title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-11 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Parental encouragement is positively associated with outdoor active play outside of school hours among 7–12 year olds link: https://peerj.com/articles/1463 last-modified: 2015-11-30 description: Background. Physical activity is important for children’s physical, mental, and social well-being. Outdoor active play is an important yet unstudied domain of children’s physical activity. The objective of this study was to determine if parental encouragement is associated with the frequency that children engage in outdoor active play outside of school hours.Methods. Participants consisted of 514 children aged 7–12 years and one of their parents. Parents completed a survey that included four questions that assessed how frequently they used verbal cues to encourage their child to play outdoors. Points were assigned to each response and averaged across the 4 questions, and based on this average participants were assigned to quintiles. The survey included seven questions that asked parents to assess how frequently their child played outdoors outside of school hours. Points were assigned to each response and summed to create an active outdoor play frequency score. General linear models assessed associations between parental encouragement and outdoor play while controlling for individual, family, and neighborhood covariates.Results. The mean outdoor active play frequency score increased significantly across quintiles of the parental encouragement score as follows: 6.0 (standard error = 0.7) in quintile 1, 9.8 (0.6) in quintile 2, 11.4 (0.6) in quintile 3, 16.2 (0.9) in quintile 4, and 23.3 (1.3) in quintile 5. After adjusting for covariates, the mean outdoor active play frequency score was almost three times higher in the highest parental encouragement quintile than in the lowest quintile (20.4 vs. 7.8).Conclusions. Parents use of verbal cues to encourage their children to play outdoors was independently associated with outdoor active play among 7–12 year olds. creator: Thomas Ferrao creator: Ian Janssen uri: https://doi.org/10.7717/peerj.1463 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ferrao and Janssen title: Biomechanical implications of skeletal muscle hypertrophy and atrophy: a musculoskeletal model link: https://peerj.com/articles/1462 last-modified: 2015-11-30 description: Muscle hypertrophy and atrophy occur frequently as a result of mechanical loading or unloading, with implications for clinical, general, and athletic populations. The effects of muscle hypertrophy and atrophy on force production and joint moments have been previously described. However, there is a paucity of research showing how hypertrophy and atrophy may affect moment arm (MA) lengths. The purpose of this model was to describe the mathematical relationship between the anatomical cross-sectional area (ACSA) of a muscle and its MA length. In the model, the ACSAs of the biceps brachii and brachialis were altered to hypertrophy up to twice their original size and to atrophy to one-half of their original size. The change in MA length was found to be proportional to the arcsine of the square root of the change in ACSA. This change in MA length may be a small but important contributor to strength, especially in sports that require large joint moments at slow joint angular velocities, such as powerlifting. The paradoxical implications of the increase in MA are discussed, as physiological factors influencing muscle contraction velocity appear to favor a smaller MA length for high velocity movements but a larger muscle MA length for low velocity, high force movements. creator: Andrew D. Vigotsky creator: Bret Contreras creator: Chris Beardsley uri: https://doi.org/10.7717/peerj.1462 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Vigotsky et al. title: Preference of a native beetle for “exoticism,” characteristics that contribute to invasive success of Costelytra zealandica (Scarabaeidae: Melolonthinae) link: https://peerj.com/articles/1454 last-modified: 2015-11-30 description: Widespread replacement of native ecosystems by productive land sometimes results in the outbreak of a native species. In New Zealand, the introduction of exotic pastoral plants has resulted in diet alteration of the native coleopteran species, Costelytra zealandica (White) (Scarabaeidae) such that this insect has reached the status of pest. In contrast, C. brunneum (Broun), a congeneric species, has not developed such a relationship with these ‘novel’ host plants. This study investigated the feeding preferences and fitness performance of these two closely related scarab beetles to increase fundamental knowledge about the mechanisms responsible for the development of invasive characteristics in native insects. To this end, the feeding preference of third instar larvae of both Costelytra species was investigated using an olfactometer device, and the survival and larval growth of the invasive species C. zealandica were compared on native and exotic host plants. Costelytra zealandica, when sampled from exotic pastures, was unable to fully utilise its ancestral native host and showed higher feeding preference and performance on exotic plants. In contrast, C. zealandica sampled from native grasslands did not perform significantly better on either host and showed similar feeding preferences to C. brunneum, which exhibited no feeding preference. This study suggests the possibility of strong intraspecific variation in the ability of C. zealandica to exploit native or exotic plants, supporting the hypothesis that such ability underpins the existence of distinct host-races in this species. creator: Marie-Caroline Lefort creator: Stéphane Boyer creator: Jessica Vereijssen creator: Rowan Sprague creator: Travis R. Glare creator: Susan P. Worner uri: https://doi.org/10.7717/peerj.1454 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lefort et al. title: Inconsistencies among secondary sources of Chukar Partridge (Alectoris chukar) introductions to the United States link: https://peerj.com/articles/1447 last-modified: 2015-11-30 description: The propagule pressure hypothesis asserts that the number of individuals released is the key determinant of whether an introduction will succeed or not. It remains to be shown whether propagule pressure is more important than either species-level or site-level factors in determining the fate of an introduction. Studies claiming to show that propagule pressure is the primary determinant of introduction success must assume that the historical record as reported by secondary sources is complete and accurate. Here, examine a widely introduced game bird, the Chukar (Alectoris chukar), to the USA. We compare the records reported by two secondary sources (Long, 1981; Lever, 1987) to those in a primary source (Christensen, 1970) and to a recent study by Sol et al. (2012). Numerous inconsistencies exist in the records reported by Sol et al. (2012), Long (1981) and Lever (1987) when compared to the primary record of Christensen (1970). As reported by Christensen (1970), very large numbers of Chukars were released unsuccessfully in some states. Our results strongly imply that factors other than sheer numbers are more important. Site-to-site differences are the most likely explanation for the variation in success. creator: Michael P. Moulton creator: Wendell P. Cropper creator: Andrew J. Broz uri: https://doi.org/10.7717/peerj.1447 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Moulton et al. title: Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa link: https://peerj.com/articles/1339 last-modified: 2015-11-30 description: Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging. creator: Steven J. Franks creator: