploration in the top of the novel tank and increased scototaxis behavior in the light-dark test, which supports the established anxiogenic effect of acute exposure to caffeine. Taurine alone did not alter basal levels of anxiety-like behavioral responses nor ameliorated the anxiogenic effects of caffeine on behavior when the two compounds were administered concurrently. None of the drug treatments altered basal levels of whole-body cortisol. The current results of this study suggest that, at least at this dose and time of exposure, taurine does not mitigate the anxiety-producing effects of caffeine when administered in combination, such as with energy drink consumption. creator: Alia O. Alia creator: Maureen L. Petrunich-Rutherford uri: https://doi.org/10.7717/peerj.7546 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Alia and Petrunich-Rutherford title: A revision of the Neotropical caddisfly genus Ascotrichia Flint, 1983 (Trichoptera, Hydroptilidae) link: https://peerj.com/articles/7560 last-modified: 2019-08-20 description: A revision of the microcaddisfly genus Ascotrichia (Trichoptera, Hydroptilidae) is provided, including a generic diagnosis, illustrations, and descriptions of males. This genus is endemic to the Neotropical region and has been recorded from countries in northern South America. Adults of the genus are notable within the family for the contrasting black and green hairs on the forewings. A total of six species are treated, three described as new: Ascotrichia adirecta sp. n. (Brazil), A. hystricosa sp. n. (Brazil), and A. simoma sp. n. (Brazil). creator: Robin E. Thomson uri: https://doi.org/10.7717/peerj.7560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Thomson title: Assessment of complementary and alternative medicine use among patients admitted to the emergency room: a descriptive study from a Turkish hospital link: https://peerj.com/articles/7584 last-modified: 2019-08-20 description: BackgroundThe main aim of this study was to assess the frequency of use of complementary and alternative medicine (CAM) in patients admitted to the emergency room (ER). Additionally, we aimed to evaluate the socio-demographic and clinical factors associated with CAM use.MethodsThis was a descriptive study. A total of 951 patients who were admitted to the ER of a tertiary hospital between October 2018 and November 2018 were enrolled. Data were obtained using a questionnaire that was prepared by the researchers considering the literature data.ResultsThe mean age of the patients was 37.98 ± 15.65 years. Of the 951 patients, 48.4% (n = 460) were female and 51.6% (n = 491) were male. The rate of patients who used CAM at least once was 47.3% (n = 450). The most frequently used CAM methods were herbal therapy (68.9%), massage (40.7%), dietary supplements (24.7%), and hijama (24.2%). Being aged 64 years or younger (p = 0.001), having an education level of university or higher (p = 0.006), having an income more than minimum wage (p = 0.016), and having a chronic disease (p = 0.003) were found to be associated with CAM use in this study.DiscussionCAM methods were used by a considerable proportion of patients admitted to the ER. Physicians should incorporate CAM use history in their patient assessments and should provide accurate and unbiased information about CAM methods. creator: Hakan Hakkoymaz creator: Burhan Fatih Koçyiğit uri: https://doi.org/10.7717/peerj.7584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hakkoymaz et al. title: Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies link: https://peerj.com/articles/7410 last-modified: 2019-08-19 description: Information on taxa distribution is a prerequisite for many research fields, and biological records are a major source of data contributing to biogeographic studies. The Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS) are important infrastructures facilitating free and open access to classical biological data from several sources in both temporal and spatial scales. Over the last ten years, high throughput sequencing (HTS) metabarcoding data have become available, which constitute a great source of detailed occurrence data. Among the global sampling projects that have contributed to such data are Tara Oceans and the Ocean Sampling Day (OSD). Integration of classical and metabarcoding data may aid a more comprehensive assessment of the geographic range of species, especially of microscopic ones such as protists. Rare, small and cryptic species are often ignored in surveys or mis-assigned with the classical approaches. Here we show how integration of data from various sources can contribute to insight in the biogeography and diversity at the genus- and species-level using Chaetoceros as study system, one of the most diverse and abundant genera among marine planktonic diatoms. Chaetoceros records were extracted from GBIF and OBIS and literature data were collected by means of a Google Scholar search. Chaetoceros references barcodes where mapped against the metabarcode datasets of Tara Oceans (210 sites) and OSD (144 sites). We compared the resolution of different data sources in determining the global distribution of the genus and provided examples, at the species level, of detection of cryptic species, endemism and cosmopolitan or restricted distributions. Our results highlighted at genus level a comparable picture from the different sources but a more complete assessment when data were integrated. Both the importance of the integration but also the challenges related to it were illustrated. Chaetoceros data collected in this study are organised and available in the form of tables and maps, providing a powerful tool and a baseline for further research in e.g., ecology, conservation and evolutionary biology. creator: Daniele De Luca creator: Wiebe H.C.F. Kooistra creator: Diana Sarno creator: Chetan C. Gaonkar creator: Roberta Piredda uri: https://doi.org/10.7717/peerj.7410 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 De Luca et al. title: A comparative study of root canal shaping using protaper universal and protaper next rotary files in preclinical dental education link: https://peerj.com/articles/7419 last-modified: 2019-08-19 description: BackgroundDentistry has undergone an evolution in endodontics practice caused by the advancement of rotary techniques for root canal preparation and their subsequent incorporation into the teaching of dentistry undergraduates. This research aimed to evaluate the shaping ability of third-year dental students as their first experience in rotary instrumentation using ProTaper Universal (PTU) and ProTaper Next (PTN) (Dentsply Maillefer) rotary instruments in simulated curved canals.MethodsForty students instrumented 200 simulated canals with a 40° curvature in resin blocks according to the manufacturer’s instructions with PTU and 39 students and 195 canals with PTN files. The canals were prepared at a speed of 300 rpm using a 16:1 reduction hand-piece powered by an electric motor (Xsmart; Dentsply Maillefer). The final apical preparation was set to F2 for the PTU and X2 for the PTN group. The change in canal curvature was evaluated based on Schneider technique using the AutoCAD 2007 software on post-digital photographs. The incidence of instrument fracture and deformation, the incidence of ledge, the change in working length (WL), and the working time were noted. The data were analyzed with Student’s t-test and Chi-Square test at a significance level of 0.05 using SPSS.ResultsPTN maintained the original canal curvature better, resulting in fewer fractures and ledges, and shaped the canals faster than the PTU (P < 0.05). The mean curves of the resin canals after the instrumentation for the PTU and PTN groups were 24.03° ± 3.14° and 25.64° ± 2.72°, respectively. Thirty-three (17.4%) PTU and 18 (9.3%) PTN files fractured (p < 0.05). Nine (4.5%) PTU and 2 (2.6%) PTN deformed (p > 0.05). The change in WL after instrumentation was 0.97 mm ± 0.95 mm in PTU and 0.96 mm ± 0.80 mm in PTN (p < 0.05). The mean times were 627 s ± 18 s for PTU and 379 s ± 18 s for PTN (p < 0.000).DiscussionPTN can be recommended in severely curved root canals in terms of maintenance of the original canal curvature, superior instrument fracture and fewer ledges. Even if training before preparation provides an acceptable level of canal shaping for preclinical students, the use of NiTi rotary instruments should be included in the undergraduate dental curriculum, contributing to an increase in the quality of root canal shaping and, consequently, to an improvement of the clinical experience of students. creator: Gül Çelik creator: Feyza Özdemir Kısacık creator: Emir Faruk Yılmaz creator: Arife Mersinlioğlu creator: İhsan Furkan Ertuğrul creator: Hikmet Orhan uri: https://doi.org/10.7717/peerj.7419 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Çelik et al.