title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1641 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Ginsenoside Rk1 bioactivity: a systematic review link: https://peerj.com/articles/3993 last-modified: 2017-11-17 description: Ginsenoside Rk1 (G-Rk1) is a unique component created by processing the ginseng plant (mainly Sung Ginseng (SG)) at high temperatures. The aim of our study was to systematically review the pharmacological effects of G-Rk1. We utilized and manually searched eight databases to select in vivo and in vitro original studies that provided information about biological, pharmaceutical effects of G-Rk1 and were published up to July 2017 with no restriction on language or study design. Out of the 156 papers identified, we retrieved 28 eligible papers in the first skimming phase of research. Several articles largely described the G-Rk1 anti-cancer activity investigating “cell viability”, “cell proliferation inhibition”, “apoptotic activity”, and “effects of G-Rk1 on G1 phase and autophagy in tumor cells” either alone or in combination with G-Rg5. Others proved that it has antiplatelet aggregation activities, anti-inflammatory effects, anti-insulin resistance, nephroprotective effect, antimicrobial effect, cognitive function enhancement, lipid accumulation reduction and prevents osteoporosis. In conclusion, G-Rk1 has a significant anti-tumor effect on liver cancer, melanoma, lung cancer, cervical cancer, colon cancer, pancreatic cancer, gastric cancer, and breast adenocarcinoma against in vitro cell lines. In vivo experiments are further warranted to confirm these effects. creator: Abdelrahman Elshafay creator: Ngo Xuan Tinh creator: Samar Salman creator: Yara Saber Shaheen creator: Eman Bashir Othman creator: Mohamed Tamer Elhady creator: Aswin Ratna Kansakar creator: Linh Tran creator: Le Van creator: Kenji Hirayama creator: Nguyen Tien Huy uri: https://doi.org/10.7717/peerj.3993 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Elshafay et al. title: Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion link: https://peerj.com/articles/4075 last-modified: 2017-11-16 description: The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was overrepresented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala’s diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials. creator: Miriam E. Shiffman creator: Rochelle M. Soo creator: Paul G. Dennis creator: Mark Morrison creator: Gene W. Tyson creator: Philip Hugenholtz uri: https://doi.org/10.7717/peerj.4075 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shiffman et al. title: Antimicrobial consumption on Austrian dairy farms: an observational study of udder disease treatments based on veterinary medication records link: https://peerj.com/articles/4072 last-modified: 2017-11-16 description: BackgroundAntimicrobial use in livestock production is an important contemporary issue, which is of public interest worldwide. Antimicrobials are not freely available to Austrian farmers and can only be administered to livestock by veterinarians, or by farmers who are trained members of the Animal Health Service. Since 2015, veterinarians have been required by law to report antimicrobials dispensed to farmers for use in food-producing animals. The study presented here went further than the statutory framework, and collected data on antimicrobials dispensed to farmers and those administered by veterinarians.MethodsSeventeen veterinary practices were enrolled in the study via convenience sampling. These veterinarians were asked to contact interested dairy farmers regarding participation in the study (respondent-driven sampling). Data were collected from veterinary practice software between 1st October 2015 and 30th September 2016. Electronic data (89.4%) were transferred via an online interface and paper records (10.6%) were entered by the authors. Antimicrobial treatments with respect to udder disease were analysed by number of defined daily doses per cow and year (nDDDvet/cow/year), based on the European Medicines Agency technical unit, Defined Daily Dose for animals (DDDvet). Descriptive statistics and the Wilcoxon rank sum test were used to analyse the results.ResultsAntimicrobial use data from a total of 248 dairy farms were collected during the study, 232 of these farms treated cows with antibiotics; dry cow therapy was excluded from the current analysis. The mean number of DDDvet/cow/year for the antimicrobial treatment of all udder disease was 1.33 DDDvet/cow/year. Of these treatments, 0.73 DDDvet/cow/year were classed as highest priority critically important