Beatriz Perez-Sweeney creator: Maya Strahl creator: Anna Nowogrodzki creator: Jennifer J. Weber creator: Rebecca Lalchan creator: Kevin P. Jordan creator: Amy Litt uri: https://doi.org/10.7717/peerj.1339 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Franks et al. title: Learning from a provisioning site: code of conduct compliance and behaviour of whale sharks in Oslob, Cebu, Philippines link: https://peerj.com/articles/1452 last-modified: 2015-11-26 description: While shark-based tourism is a rapidly growing global industry, there is ongoing controversy about the effects of provisioning on the target species. This study investigated the effect of feeding on whale sharks (Rhincodon typus) at a provisioning site in Oslob, Cebu, in terms of arrival time, avoidance and feeding behaviour using photo-identification and focal follows. Additionally, compliance to the code of conduct in place was monitored to assess tourism pressure on the whale sharks. Newly identified sharks gradually arrived earlier to the provisioning site after their initial sighting, indicating that the animals learn to associate the site with food rewards. Whale sharks with a long resighting history showed anticipatory behaviour and were recorded at the site on average 5 min after the arrival of feeder boats. Results from a generalised linear mixed model indicated that animals with a longer resighting history were less likely to show avoidance behaviour to touches or boat contact. Similarly, sequential data on feeding behaviour was modelled using a generalised estimating equations approach, which suggested that experienced whale sharks were more likely to display vertical feeding behaviour. It was proposed that the continuous source of food provides a strong incentive for the modification of behaviours, i.e., learning, through conditioning. Whale sharks are large opportunistic filter feeders in a mainly oligotrophic environment, where the ability to use novel food sources by modifying their behaviour could be of great advantage. Non-compliance to the code of conduct in terms of minimum distance to the shark (2 m) increased from 79% in 2012 to 97% in 2014, suggesting a high tourism pressure on the whale sharks in Oslob. The long-term effects of the observed behavioural modifications along with the high tourism pressure remain unknown. However, management plans are traditionally based on the precautionary principle, which aims to take preventive actions even if data on cause and effect are still inconclusive. Hence, an improved enforcement of the code of conduct coupled with a reduction in the conditioning of the whale sharks through provisioning were proposed to minimise the impacts on whale sharks in Oslob. creator: Anna Schleimer creator: Gonzalo Araujo creator: Luke Penketh creator: Anna Heath creator: Emer McCoy creator: Jessica Labaja creator: Anna Lucey creator: Alessandro Ponzo uri: https://doi.org/10.7717/peerj.1452 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Schleimer et al. title: The effectiveness of sputum pH analysis in the prediction of response to therapy in patients with pulmonary tuberculosis link: https://peerj.com/articles/1448 last-modified: 2015-11-26 description: Purpose. The predictive factor of response to antituberculous therapy has not been fully elucidated. Airway acidity has been thought to be a potential indicator of the bactericidal activity. Therefore, we hypothesized that monitoring airway acidity by measuring sputum pH could predict response to therapy.Methods. A total of 47 patients having newly diagnosed, smear-positive, active pulmonary tuberculosis were enrolled between October 2011 and March 2014. Sputum samples were serially analyzed before and after treatment. Eligible patients who initiated a standard 6-month treatment were monitored for the length of time to sputum smear and culture conversion.Results. There were 39 patients who completed a 2-month intensive phase of isoniazid, rifampicin, pyrazinamide, and ethambutol therapy followed by a 4-month continuation phase of isoniazid and rifampicin. Although factors including age, cavitation, sputum grade, and use of an acid-suppressant were associated with initial low sputum pH in univariate analysis, multivariate analysis revealed that only age ≥61 years was a statistically important factor predicting low pH value (p = 0.005). Further outcome analysis showed that initial low sputum pH before treatment was the only factor significantly associated with shorter length of time to both sputum smear and culture conversion (p = 0.034 and 0.019, respectively) independent of the effects of age, sputum bacterial load, extent of lung lesion, and cavitation. Thus, initial low sputum pH indicated favorable response to anti-tuberculosis therapy.Conclusions. Measuring sputum pH is an easy and inexpensive way of predicting response to standard combination therapy in patients with pulmonary tuberculosis. creator: Makoto Masuda creator: Takashi Sato creator: Kentaro Sakamaki creator: Makoto Kudo creator: Takeshi Kaneko creator: Yoshiaki Ishigatsubo uri: https://doi.org/10.7717/peerj.1448 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Masuda et al. title: Ranking, selecting, and prioritising genes with desirability functions link: https://peerj.com/articles/1444 last-modified: 2015-11-26 description: In functional genomics experiments, researchers often select genes to follow-up or validate from a long list of differentially expressed genes. Typically, sharp thresholds are used to bin genes into groups such as significant/non-significant or fold change above/below a cut-off value, and ad hoc criteria are also used such as favouring well-known genes. Binning, however, is inefficient and does not take the uncertainty of the measurements into account. Furthermore, p-values, fold-changes, and other outcomes are treated as equally important, and relevant genes may be overlooked with such an approach. Desirability functions are proposed as a way to integrate multiple selection criteria for ranking, selecting, and prioritising genes. These functions map any variable to a continuous 0–1 scale, where one is maximally desirable and zero is unacceptable. Multiple selection criteria are then combined to provide an overall desirability that is used to rank genes. In addition to p-values and fold-changes, further experimental results and information contained in databases can be easily included as criteria. The approach is demonstrated with a breast cancer microarray data set. The functions and an example data set can be found in the desiR package on CRAN (https://cran.r-project.org/web/packages/desiR/) and the development version is available on GitHub (https://github.com/stanlazic/desiR). creator: Stanley E. Lazic uri: https://doi.org/10.7717/peerj.1444 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lazic title: Intensity of bouted and sporadic physical activity and the metabolic syndrome in adults link: https://peerj.com/articles/1437 last-modified: 2015-11-26 description: Background. Physical activity guidelines for adults only recognize the health benefits of accumulating bouted moderate-to-vigorous physical activity (MVPA), or MVPA occurring over at least 10 consecutive minutes. There is a lack of evidence supporting the health benefits of other patterns and intensities of activity including sporadic MVPA (i.e., MVPA occurring in periods of fewer than 10 consecutive minutes) and light intensity physical activity (LIPA). The objective of this study was to examine the health benefits associated with physical activity that does not meet the physical activity guidelines criteria for bouted MVPA. Specifically, we examined the association between sporadic MVPA and bouted and sporadic LIPA with the metabolic syndrome.Methods. We studied a