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Xiao-Yong Zhan, Qing-Yi Zhu
Background: L. pneumophila is the main causative agent of Legionnaires' disease. Free-living amoeba in natural aquatic environments is the reservoir and shelter for L. pneumophila. From natural water sources, L. pneumophila can colonize artificial environments such as cooling towers and hot-water systems, and then spread in aerosols, infecting the susceptible person. Therefore, molecular phylogeny and genetic variability of L. pneumophila from different sources (natural water, artificial water, and human lung tissue) might be distinct because of the selection pressure in different environments...
2017: PeerJ
Yan Chen, Yining Liu, Min Du, Wengang Zhang, Ling Xu, Xue Gao, Lupei Zhang, Huijiang Gao, Lingyang Xu, Junya Li, Min Zhao
Integrating genomic information into cattle breeding is an important approach to exploring genotype-phenotype relationships for complex traits related to diary and meat production. To assist with genomic-based selection, a reference map of interactome is needed to fully understand and identify the functional relevant genes. To this end, we constructed a co-expression analysis of 92 tissues and this represents the systematic exploration of gene-gene relationship in Bos taurus. By using robust WGCNA (Weighted Gene Correlation Network Analysis), we described the gene co-expression network of 5,000 protein-coding genes with majority variations in expression across 92 tissues...
2017: PeerJ
David G Delaney, Lida T Teneva, Kostantinos A Stamoulis, Jonatha L Giddens, Haruko Koike, Tom Ogawa, Alan M Friedlander, John N Kittinger
Sustainable fisheries management is key to restoring and maintaining ecological function and benefits to people, but it requires accurate information about patterns of resource use, particularly fishing pressure. In most coral reef fisheries and other data-poor contexts, obtaining such information is challenging and remains an impediment to effective management. We developed the most comprehensive regional view of shore-based fishing effort and catch published to date, to show detailed fishing patterns from across the main Hawaiian Islands (MHI)...
2017: PeerJ
Katrina S Luzon, Mei-Fang Lin, Ma Carmen A Ablan Lagman, Wilfredo Roehl Y Licuanan, Chaolun Allen Chen
Background: The corallum is crucial in building coral reefs and in diagnosing systematic relationships in the order Scleractinia. However, molecular phylogenetic analyses revealed a paraphyly in a majority of traditional families and genera among Scleractinia showing that other biological attributes of the coral, such as polyp morphology and reproductive traits, are underutilized. Among scleractinian genera, the Euphyllia, with nine nominal species in the Indo-Pacific region, is one of the groups that await phylogenetic resolution...
2017: PeerJ
Paula Simó-Mirabet, M Carla Piazzon, Josep Alvar Calduch-Giner, Álvaro Ortiz, Mónica Puyalto, Ariadna Sitjà-Bobadilla, Jaume Pérez-Sánchez
Background: The increased demand for fish protein has led to the intensification of aquaculture practices which are hampered by nutritional and health factors affecting growth performance. To solve these problems, antibiotics have been used for many years in the prevention, control and treatment against disease as well as growth promoters to improve animal performance. Nowadays, the use of antibiotics in the European Union and other countries has been completely or partially banned as a result of the existence of antibiotic cross-resistance...
2017: PeerJ
Shuang Qiu, Hongxuan Sun, Yawen Liu, Joseph Sam Kanu, Ri Li, Yaqin Yu, Xufeng Huang, Bo Li, Xiangyang Zhang
[This corrects the article DOI: 10.7717/peerj.2869.].
2017: PeerJ
Anders K Nilsson, Mats X Andersson
A striking and unexpected biochemical phenotype was found in an insertion mutant line in the model plant Arabidopsis thaliana. One of two investigated insertion mutant lines in the gene encoding the phosphate transporter PHT4;1 demonstrated a prominent loss of trienoic fatty acids, whereas the other insertion line was indistinguishable from wild type in this aspect. We demonstrate that the loss of trienoic fatty acids was due to a remnant inactive negative selection marker gene in this particular transposon tagged line, pht4;1-3...