antimicrobials (HPCIAs), according to the World Health Organization (WHO) definition. The Wilcoxon rank sum test determined a statistically significant difference between the median number of DDDvet/cow/year for acute and chronic mastitis treatment (W = 10,734, p < 0.001). The most commonly administered antimicrobial class for the treatment of acute mastitis was beta-lactams. Intramammary penicillin was used at a mean of 0.63 DDDvet/cow/year, followed by the third generation cephalosporin, cefoperazone, (a HPCIA) at 0.60 DDDvet/cow/year. Systemic antimicrobial treatments were used at a lower overall level than intramammary treatments for acute mastitis.DiscussionThis study demonstrated that Austrian dairy cows in the study population were treated with antimicrobial substances for udder diseases at a relatively low frequency, however, a substantial proportion of these treatments were with substances considered critically important for human health. While it is vital that sick cows are treated, reductions in the overall use of antimicrobials, and critically important substances in particular, are still possible. creator: Clair L. Firth creator: Annemarie Käsbohrer creator: Corina Schleicher creator: Klemens Fuchs creator: Christa Egger-Danner creator: Martin Mayerhofer creator: Hermann Schobesberger creator: Josef Köfer creator: Walter Obritzhauser uri: https://doi.org/10.7717/peerj.4072 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Firth et al. title: HRV-derived data similarity and distribution index based on ensemble neural network for measuring depth of anaesthesia link: https://peerj.com/articles/4067 last-modified: 2017-11-16 description: Evaluation of depth of anaesthesia (DoA) is critical in clinical surgery. Indices derived from electroencephalogram (EEG) are currently widely used to quantify DoA. However, there are known to be inaccurate under certain conditions; therefore, experienced anaesthesiologists rely on the monitoring of vital signs such as body temperature, pulse rate, respiration rate, and blood pressure to control the procedure. Because of the lack of an ideal approach for quantifying level of consciousness, studies have been conducted to develop improved methods of measuring DoA. In this study, a short-term index known as the similarity and distribution index (SDI) is proposed. The SDI is generated using heart rate variability (HRV) in the time domain and is based on observations of data distribution differences between two consecutive 32 s HRV data segments. A comparison between SDI results and expert assessments of consciousness level revealed that the SDI has strong correlation with anaesthetic depth. To optimise the effect, artificial neural network (ANN) models were constructed to fit the SDI, and ANN blind cross-validation was conducted to overcome random errors and overfitting problems. An ensemble ANN was then employed and was discovered to provide favourable DoA assessment in comparison with commonly used Bispectral Index. This study demonstrated the effectiveness of this method of DoA assessment, and the results imply that it is feasible and meaningful to use the SDI to measure DoA with the additional use of other measurement methods, if appropriate. creator: Quan Liu creator: Li Ma creator: Ren-Chun Chiu creator: Shou-Zen Fan creator: Maysam F. Abbod creator: Jiann-Shing Shieh uri: https://doi.org/10.7717/peerj.4067 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liu et al. title: Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study link: https://peerj.com/articles/4064 last-modified: 2017-11-16 description: AimsPeriodontitis and psoriatic disease, including psoriasis (PS) and psoriatic arthritis (PsA), share the common risk factors and co-morbidities. However, the risk of periodontitis in patients with psoriatic disease still needs further investigation. This study was a nationwide population-based retrospective cohort study assessing the risk of periodontitis from psoriatic disease exposure.Materials and MethodsPatients with newly diagnosed psoriatic disease from 2003 to 2012 were identified from the Taiwanese National Health Insurance Research Database. The 1:4 ratio propensity score matched controls were selected from no psoriatic disease participations. The subsequent risk of periodontitis was evaluated in exposure and comparison groups. Multiple Cox proportional hazard models were used for the estimation.ResultsA total of 3,487 psoriatic disease patients and 13,948 controls were identified. Incidence rate of periodontitis was higher in patients with PsA. The adjusted hazard ratio (aHRs) for