representative cross-sectional sample of 1,974 adults aged 20 years and older from the 2003–2006 US National Health and Nutrition Examination Survey. Physical activity was measured over 7 days using Actigraph AM-7164 accelerometers. Each minute over the 7-day measurement period was classified as being of a sedentary, light, or moderate-to-vigorous intensity. A 10 min threshold differentiated bouted activity from sporadic activity. Average minutes/day of sporadic LIPA, sporadic MVPA, bouted LIPA, bouted MVPA, and embedded MVPA (MVPA occurring within bouts of primarily LIPA) were calculated. Metabolic syndrome status was determined using established criteria. Associations were examined using logistic regression and controlled for relevant covariates.Results. For every 30 min/day of physical activity, the odds ratio (95% confidence interval) of the metabolic syndrome was reduced by 4% (1–7%) for bouted LIPA, 64% (51–71%) for bouted MVPA, and 57% (45–67%) for embedded MVPA. Sporadic LIPA was not independently associated with the metabolic syndrome. We could not examine the association between sporadic MVPA and the metabolic syndrome because participants accumulated such a marginal amount of this type of activity (i.e., median = 2 min/day, only 11% of participants accumulated ≥5 min/day).Conclusion. The intensity of non-bouted activity is important, as embedded MVPA had a stronger association with the metabolic syndrome than sporadic LIPA and a comparable association to bouted MVPA. creator: Jordan Robson creator: Ian Janssen uri: https://doi.org/10.7717/peerj.1437 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Robson and Janssen title: Prediction of cancer cell sensitivity to natural products based on genomic and chemical properties link: https://peerj.com/articles/1425 last-modified: 2015-11-26 description: Natural products play a significant role in cancer chemotherapy. They are likely to provide many lead structures, which can be used as templates for the construction of novel drugs with enhanced antitumor activity. Traditional research approaches studied structure-activity relationship of natural products and obtained key structural properties, such as chemical bond or group, with the purpose of ascertaining their effect on a single cell line or a single tissue type. Here, for the first time, we develop a machine learning method to comprehensively predict natural products responses against a panel of cancer cell lines based on both the gene expression and the chemical properties of natural products. The results on two datasets, training set and independent test set, show that this proposed method yields significantly better prediction accuracy. In addition, we also demonstrate the predictive power of our proposed method by modeling the cancer cell sensitivity to two natural products, Curcumin and Resveratrol, which indicate that our method can effectively predict the response of cancer cell lines to these two natural products. Taken together, the method will facilitate the identification of natural products as cancer therapies and the development of precision medicine by linking the features of patient genomes to natural product sensitivity. creator: Zhenyu Yue creator: Wenna Zhang creator: Yongming Lu creator: Qiaoyue Yang creator: Qiuying Ding creator: Junfeng Xia creator: Yan Chen uri: https://doi.org/10.7717/peerj.1425 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Yue et al. title: Pathways from marine protected area design and management to ecological success link: https://peerj.com/articles/1424 last-modified: 2015-11-26 description: Using an international dataset compiled from 121 sites in 87 marine protected areas (MPAs) globally (Edgar et al., 2014), I assessed how various configurations of design and management conditions affected MPA ecological performance, measured in terms of fish species richness and biomass. The set-theoretic approach used Boolean algebra to identify pathways that combined up to five ‘NEOLI’ (No-take, Enforced, Old, Large, Isolated) conditions and that were sufficient for achieving positive, and negative, ecological outcomes. Ecological isolation was overwhelming the most important condition affecting ecological outcomes but Old and Large were also conditions important for achieving high levels of biomass among large fishes (jacks, groupers, sharks). Solution coverage was uniformly low (<0.35) for all models of positive ecological performance suggesting the presence of numerous other conditions and pathways to ecological success that did not involve the NEOLI conditions. Solution coverage was higher (>0.50) for negative results (i.e., the absence of high biomass) among the large commercially-exploited fishes, implying asymmetries in how MPAs may rebuild populations on the one hand and, on the other, protect against further decline. The results revealed complex interactions involving MPA design, implementation, and management conditions that affect MPA ecological performance. In general terms, the presence of no-take regulations and effective enforcement were insufficient to ensure MPA effectiveness on their own. Given the central role of ecological isolation in securing ecological benefits from MPAs, site selection in the design phase appears critical for success. creator: Murray A. Rudd uri: https://doi.org/10.7717/peerj.1424 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Rudd title: Geographic variation and genetic structure in the Bahama Oriole (Icterus northropi), a critically endangered synanthropic species link: https://peerj.com/articles/1421 last-modified: 2015-11-26 description: Bird species may exhibit unexpected population structuring over small distances, with gene flow restricted by geographic features such as water or mountains. The Bahama Oriole (Icterus northropi) is a critically endangered, synanthropic island endemic with a declining population of fewer than 300 individuals. It now remains only on Andros Island (The Bahamas), which is riddled with waterways that past studies assumed did not hinder gene flow. We examined 1,858 base pairs of mitochondrial DNA sequenced from four gene regions in 14 birds (roughly 5% of the remaining population) found on the largest land masses of Andros Island (North Andros and Mangrove Cay/South Andros). We sought to discern genetic structuring between the remaining subpopulations and its relationship to current conservation concerns. Four unique haplotypes were identified, with only one shared between the two subpopulations. Nucleotide and haplotype diversity were higher for the North Andros subpopulation than for the Mangrove Cay/South Andros subpopulation. Analysis of molecular variance (AMOVA) yielded a Wright’s fixation index (Fst) of 0.60 (PFst = 0.016), with 40.2% of the molecular variation explained by within-population differences and 59.8% by among-population differences. Based on the mitochondrial regions examined in this study, we suggest the extant subpopulations of Bahama Oriole exhibit significant population structuring over short distances, consistent with some other non-migratory tropical songbird species. creator: Melissa R. Price creator: Carl Person creator: William K. Hayes uri: https://doi.org/10.7717/peerj.1421 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Price et al. title: TLR4 Asp299Gly (rs4986790) polymorphism and coronary artery disease: a meta-analysis link: https://peerj.com/articles/1412 last-modified: 2015-11-26 description: Background. Previous studies have shown conflicting results on the association between toll-like receptor 4 (TLR4) Asp299Gly (rs4986790) polymorphism and coronary artery disease (CAD). The aim of this study was to evaluate the influence of TLR4 Asp299Gly polymorphism on CAD risk, CRP level and the number of stenotic coronary arteries, as