title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1619 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Distribution and seasonal differences in Pacific Lamprey and Lampetra spp eDNA across 18 Puget Sound watersheds link: https://peerj.com/articles/4496 last-modified: 2018-03-16 description: Lampreys have a worldwide distribution, are functionally important to ecological communities and serve significant roles in many cultures. In Pacific coast drainages of North America, lamprey populations have suffered large declines. However, lamprey population status and trends within many areas of this region are unknown and such information is needed for advancing conservation goals. We developed two quantitative PCR-based, aquatic environmental DNA (eDNA) assays for detection of Pacific Lamprey (Entosphenus tridentatus) and Lampetra spp, using locked nucleic acids (LNAs) in the probe design. We used these assays to characterize the spatial distribution of lamprey in 18 watersheds of Puget Sound, Washington, by collecting water samples in spring and fall. Pacific Lamprey and Lampetra spp were each detected in 14 watersheds and co-occurred in 10 watersheds. Lamprey eDNA detection rates were much higher in spring compared to fall. Specifically, the Pacific Lamprey eDNA detection rate was 3.5 times higher in spring and the Lampetra spp eDNA detection rate was 1.5 times higher in spring even though larval lamprey are present in streams year-round. This significant finding highlights the importance of seasonality on eDNA detection. Higher stream discharge in the fall likely contributed to reduced eDNA detection rates, although seasonal life history events may have also contributed. These eDNA assays differentiate Pacific Lamprey and Lampetra spp across much of their range along the west coast of North America. Sequence analysis indicates the Pacific Lamprey assay also targets other Entosphenus spp and indicates the Lampetra spp assay may have limited or no capability of detecting Lampetra in some locations south of the Columbia River Basin. Nevertheless, these assays will serve as a valuable tool for resource managers and have direct application to lamprey conservation efforts, such as mapping species distributions, occupancy modeling, and monitoring translocations and reintroductions. creator: Carl O. Ostberg creator: Dorothy M. Chase creator: Michael C. Hayes creator: Jeffrey J. Duda uri: https://doi.org/10.7717/peerj.4496 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: The use of nutritional supplements to induce ketosis and reduce symptoms associated with keto-induction: a narrative review link: https://peerj.com/articles/4488 last-modified: 2018-03-16 description: BackgroundAdaptation to a ketogenic diet (keto-induction) can cause unpleasant symptoms, and this can reduce tolerability of the diet. Several methods have been suggested as useful for encouraging entry into nutritional ketosis (NK) and reducing symptoms of keto-induction. This paper reviews the scientific literature on the effects of these methods on time-to-NK and on symptoms during the keto-induction phase.MethodsPubMed, Science Direct, CINAHL, MEDLINE, Alt Health Watch, Food Science Source and EBSCO Psychology and Behavioural Sciences Collection electronic databases were searched online. Various purported ketogenic supplements were searched along with the terms “ketogenic diet”, “ketogenic”, “ketosis” and ketonaemia (/ ketonemia). Additionally, author names and reference lists were used for further search of the selected papers for related references.ResultsEvidence, from one mouse study, suggests that leucine doesn’t significantly increase beta-hydroxybutyrate (BOHB) but the addition of leucine to a ketogenic diet in humans, while increasing the protein-to-fat ratio of the diet, doesn’t reduce ketosis. Animal studies indicate that the short chain fatty acids acetic acid and butyric acid, increase ketone body concentrations. However, only one study has been performed in humans. This demonstrated that butyric acid is more ketogenic than either leucine or an 8-chain monoglyceride. Medium-chain triglycerides (MCTs) increase BOHB in a linear, dose-dependent manner, and promote both ketonaemia and ketogenesis. Exogenous ketones promote ketonaemia but may inhibit ketogenesis.ConclusionsThere is a clear ketogenic effect of supplemental MCTs; however, it is unclear whether they independently improve time to NK and reduce symptoms of keto-induction. There is limited research on the potential for other supplements to improve time to NK and reduce symptoms of keto-induction. Few studies have specifically evaluated symptoms and adverse effects of a ketogenic diet during the induction phase. Those that have typically were not designed to evaluate these variables as primary outcomes, and thus, more research is required to elucidate the role that supplementation might play in encouraging ketogenesis, improve time to NK, and reduce symptoms associated with keto-induction. creator: Cliff J. d C. Harvey creator: Grant M. Schofield creator: Micalla Williden uri: https://doi.org/10.7717/peerj.4488 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Harvey et al. title: pcr: an R package for quality assessment, analysis and testing of qPCR data link: https://peerj.com/articles/4473 last-modified: 2018-03-16 description: BackgroundReal-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions.MethodsWe developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest.ResultsUsing two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable.ConclusionThe pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way. creator: Mahmoud Ahmed creator: Deok Ryong Kim uri: https://doi.org/10.7717/peerj.4473 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ahmed and Kim title: Characterization of the salivary microbiome in people with obesity link: https://peerj.com/articles/4458 last-modified: 2018-03-16 description: BackgroundThe interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs.MethodsWe characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases.ResultsThe salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls.DiscussionOur study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases. creator: Yujia Wu creator: Xiaopei Chi creator: Qian Zhang creator: Feng Chen creator: Xuliang Deng uri: https://doi.org/10.7717/peerj.4458 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wu et al. title: Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot link: https://peerj.com/articles/4388 last-modified: 2018-03-16 description: Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes—the world’s richest and most diverse biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contributed roughly equally to the high Andean (i.e., páramo) flora. Here we infer the evolutionary history of the southern hemisphere plant genus Gunnera, a lineage with a rich fossil history and an important ecological role as an early colonising species characteristic of wet, montane environments. Our results show striking contrasts in species diversification, where some species may have persisted for some 90 million years, and whereas others date to less than 2 Ma since origination. The outstanding longevity of the group is likely linked to a high degree of niche conservatism across its highly disjunct range, whereby Gunnera tracks damp and boggy soils in cool habitats. Colonisation of the northern Andes is related to Quaternary climate change, with subsequent rapid diversification appearing to be driven by their ability to take advantage of environmental opportunities. This study demonstrates the composite origin of a mega-diverse biota. creator: Christine D. Bacon creator: Francisco J. Velásquez-Puentes creator: Luis Felipe Hinojosa creator: Thomas Schwartz creator: Bengt Oxelman creator: Bernard Pfeil creator: Mary T.K. Arroyo creator: Livia Wanntorp creator: Alexandre Antonelli uri: https://doi.org/10.7717/peerj.4388 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bacon et al. title: The right thalamus may play an important role in anesthesia-awakening regulation in frogs link: https://peerj.com/articles/4516 last-modified: 2018-03-15 description: BackgroundPrevious studies have shown that the mammalian thalamus is a key structure for anesthesia-induced unconsciousness and anesthesia-awakening regulation. However, both the dynamic characteristics and probable lateralization of thalamic functioning during anesthesia-awakening regulation are not fully understood, and little is known of the evolutionary basis of the role of the thalamus in anesthesia-awakening regulation.MethodsAn amphibian species, the South African clawed frog (Xenopus laevis) was used in the present study. The frogs were immersed in triciane methanesulfonate (MS-222) for general anesthesia. Electroencephalogram (EEG) signals were recorded continuously from both sides of the telencephalon, diencephalon (thalamus) and mesencephalon during the pre-anesthesia stage, administration stage, recovery stage and post-anesthesia stage. EEG data was analyzed including calculation of approximate entropy (ApEn) and permutation entropy (PE).ResultsBoth ApEn and PE values differed significantly between anesthesia stages, with the highest values occurring during the awakening period and the lowest values during the anesthesia period. There was a significant correlation between the stage durations and ApEn or PE values during anesthesia-awakening cycle primarily for the right diencephalon (right thalamus). ApEn and PE values for females were significantly higher than those for males.DiscussionApEn and PE measurements are suitable for estimating depth of anesthesia and complexity of amphibian brain activity. The right thalamus appears physiologically positioned to play an important role in anesthesia-awakening regulation in frogs indicating an early evolutionary origin of the role of the thalamus in arousal and consciousness in land vertebrates. Sex differences exist in the neural regulation of general anesthesia in frogs. creator: Yanzhu Fan creator: Xizi Yue creator: Fei Xue creator: Steven E. Brauth creator: Yezhong Tang creator: Guangzhan Fang uri: https://doi.org/10.7717/peerj.4516 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fan et al. title: Recalibrating the body: visuotactile ventriloquism aftereffect link: https://peerj.com/articles/4504 last-modified: 2018-03-15 description: Visuotactile ventriloquism is a recently reported effect showing that somatotopic tactile representations (namely, representation of location along the surface of one’s arm) can be biased by simultaneous presentation of a visual stimulus in a spatial localization task along the surface of the skin. Here we investigated whether the exposure to discrepancy between tactile and visual stimuli on the skin can induce lasting changes in the somatotopic representations of space. We conducted an experiment investigating this question by asking participants to perform a localization task that included unisensory and bisensory trials, before and after exposure to spatially discrepant visuotactile stimuli. Participants localized brief flashes of light and brief vibrations that were presented along the surface of their forearms, and were presented either individually (unisensory conditions) or were presented simultaneously at the same location or different locations. We then compared the localization of tactile stimuli in unisensory tactile conditions before and after the exposure to discrepant bisensory stimuli. After exposure, participants exhibited a shift in their tactile localizations in the direction of the visual stimulus that was presented during the exposure block. These results demonstrate that the somatotopic spatial representations are capable of rapidly recalibrating after a very brief exposure to visually discrepant stimuli. creator: Majed Samad creator: Ladan Shams uri: https://doi.org/10.7717/peerj.4504 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Samad and Shams title: Electroencephalographic modulations during an open- or closed-eyes motor task link: https://peerj.com/articles/4492 last-modified: 2018-03-15 description: There is fundamental knowledge