moderate/severe periodontitis were 0.85 (95% CI [0.65–1.11]) in PS group and 1.66 (95% CI [0.99–2.78]) in PsA group. The aHRs of PsA were increased over time, aHRs was changed from 0.65 (0–11 months from index date) to 1.34 (≥12 months from index date) in all types of periodontitis and from 1.09 to 1.79 in moderate/severe periodontitis group, respectively.ConclusionsThe increased risk of periodontitis was observed, especially the association between PsA and moderate/severe periodontitis. The patients with psoriatic disease should receive regular periodontal evaluation. creator: Ni-Yu Su creator: Jing-Yang Huang creator: Chien-Jen Hu creator: Hui-Chieh Yu creator: Yu-Chao Chang uri: https://doi.org/10.7717/peerj.4064 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Su et al. title: Adult zebra finches rehearse highly variable song patterns during sleep link: https://peerj.com/articles/4052 last-modified: 2017-11-16 description: Brain activity during sleep is fairly ubiquitous and the best studied possible function is a role in memory consolidation, including motor memory. One suggested mechanism of how neural activity effects these benefits is through reactivation of neurons in patterns resembling those of the preceding experience. The specific patterns of motor activation replayed during sleep are largely unknown for any system. Brain areas devoted to song production in the songbird brain exhibit spontaneous song-like activity during sleep, but single cell neural recordings did not permit detection of the specific song patterns. We have now discovered that this sleep activation can be detected in the muscles of the vocal organ, thus providing a unique window into song-related brain activity at night. We show that male zebra finches (Taeniopygia guttata) frequently exhibit spontaneous song-like activity during the night, but that the fictive song patterns are highly variable and uncoordinated compared to the highly stereotyped day-time song production. This substantial variability is not consistent with the idea that night-time activity replays day-time experiences for consolidation. Although the function of this frequent activation is unknown, it may represent a mechanism for exploring motor space or serve to generate internal error signals that help maintain the high stereotypy of day-time song. In any case, the described activity supports the emerging insight that brain activity during sleep may serve a variety of functions. creator: Brent K. Young creator: Gabriel B. Mindlin creator: Ezequiel Arneodo creator: Franz Goller uri: https://doi.org/10.7717/peerj.4052 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Young et al. title: Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans” link: https://peerj.com/articles/4046 last-modified: 2017-11-16 description: Hörnig, Haug & Haug (2017) published a description of a new specimen of Santanmantis axelrodi MB.I.2068, an extinct species of praying mantis from the Crato Formation of Brazil. According to Hörnig, Haug & Haug (2017), the discovery of this new specimen brought with it implications for praying mantis character evolution and predatory behavior; it is with these lines of reasoning that we find fault. More specifically, we point to four flawed assumptions in their study that led to their unsubstantiated conclusion that S. axelrodi employed their mesothoracic legs in prey capture. creator: Sydney K. Brannoch creator: Gavin J. Svenson uri: https://doi.org/10.7717/peerj.4046 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Brannoch and Svenson title: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro link: https://peerj.com/articles/4017 last-modified: 2017-11-16 description: Gastrointestinal mucositis is a debilitating side effect of chemotherapy treatment, with currently no treatment available. As changes in microbial composition have been reported upon chemotherapy treatment in vivo, it is thought that gut microbiota dysbiosis contribute to the mucositis etiology. Yet it is not known whether chemotherapeutics directly cause microbial dysbiosis, thereby increasing mucositis risk, or whether the chemotherapeutic subjected host environment disturbs the microbiome thereby aggravating the disease. To address this question, we used the M-SHIME®, an in vitro mucosal simulator of the human intestinal microbial ecosystem, as an experimental setup that excludes the host factor. The direct impact of two chemotherapeutics, 5-fluorouracil (5-FU) and SN-38 (active metabolite of irinotecan), on the luminal and mucosal gut microbiota from several human donors was investigated through