well as to investigate whether G allele carriers would benefit more from statin treatment.Methods. PubMed, EMBASE, and CNKI databases were searched until May 2015. All the statistical tests were performed using R version 3.1.2. Odds ratio (OR) and 95% confidence interval (CI) were used to assess the association between TLR4 Asp299Gly polymorphism and CAD risk, the number of stenotic vessels, and the incidence of cardiovascular events according to statin-treated patients. Weighted mean difference (WMD) was calculated for the association between Asp299Gly and CRP level.Results. Overall, 12 case-control studies with 10,258 cases and 5,891 controls were included, and no association of TLR4Asp299Gly polymorphism with CAD was found (G allele vs. A allele: OR = 0.97, 95% CI [0.81–1.17], P = 0.75; AA vs. GG + AG: OR = 0.97, 95% CI [0.80–1.18], P = 0.76; GG vs. AG + AA: OR = 1.08, 95% CI [0.57–2.02], P = 0.82; AG vs. AA + GG: OR = 1.03, 95% CI [0.85–1.25], P = 0.74). Also, no association was noted between Asp299Gly and CRP level (WMD = −0.10, 95% CI [−0.62, 0.41], P = 0.69). Furthermore, no synergistic effect of statin and 299Gly was reported (Statin_AA vs. Statin_AG/GG: OR = 1.12, 95% CI [0.41–3.09], P = 0.82).Discussion. This meta-analysis suggests no association of TLR4 Asp299Gly polymorphism with CAD and CRP level. It is further indicated that the G allele carriers may not benefit more from statin treatment. Further studies should include large sample size and high-quality literature to understand this issue in depth. creator: Rui Chen creator: Ning Gu creator: Ying Gao creator: Wei Cen uri: https://doi.org/10.7717/peerj.1412 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Chen et al. title: Adaptive divergence in resistance to herbivores in Datura stramonium link: https://peerj.com/articles/1411 last-modified: 2015-11-26 description: Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations of Datura stramonium, we compared the degree of phenotypic differentiation (PST) of leaf resistance traits (trichome density, atropine and scopolamine concentration) against neutral genetic differentiation (FST) at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher than FST across the range of trait heritability values. In contrast, genetic differentiation in trichome density was different from FST only when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits in D. stramonium. creator: Guillermo Castillo creator: Pedro L. Valverde creator: Laura L. Cruz creator: Johnattan Hernández-Cumplido creator: Guadalupe Andraca-Gómez creator: Juan Fornoni creator: Edson Sandoval-Castellanos creator: Erika Olmedo-Vicente creator: César M. Flores-Ortiz creator: Juan Núñez-Farfán uri: https://doi.org/10.7717/peerj.1411 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Castillo et al. title: Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery link: https://peerj.com/articles/1398 last-modified: 2015-11-26 description: Background. Preterm Premature Rupture of Membranes (PPROM) is a major leading cause of preterm births. While the cause for PPROM remains unidentified, it is anticipated to be due to subclinical infection, since a large proportion of PPROM patients display signs of chorioamnionitis. Since subclinical infections can be facilitated by dysbiosis, our goal was to characterize the vaginal microbiome and amniotic fluid discharge upon PPROM, through latency antibiotic treatment, and until delivery, to detect the presence of pathogens, microbiota alteration, and microbial response to treatment.Methods. Enrolled subjects (15) underwent routine institutional antenatal care for PPROM, including the administration of latency antibiotics. Serial vaginal swabs were obtained from diagnosis of PPROM through delivery and the sequencing of the V3–V5 region of the 16S rRNA gene was performed for all collected samples.Results. The results show that Lactobacilli species were markedly decreased when compared to vaginal swabs collected from uncomplicated pregnancy subjects with a matched gestational time. Prevotella and Peptoniphilus were the most prevalent taxa in PPROM subjects at presentation. The vaginal microbiome of the PPROM subjects varied substantially intra- and inter-subjects. Several taxa were found to be significantly reduced during and after the antibiotic treatment: Weeksella, Lachnospira, Achromobacter, and Pediococcus. In contrast, Peptostreptococcus and Tissierellaceae ph2 displayed a significant increase after the antibiotic treatment. However, the relative abundance of Lactobacillus, Prevotella, and Peptoniphilus was not substantially impacted during the hospitalization of the PPROM subjects. The deficiency of Lactobacillus, and constancy of known pathogenic species, such as Prevotella and Peptoniphilus during and after antibiotics, highlights the persistent dysbiosis and warrants further investigation into mitigating approaches.Discussion. PPROM is responsible for one third of all preterm births. It is thought that subclinical infection is a crucial factor in the pathophysiology of PPROM because 25–40% of patients present signs of chorioamnionitis on amniocentesis. Here we sought to directly assess the bacterial content of the vagina and leaking amniotic fluid of subjects at presentation, throughout treatment and up until delivery, in order to search for common pathogens, microbiota changes, and microbial response to latency antibiotic treatment. We have found that the vaginal microbiome of PPROM subjects is highly variable and displays significant changes to treatment. However, the unchanging deficiency of Lactobacillus, and persistence of known pathogenic species, such as Prevotella and Peptoniphilus from presentation, through antibiotic treatment and up until delivery, highlights the persistent dysbiosis and warrants further investigation into mitigating approaches. creator: Elizabeth A. Baldwin creator: Marina Walther-Antonio creator: Allison M. MacLean creator: Daryl M. Gohl creator: Kenneth B. Beckman creator: Jun Chen creator: Bryan White creator: Douglas J. Creedon creator: Nicholas Chia uri: https://doi.org/10.7717/peerj.1398 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Baldwin et al. title: A questionnaire study of injections prescribed and dispensed for patients diagnosed with mild/moderate community-acquired pneumonia in Mongolia link: https://peerj.com/articles/1375 last-modified: 2015-11-26 description: Purpose. The study aimed to determine the extent of and factors influencing the prescribing of injections for the treatment of mild/moderate community acquired pneumonia (CAP) in Mongolia.Methods. Questionnaires were developed and administered to medication providers (34 Pharmacists, 27 pharmacy technicians) and prescribers (22 general doctors and 49 medical specialists) working in Mongolia.Results. Cefalosporins were prescribed for patients with mild pneumonia and doctors tended to prescribe injectable cefalosporins (cefazolin) rather than oral dosage forms. This was supported by the questionnaire study with pharmacists and pharmacy technicians. Additionally, 23 pharmacists and pharmacy technicians indicated that OTC injectable cefalosporins (37.7%) and injectable aminopenicillins (33,9%) were frequently sold by pharmacies for the treatment of mild/moderate CAP. Doctors and particularly pharmacists in the questionnaire studies indicated choosing an injection was to avoid non-compliance problems.Conclusion. High levels of injectable prescribing of antibiotics were found in non-hospitalized patients with CAP in Mongolia. This prevalence level indicated that inappropriate injection prescribing is a public health hazard for Mongolia and requires consideration by the appropriate authorities. creator: Gereltuya Dorj creator: Delia Hendrie creator: Richard W. Parsons creator: Bruce Sunderland uri: https://doi.org/10.7717/peerj.1375 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Dorj et al. title: Reference genes selection for transcript normalization in kenaf (Hibiscus cannabinus L.) under salinity and drought stress link: https://peerj.com/articles/1347 last-modified: 2015-11-26 description: Kenaf (Hibiscus cannabinus) is an economic and ecological fiber crop but suffers severe losses in fiber yield and quality under the stressful conditions of excess salinity and drought. To explore the mechanisms by which kenaf responds to excess salinity and drought, gene expression was performed at the transcriptomic level using RNA-seq. Thus, it is crucial to have a suitable set of reference genes to normalize target gene expression in kenaf under different conditions using real-time quantitative reverse transcription-PCR (qRT-PCR). In this study, we selected 10 candidate reference genes from the kenaf transcriptome and assessed their expression stabilities by qRT-PCR in 14 NaCl- and PEG-treated samples using geNorm, NormFinder, and BestKeeper. The results indicated that TUBα and 18S rRNA were the optimum reference genes under conditions of excess salinity and drought in kenaf. Moreover, TUBα and 18S rRNA were used singly or in combination as reference genes to validate the expression levels of WRKY28 and WRKY32 in NaCl- and PEG-treated samples by qRT-PCR. The results further proved the reliability of the two selected reference genes. This work will benefit future studies on gene expression and lead to a better understanding of responses to excess salinity and drought in kenaf. creator: Xiaoping Niu creator: Jianmin Qi creator: Meixia Chen creator: Gaoyang Zhang creator: Aifen Tao creator: Pingping Fang creator: Jiantang Xu creator: Sandra A. Onyedinma creator: Jianguang Su uri: https://doi.org/10.7717/peerj.1347 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Niu et al. title: Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus link: https://peerj.com/articles/1445 last-modified: 2015-11-24 description: Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons. creator: Bryan G. Falk creator: Robert N. Reed uri: https://doi.org/10.7717/peerj.1445 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Falk and Reed title: A tide prediction and tide height control system for laboratory mesocosms link: https://peerj.com/articles/1442 last-modified: 2015-11-24 description: Experimental mesocosm studies of rocky shore and estuarine intertidal systems may benefit from the application of natural tide cycles to better replicate variation in immersion time, water depth, and attendant fluctuations in abiotic and edaphic conditions. Here we describe a stand-alone microcontroller tide prediction open-source software program, coupled with a mechanical tidal elevation control system, which allows continuous adjustment of aquarium water depths in synchrony with local tide cycles. We used this system to monitor the growth of Spartina foliosa marsh cordgrass and scale insect herbivores at three simulated shore elevations in laboratory mesocosms. Plant growth decreased with increasing shore elevation, while scale insect population growth on the plants was not strongly affected by immersion time. This system shows promise for a range of laboratory mesocosm studies where natural tide cycling could impact organism performance or behavior, while the tide prediction system could additionally be utilized in field experiments where treatments need to be applied at certain stages of the tide cycle. creator: Luke P. Miller creator: Jeremy D. Long uri: https://doi.org/10.7717/peerj.1442 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Miller and Long title: Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing link: https://peerj.com/articles/1441 last-modified: 2015-11-24 description: Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0–2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5′ and 3′ UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species. creator: Adam D. Hargreaves creator: John F. Mulley uri: https://doi.org/10.7717/peerj.1441 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hargreaves and Mulley title: Spatial patterns of coral survivorship: impacts of adult proximity versus other drivers of localized mortality link: https://peerj.com/articles/1440 last-modified: 2015-11-24 description: Species-specific enemies may promote prey coexistence through negative distance- and density-dependent survival of juveniles near conspecific adults. We tested this mechanism by transplanting juvenile-sized fragments of the brooding corals Pocillopora damicornis and Seriatopora hystrix 3, 12, 24 and 182 cm up- and down-current of conspecific adults and monitoring their survival and condition over time. We also characterized the spatial distribution of P. damicornis and S. hystrix within replicate plots on three Fijian reef flats and measured the distribution of small colonies within 2 m of larger colonies of each species. Juvenile-sized transplants exhibited no differences in survivorship as a function of distance from adult P. damicornis or S. hystrix. Additionally, both P. damicornis and S. hystrix were aggregated rather than overdispersed on natural reefs. However, a pattern of juveniles being aggregated near adults while larger (and probably older) colonies were not suggests that greater mortality near large adults could occur over longer periods of time or that size-dependent mortality was occurring. While we found minimal evidence of greater mortality of small colonies near adult conspecifics in our transplant experiments, we did document hot-spots of species-specific corallivory. We detected spatially localized and temporally persistent predation on P. damicornis by the territorial triggerfish Balistapus undulatus. This patchy predation did not occur for S. hystrix. This variable selective regime in an otherwise more uniform environment could be one mechanism maintaining diversity of corals on Indo-Pacific reefs. creator: David A. Gibbs creator: Mark E. Hay uri: https://doi.org/10.7717/peerj.1440 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gibbs and Hay title: A critical survey of vestigial structures in the postcranial skeletons of extant mammals link: https://peerj.com/articles/1439 last-modified: 2015-11-24 description: In the Mammalia, vestigial skeletal structures abound but have not previously been the focus of study, with a few exceptions (e.g., whale pelves). Here we use a phylogenetic bracketing approach to identify vestigial structures in mammalian postcranial skeletons and present a descriptive survey of such structures in the Mammalia. We also correct previous misidentifications, including the previous misidentification of vestigial caviid metatarsals as sesamoids. We also examine the phylogenetic distribution of vestigiality and loss. This distribution indicates multiple vestigialization and loss events in mammalian skeletal structures, especially in the hand and foot, and reveals no correlation in such events between mammalian fore and hind limbs. creator: Phil Senter creator: John G. Moch uri: https://doi.org/10.7717/peerj.1439 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Senter and Moch title: Measuring health disparities: a comparison of absolute and relative disparities link: https://peerj.com/articles/1438 last-modified: 2015-11-24 description: Monitoring national trends in disparities in different diseases could provide measures to evaluate the impact of intervention programs designed to reduce health disparities. In the US, most of the reports that track health disparities provided either relative or absolute disparities or both. However, these two measures of disparities are not only different in scale and magnitude but also