that during the resting state cerebral activity recorded by electroencephalography (EEG) is strongly modulated by the eyes-closed condition compared to the eyes-open condition, especially in the occipital lobe. However, little research has demonstrated the influence of the eyes-closed condition on the motor cortex, particularly during a self-paced movement. This prompted the question: How does the motor cortex activity change between the eyes-closed and eyes-open conditions? To answer this question, we recorded EEG signals from 15 voluntary healthy subjects who performed a simple motor task (i.e., a voluntary isometric flexion of the right-hand index) under two conditions: eyes-closed and eyes-open. Our results confirmed strong modulation in the mu rhythm (7–13 Hz) with a large event-related desynchronisation. However, no significant differences have been observed in the beta band (15–30 Hz). Furthermore, evidence suggests that the eyes-closed condition influences the behaviour of subjects. This study gives us greater insight into the motor cortex and could also be useful in the brain-computer interface (BCI) domain. creator: Sébastien Rimbert creator: Rahaf Al-Chwa creator: Manuel Zaepffel creator: Laurent Bougrain uri: https://doi.org/10.7717/peerj.4492 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rimbert et al. title: Measuring short distance dispersal of Alliaria petiolata and determining potential long distance dispersal mechanisms link: https://peerj.com/articles/4477 last-modified: 2018-03-15 description: IntroductionAlliaria petiolata, an herbaceous plant, has invaded woodlands in North America. Its ecology has been thoroughly studied, but an overlooked aspect of its biology is seed dispersal distances and mechanisms. We measured seed dispersal distances in the field and tested if epizoochory is a potential mechanism for long-distance seed dispersal.MethodsDispersal distances were measured by placing seed traps in a sector design around three seed point sources, which consisted of 15 second-year plants transplanted within a 0.25 m radius circle. Traps were placed at intervals ranging from 0.25–3.25 m from the point source. Traps remained in the field until a majority of seeds were dispersed. Eight probability density functions were fitted to seed trap counts via maximum likelihood. Epizoochory was tested as a potential seed dispersal mechanism for A. petiolata through a combination of field and laboratory experiments. To test if small mammals transport A. petiolata seeds in their fur, experimental blocks were placed around dense A. petiolata patches. Each block contained a mammal inclusion treatment (MIT) and control. The MIT consisted of a wood-frame (31 × 61× 31 cm) covered in wire mesh, except for the two 31 × 31 cm ends, placed over a germination tray filled with potting soil. A pan filled with bait was placed in the center of the tray. The control frame (11 × 31 × 61 cm) was placed over a germination tray and completely covered in wire mesh to exclude animal activity. Treatments were in the field for peak seed dispersal. In March, trays were moved to a greenhouse and A. petiolata seedlings were counted and then compared between treatments. To determine if A. petiolata seeds attach to raccoon (Procyon lotor) and white-tailed deer (Odocoileus virginianus) fur, wet and dry seeds were dropped onto wet and dry fur. Furs were rotated 180 degrees and the seeds that remained attached were counted. To measure seed retention, seeds were dropped on furs and rotated as before, then the furs were agitated for one hour. The seeds retained in the fur were counted.ResultsFor the seed dispersal experiment, the 2Dt function provided the best fit and was the most biologically meaningful. It predicted that seed density rapidly declined with distance from the point source. Mean dispersal distance was 0.52 m and 95% of seeds dispersed within 1.14 m. The epizoochory field experiment showed increased mammal activity and A. petiolata seedlings in germination trays of the MIT compared to control. Laboratory studies showed 3–26% of seeds were attached and retained by raccoon and deer fur. Retention significantly increased if either seed or fur were wet (57–98%).DiscussionWithout animal seed vectors, most seeds fall within a short distance of the seed source; however, long distance dispersal may be accomplished by epizoochory. Our data are consistent with A. petiolata’s widespread distribution and development of dense clusters of the species in invaded areas. creator: Christopher A. Loebach creator: Roger C. Anderson uri: https://doi.org/10.7717/peerj.4477 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Loebach and Anderson title: Detection of linear features including bone and skin areas in ultrasound images of joints link: https://peerj.com/articles/4411 last-modified: 2018-03-15 description: Identifying the separate parts in ultrasound images such as bone and skin plays a crucial role in the synovitis detection task. This paper presents a detector of bone and skin regions in the form of a classifier which is trained on a set of annotated images. Selected regions have labels: skin or bone or none. Feature vectors used by the classifier are assigned to image pixels as a result of passing the image through the bank of linear and nonlinear filters. The filters include Gaussian blurring filter, its first and second order derivatives, Laplacian as well as positive and negative threshold operations applied to the filtered images. We compared multiple supervised learning classifiers including Naive Bayes, k-Nearest Neighbour, Decision Trees, Random Forest, AdaBoost and Support Vector Machines (SVM) with various kernels, using four classification performance scores and computation time. The Random Forest classifier was selected for the final use, as it gives the best overall evaluation results. creator: Artur Bąk creator: Jakub Segen creator: Kamil Wereszczyński creator: Pawel Mielnik creator: Marcin Fojcik creator: Marek Kulbacki uri: https://doi.org/10.7717/peerj.4411 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bąk et al.