monitoring fermentation activity and next generation sequencing. At a dose of 10 µM in the mucosal environment, 5-FU impacted the functionality and composition of the colon microbiota to a minor extent. Similarly, a daily dose of 10 µM SN-38 in the luminal environment did not cause significant changes in the functionality or microbiome composition. As our mucosal model does not include a host-compartment, our findings strongly indicate that a putative microbial contribution to mucositis is initially triggered by an altered host environment upon chemotherapy. creator: Eline Vanlancker creator: Barbara Vanhoecke creator: Andrea Stringer creator: Tom Van de Wiele uri: https://doi.org/10.7717/peerj.4017 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vanlancker et al. title: Sediment tolerance mechanisms identified in sponges using advanced imaging techniques link: https://peerj.com/articles/3904 last-modified: 2017-11-16 description: Terrestrial runoff, resuspension events and dredging can affect filter-feeding sponges by elevating the concentration of suspended sediments, reducing light intensity, and smothering sponges with sediments. To investigate how sponges respond to pressures associated with increased sediment loads, the abundant and widely distributed Indo-Pacific species Ianthella basta was exposed to elevated suspended sediment concentrations, sediment deposition, and light attenuation for 48 h (acute exposure) and 4 weeks (chronic exposure). In order to visualise the response mechanisms, sponge tissue was examined by 3D X-ray microscopy and scanning electron microscopy (SEM). Acute exposures resulted in sediment rapidly accumulating in the aquiferous system of I. basta, although this sediment was fully removed within three days. Sediment removal took longer (>2 weeks) following chronic exposures, and I. basta also exhibited tissue regression and a smaller aquiferous system. The application of advanced imaging approaches revealed that I. basta employs a multilevel system for sediment rejection and elimination, containing both active and passive components. Sponges responded to sediment stress through (i) mucus production, (ii) exclusion of particles by incurrent pores, (iii) closure of oscula and pumping cessation, (iv) expulsion of particles from the aquiferous system, and (v) tissue regression to reduce the volume of the aquiferous system, thereby entering a dormant state. These mechanisms would result in tolerance and resilience to exposure to variable and high sediment loads associated with both anthropogenic impacts like dredging programs and natural pressures like flood events. creator: Brian W. Strehlow creator: Mari-Carmen Pineda creator: Alan Duckworth creator: Gary A. Kendrick creator: Michael Renton creator: Muhammad Azmi Abdul Wahab creator: Nicole S. Webster creator: Peta L. Clode uri: https://doi.org/10.7717/peerj.3904 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Strehlow et al. title: Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts link: https://peerj.com/articles/4063 last-modified: 2017-11-15 description: Specific regulation and activation of focal adhesion kinase (FAK) are thought to be important for focal adhesion formation, and activation of Rho-kinase has been suggested to play a role in determining the effects of FAK on the formation of stress fibers and focal adhesions. To clarify the role of FAK in stress fiber formation and focal adhesion organization, the author examined the formation of new stress fibers and focal adhesions by activation of Rho-kinase in FAK knockout (FAK–/–) fibroblasts. FAK–/– cells were elliptical in shape, and showed reduced numbers of stress fibers and focal adhesions in the central part of the cells along with large focal adhesions in the peripheral regions. Activation of Rho-kinase in FAK–/– cells transiently increased the actin filaments in the cell center, but these did not form typical thick stress fibers. Moreover, only plaque-like structures as the origins of newly formed focal adhesions were observed in the center of the cell. Furthermore, introduction of an exogenous GFP-labeled FAK gene into FAK–/– cells resulted in increased numbers of stress fibers and focal adhesions in the center of the cells, which showed typical fibroblast morphology. These results indicated that FAK plays an important role in the formation of stress fibers and focal adhesions as well as in regulation of cell shape and morphology with the activation of Rho-kinase. creator: Kazuo Katoh uri: https://doi.org/10.7717/peerj.4063 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Katoh