the temporal changes in the magnitudes of these measures can occur in opposite directions. The trends for absolute disparity and relative disparity could move in opposite directions when the prevalence of disease in the two populations being compared either increase or decline simultaneously. If the absolute disparity increases but relative disparity declines for consecutive time periods, the absolute disparity increases but relative disparity declines for the combined time periods even with a larger increase in absolute disparity during the combined time periods. Based on random increases or decreases in prevalence of disease for two population groups, there is a higher chance the trends of these two measures could move in opposite directions when the prevalence of disease for the more advantaged group is very small relative to the prevalence of disease for the more disadvantaged group. When prevalence of disease increase or decrease simultaneously for two populations, the increase or decrease in absolute disparity has to be sufficiently large enough to warrant a corresponding increase or decrease in relative disparity. When absolute disparity declines but relative disparity increases, there is some progress in reducing disparities, but the reduction in absolute disparity is not large enough to also reduce relative disparity. When evaluating interventions to reduce health disparities using these two measures, it is important to consider both absolute and relative disparities and consider all the scenarios discussed in this paper to assess the progress towards reducing or eliminating health disparities. creator: Ramal Moonesinghe creator: Gloria L.A. Beckles uri: https://doi.org/10.7717/peerj.1438 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Moonesinghe and Beckles title: Dynamics in benthic community composition and influencing factors in an upwelling-exposed coral reef on the Pacific coast of Costa Rica link: https://peerj.com/articles/1434 last-modified: 2015-11-24 description: Seasonal upwelling at the northern Pacific coast of Costa Rica offers the opportunity to investigate the effects of pronounced changes in key water parameters on fine-scale dynamics of local coral reef communities. This study monitored benthic community composition at Matapalo reef (10.539°N, 85.766°W) by weekly observations of permanent benthic quadrats from April 2013 to April 2014. Monitoring was accompanied by surveys of herbivore abundance and biomass and measurements of water temperature and inorganic nutrient concentrations. Findings revealed that the reef-building corals Pocillopora spp. exhibited an exceptional rapid increase from 22 to 51% relative benthic cover. By contrast, turf algae cover decreased from 63 to 24%, resulting in a corresponding increase in crustose coralline algae cover. The macroalga Caulerpa sertularioides covered up to 15% of the reef in April 2013, disappeared after synchronized gamete release in May, and subsequently exhibited slow regrowth. Parallel monitoring of influencing factors suggest that C. sertularioides cover was mainly regulated by their reproductive cycle, while that of turf algae was likely controlled by high abundances of herbivores. Upwelling events in February and March 2014 decreased mean daily seawater temperatures by up to 7 °C and increased nutrient concentrations up to 5- (phosphate) and 16-fold (nitrate) compared to mean values during the rest of the year. Changes in benthic community composition did not appear to correspond to the strong environmental changes, but rather shifted from turf algae to hard coral dominance over the entire year of observation. The exceptional high dynamic over the annual observation period encourages further research on the adaptation potential of coral reefs to environmental variability. creator: Ines Stuhldreier creator: Celeste Sánchez-Noguera creator: Florian Roth creator: Carlos Jiménez creator: Tim Rixen creator: Jorge Cortés creator: Christian Wild uri: https://doi.org/10.7717/peerj.1434 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Stuhldreier et al. title: Radiocesium concentrations in wild mushrooms collected in Kawauchi Village after the accident at the Fukushima Daiichi Nuclear Power Plant link: https://peerj.com/articles/1427 last-modified: 2015-11-24 description: It is well known from the experience after the 1986 accident at the Chernobyl Nuclear Power Plant that radiocesium tends to concentrate in wild mushrooms. In this study, we collected wild mushrooms from the Kawauchi Village of Fukushima Prefecture, located within 30 km of the Fukushima Daiichi Nuclear Power Plant, and evaluated their radiocesium concentrations to estimate the risk of internal radiation exposure in local residents. We found that radioactive cesium exceeding 100 Bq/kg was detected in 125 of 154 mushrooms (81.2%). We calculated committed effective doses based on 6,278 g per year (age > 20 years, 17.2 g/day), the average intake of Japanese citizens, ranging from doses of 0.11–1.60 mSv, respectively. Although committed effective doses are limited even if residents eat contaminated foods several times, we believe that comprehensive risk-communication based on the results of the radiocesium measurements of food, water, and soil is necessary for the recovery of Fukushima after this nuclear disaster. creator: Kanami Nakashima creator: Makiko Orita creator: Naoko Fukuda creator: Yasuyuki Taira creator: Naomi Hayashida creator: Naoki Matsuda creator: Noboru Takamura uri: https://doi.org/10.7717/peerj.1427 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Nakashima et al. title: Datziinae as a new subfamily name for the unavailable name Protopsychodinae Stebner et al., 2015, (Diptera: Psychodidae) link: https://peerj.com/articles/1423 last-modified: 2015-11-24 description: In a recent paper a new subfamily of Psychodidae was inadequately named Protopsychodinae. This nomenclatural act cannot be considered as a valid name under ICZN regulations because the subfamily name is not based on the type genus DatziaStebner et al., 2015, and furthermore the fossil genus ProtopsychodaAzar et al., 1999 was originally described under the subfamily Psychodinae. Therefore, the new family-group name Datziinae is herein proposed. creator: Frauke Stebner creator: Mónica M. Solórzano Kraemer creator: Sergio Ibáñez-Bernal creator: Rüdiger Wagner uri: https://doi.org/10.7717/peerj.1423 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Stebner et al. title: A predictive screening tool to detect diabetic retinopathy or macular edema in primary health care: construction, validation and implementation on a mobile application link: https://peerj.com/articles/1404 last-modified: 2015-11-24 description: The most described techniques used to detect diabetic retinopathy and diabetic macular edema have to be interpreted correctly, such that a person not specialized in ophthalmology, as is usually the case of a primary care physician, may experience difficulties with their interpretation; therefore we constructed, validated and implemented as a mobile app a new tool to detect diabetic retinopathy or diabetic macular edema (DRDME) using simple objective variables. We undertook a cross-sectional, observational study of a sample of 142 eyes from Spanish diabetic patients suspected of having DRDME in 2012–2013. Our outcome was DRDME and the secondary variables were: type of diabetes, gender, age, glycated hemoglobin (HbA1c), foveal thickness and visual acuity (best corrected). The sample was divided into two parts: 80% to construct the tool and 20% to validate it. A binary logistic regression model was used to predict DRDME. The resulting model was transformed into a scoring system. The area under the ROC curve (AUC) was calculated and risk groups established. The tool