2017: PeerJ
Chong Chen, Hiromi Kayama Watanabe, Junichi Miyazaki, Shinsuke Kawagucci
Background: The 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...
2017: PeerJ
Toshiaki Ara, Norio Sogawa
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...
2017: PeerJ
Xin Cheng, Shunxing Jiang, Xiaolin Wang, Alexander W A Kellner
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...
2017: PeerJ
Malia A Gehan, Noah Fahlgren, Arash Abbasi, Jeffrey C Berry, Steven T Callen, Leonardo Chavez, Andrew N Doust, Max J Feldman, Kerrigan B Gilbert, John G Hodge, J Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael Miller, Eric Platon, Monica Tessman, Tony Sax
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...
2017: PeerJ
Chase D Brownstein
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...
2017: PeerJ
Isabela Coelho Marocolo, Gustavo Ribeiro da Mota, André Monteiro Londe, Stephen D Patterson, Octávio Barbosa Neto, Moacir Marocolo
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)...
2017: PeerJ
Andreas Schneck
Background: Publication 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. Methods: Four 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...
2017: PeerJ
James Steele, Andreas Endres, James Fisher, Paulo Gentil, Jürgen Giessing
'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...
2017: PeerJ
Sheng Yang, Jing Sui, Geyu Liang
Background: Lung 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 Results: The present study investigated LUSC-specific key microRNAs (miRNAs) from large-scale samples in TCGA...
2017: PeerJ
Salvador Zarco-Perello, Nuno Simões
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...
2017: PeerJ
Talya Shragai, Xiaoge Ping, Cameron Arakaki, Dennis Garlick, Daniel T Blumstein, Aaron P Blaisdell
Prior work in our lab has shown that an expanding image on a computer screen elicits a hiding response in the Caribbean terrestrial hermit crab (Coenobita clypeatus). We conducted two experiments to identify what properties of the expanding stimulus contribute to its effectiveness as a visual threat. First we found that an expanding geometric star evoked a strong hiding response while a contracting or full-sized stationary star did not. A second experiment revealed that the more quickly the stimulus expanded the shorter the latency to hide...
2017: PeerJ
Edilson Hobold, Vitor Pires-Lopes, Rossana Gómez-Campos, Miguel de Arruda, Cynthia Lee Andruske, Jaime Pacheco-Carrillo, Marco Antonio Cossio-Bolaños
Background: The importance of assessing body fat variables and physical fitness tests plays an important role in monitoring the level of activity and physical fitness of the general population. The objective of this study was to develop reference norms to evaluate the physical fitness aptitudes of children and adolescents based on age and sex from the lake region of Itaipú, Brazil. Methods: A descriptive cross-sectional study was carried out with 5,962 students (2,938 males and 3,024 females) with an age range of 6...
2017: PeerJ
Sajia Akhter, Ramy K Aziz, Mona T Kashef, Eslam S Ibrahim, Barbara Bailey, Robert A Edwards
The amino acid content of the proteins encoded by a genome may predict the coding potential of that genome and may reflect lifestyle restrictions of the organism. Here, we calculated the Kullback-Leibler divergence from the mean amino acid content as a metric to compare the amino acid composition for a large set of bacterial and phage genome sequences. Using these data, we demonstrate that (i) there is a significant difference between amino acid utilization in different phylogenetic groups of bacteria and phages; (ii) many of the bacteria with the most skewed amino acid utilization profiles, or the bacteria that host phages with the most skewed profiles, are endosymbionts or parasites; (iii) the skews in the distribution are not restricted to certain metabolic processes but are common across all bacterial genomic subsystems; (iv) amino acid utilization profiles strongly correlate with GC content in bacterial genomes but very weakly correlate with the G+C percent in phage genomes...
2017: PeerJ
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