was validated by calculating the AUC and comparing expected events with observed events. The construction sample (n = 106) had 35 DRDME (95% CI [24.1–42.0]), and the validation sample (n = 36) had 12 DRDME (95% CI [17.9–48.7]). Factors associated with DRDME were: HbA1c (per 1%) (OR = 1.36, 95% CI [0.93–1.98], p = 0.113), foveal thickness (per 1 µm) (OR = 1.03, 95% CI [1.01–1.04], p < 0.001) and visual acuity (per unit) (OR = 0.14, 95% CI [0.00–0.16], p < 0.001). AUC for the validation: 0.90 (95% CI [0.75–1.00], p < 0.001). No significant differences were found between the expected and the observed outcomes (p = 0.422). In conclusion, we constructed and validated a simple rapid tool to determine whether a diabetic patient suspected of having DRDME really has it. This tool has been implemented on a mobile app. Further validation studies are required in the general diabetic population. creator: Cesar Azrak creator: Antonio Palazón-Bru creator: Manuel Vicente Baeza-Díaz creator: David Manuel Folgado-De la Rosa creator: Carmen Hernández-Martínez creator: José Juan Martínez-Toldos creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.1404 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Azrak et al. title: Are neonicotinoid insecticides driving declines of widespread butterflies? link: https://peerj.com/articles/1402 last-modified: 2015-11-24 description: There has been widespread concern that neonicotinoid pesticides may be adversely impacting wild and managed bees for some years, but recently attention has shifted to examining broader effects they may be having on biodiversity. For example in the Netherlands, declines in insectivorous birds are positively associated with levels of neonicotinoid pollution in surface water. In England, the total abundance of widespread butterfly species declined by 58% on farmed land between 2000 and 2009 despite both a doubling in conservation spending in the UK, and predictions that climate change should benefit most species. Here we build models of the UK population indices from 1985 to 2012 for 17 widespread butterfly species that commonly occur at farmland sites. Of the factors we tested, three correlated significantly with butterfly populations. Summer temperature and the index for a species the previous year are both positively associated with butterfly indices. By contrast, the number of hectares of farmland where neonicotinoid pesticides are used is negatively associated with butterfly indices. Indices for 15 of the 17 species show negative associations with neonicotinoid usage. The declines in butterflies have largely occurred in England, where neonicotinoid usage is at its highest. In Scotland, where neonicotinoid usage is comparatively low, butterfly numbers are stable. Further research is needed urgently to show whether there is a causal link between neonicotinoid usage and the decline of widespread butterflies or whether it simply represents a proxy for other environmental factors associated with intensive agriculture. creator: Andre S. Gilburn creator: Nils Bunnefeld creator: John McVean Wilson creator: Marc S. Botham creator: Tom M. Brereton creator: Richard Fox creator: Dave Goulson uri: https://doi.org/10.7717/peerj.1402 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gilburn et al. title: Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid link: https://peerj.com/articles/1429 last-modified: 2015-11-19 description: Background. Harmful Algal Blooms (HABs) responsible for Diarrhetic Shellfish Poisoning (DSP) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the primary cause of acute DSP intoxications. Although several studies have described the molecular effects of high OA concentrations on sentinel organisms (e.g., bivalve molluscs), the effect of prolonged exposures to low (sublethal) OA concentrations is still unknown. In order to fill this gap, this work combines Next-Generation sequencing and custom-made microarray technologies to develop an unbiased characterization of the transcriptomic response of mussels during early stages of a DSP bloom.Methods. Mussel specimens were exposed to a HAB episode simulating an early stage DSP bloom (200 cells/L of the dinoflagellate Prorocentrum lima for 24 h). The unbiased characterization of the transcriptomic responses triggered by OA was carried out using two complementary methods of cDNA library preparation: normalized and Suppression Subtractive Hybridization (SSH). Libraries were sequenced and read datasets were mapped to Gene Ontology and KEGG databases. A custom-made oligonucleotide microarray was developed based on these data, completing the expression analysis of digestive gland and gill tissues.Results. Our findings show that exposure to sublethal concentrations of OA is enough to induce gene expression modifications in the mussel Mytilus. Transcriptomic analyses revealed an increase in proteasomal activity, molecular transport, cell cycle regulation, energy production and immune activity in mussels. Oppositely, a number of transcripts hypothesized to be responsive to OA (notably the Serine/Threonine phosphatases PP1 and PP2A) failed to show substantial modifications. Both digestive gland and gill tissues responded similarly to OA, although expression modifications were more dramatic in the former, supporting the choice of this tissue for future biomonitoring studies.Discussion. Exposure to OA concentrations within legal limits for safe consumption of shellfish is enough to disrupt important cellular processes in mussels, eliciting sharp transcriptional changes as a result. By combining the study of cDNA libraries and a custom-made OA-specific microarray, our work provides a comprehensive characterization of the OA-specific transcriptome, improving the accuracy of the analysis of expresion profiles compared to single-replicated RNA-seq methods. The combination of our data with related studies helps understanding the molecular mechanisms underlying molecular responses to DSP episodes in marine organisms, providing useful information to develop a new generation of tools for the monitoring of OA pollution. creator: Victoria Suarez-Ulloa creator: Juan Fernandez-Tajes creator: Vanessa Aguiar-Pulido creator: M. Veronica Prego-Faraldo creator: Fernanda Florez-Barros creator: Alexia Sexto-Iglesias creator: Josefina Mendez creator: Jose M. Eirin-Lopez uri: https://doi.org/10.7717/peerj.1429 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Suarez-Ulloa et al. title: Lipopolysaccharide induces a downregulation of adiponectin receptors in-vitro and in-vivo link: https://peerj.com/articles/1428 last-modified: 2015-11-19 description: Background. Adipose tissue contributes to the inflammatory response through production of cytokines, recruitment of macrophages and modulation of the adiponectin system. Previous studies have identified a down-regulation of adiponectin in pathologies characterised by acute (sepsis and endotoxaemia) and chronic inflammation (obesity and type-II diabetes mellitus). In this study, we investigated the hypothesis that LPS would reduce adiponectin receptor expression in a murine model of endotoxaemia and in adipoocyte and myocyte cell cultures.Methods. 25 mg/kg LPS was injected intra-peritoneally into C57BL/6J mice, equivalent volumes of normal saline were used in control animals. Mice were killed at 4 or 24 h post injection and tissues harvested. Murine adipocytes (3T3-L1) and myocytes (C2C12) were grown in standard culture, treated with LPS (0.1 µg/ml–10 µg/ml) and harvested at 4 and 24 h. RNA was extracted and qPCR was conducted according to standard protocols and relative expression was calculated.Results. After LPS treatment there was a significant reduction after 4 h in gene expression of adipo R1 in muscle and peri-renal fat and of adipo R2 in liver, peri-renal fat and abdominal wall subcutaneous fat. After 24 h, significant reductions were limited to muscle. Cell culture extracts showed varied changes with reduction in adiponectin and adipo R2 gene expression only in adipocytes.Conclusions. LPS reduced adiponectin receptor gene expression in several tissues including adipocytes. This reflects a down-regulation of this anti-inflammatory and insulin-sensitising pathway in response to LPS. The trend towards base line after 24 h in tissue depots may reflect counter-regulatory mechanisms. Adiponectin receptor regulation differs in the tissues investigated. creator: Alison Hall creator: Martin Leuwer creator: Paul Trayhurn creator: Ingeborg D. Welters uri: https://doi.org/10.7717/peerj.1428 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hall et al. title: The smell of success: the amount of prey consumed by predators determines the strength and range of cascading non-consumptive effects link: https://peerj.com/articles/1426 last-modified: 2015-11-19 description: We examined whether chemically mediated risk perception by prey and the effects of changes in prey behavior on basal resources vary as a function of the amount of prey biomass consumed by the predator. We studied these issues using a tritrophic system composed of blue crabs, Callinectes sapidus (top predator), mud crabs Panopeus herbstii (intermediate prey), and oysters Crassostrea virginica (basal resource). Working in a well characterized field environment where experiments preserve natural patterns of water flow, we found that biomass consumed by a predator determines the range, intensity and nature of prey aversive responses. Predators that consume large amounts of prey flesh more strongly diminish consumption of basal resources by prey and exert effects over a larger range (in space and time) compared to predators that have eaten less. Less well-fed predators produce weaker effects, with the consequence that behaviorally mediated cascades preferentially occur in refuge habitats. Well-fed predators affected prey behavior and increased basal resources up to distances of 1–1.5 m, whereas predators fed restricted diet evoked changes in prey only when they were extremely close, typically 50 cm or less. Thus, consumptive and non-consumptive effects may be coupled; predators that have a greater degree of predatory success will affect prey traits more strongly and non-consumptive and consumptive effects may fluctuate in tandem, with some lag. Moreover, differences among predators in their degree of prey capture will create spatial and temporal variance in risk cue availability in the absence of underlying environmental effects. creator: Marc Weissburg creator: Jeffrey Beauvais uri: https://doi.org/10.7717/peerj.1426 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Weissburg and Beauvais title: Spintharus flavidus in the Caribbean—a 30 million year biogeographical history and radiation of a ‘widespread species’ link: https://peerj.com/articles/1422 last-modified: 2015-11-19 description: The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species,’ presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spider Spintharus flavidus Hentz, 1850 (Theridiidae) is one of two described Spintharus species and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis, Spintharus “flavidus” predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by known S. flavidus biology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis of S. flavidus with the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others are single island endemics. While limited taxon sampling, with a single specimen from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum, S. “flavidus” is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis. creator: Austin Dziki creator: Greta J. Binford creator: Jonathan A. Coddington creator: Ingi Agnarsson uri: https://doi.org/10.7717/peerj.1422 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Dziki et al. title: Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data link: https://peerj.com/articles/1419 last-modified: 2015-11-19 description: Motivation. Alternative splicing events (ASEs) are prevalent in the transcriptome of eukaryotic species and are known to influence many biological phenomena. The identification and quantification of these events are crucial for a better understanding of biological processes. Next-generation DNA sequencing technologies have allowed deep characterization of transcriptomes and made it possible to address these issues. ASEs analysis, however, represents a challenging task especially when many different samples need to be compared. Some popular tools for the analysis of ASEs are known to report thousands of events without annotations and/or graphical representations. A new tool for the identification and visualization of ASEs is here described, which can be used by biologists without a solid bioinformatics background.Results. A software suite named Splicing Express was created to perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms. Its major goal is to serve the needs of biomedical researchers who do not have bioinformatics skills. Splicing Express performs automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. The identification of ASEs is done by a known algorithm previously implemented in another tool named Splooce. As a final result, Splicing Express creates a set of HTML files composed of graphics and tables designed to describe the expression profile of ASEs among all analyzed samples. By using RNA-Seq data from the Illumina Human Body Map and the Rat Body Map, we show that Splicing Express is able to perform all tasks in a straightforward way, identifying well-known specific events.Availability and Implementation.Splicing Express is written in Perl and is suitable to run only in UNIX-like systems. More details can be found at: http://www.bioinformatics-brazil.org/splicingexpress. creator: Jose E. Kroll creator: Jihoon Kim creator: Lucila Ohno-Machado creator: Sandro J. de Souza uri: https://doi.org/10.7717/peerj.1419 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kroll et al. title: Rapid drop in the reproduction number during the Ebola outbreak in the Democratic Republic of Congo link: https://peerj.com/articles/1418 last-modified: 2015-11-19 description: The Democratic Republic of Congo (DRC) experienced a confined rural outbreak of Ebola virus disease (EVD) with 69 reported cases from July to October 2014. Understanding the transmission dynamics during the outbreak can provide important information for anticipating and controlling future EVD epidemics. I fitted an EVD transmission model to previously published data of this outbreak and estimated the basic reproduction number R0 = 5.2 (95% CI [4.0–6.7]). The model suggests that the net reproduction number Rt fell below unity 28 days (95% CI [25–34] days) after the onset of symptoms in the index case. This study adds to previous epidemiological descriptions of the 2014 EVD outbreak in DRC, and is consistent with the notion that a rapid implementation of control interventions helped reduce further spread. creator: Christian L. Althaus uri: https://doi.org/10.7717/peerj.1418 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Althaus title: Tools for quantitative form description; an evaluation of different software packages for semi-landmark analysis link: https://peerj.com/articles/1417 last-modified: 2015-11-19 description: The challenging complexity of biological structures has led to the development of several methods for quantitative analyses of form. Bones are shaped by the interaction of historical (phylogenetic), structural, and functional constrains. Consequently, bone shape has been investigated intensively in an evolutionary context. Geometric morphometric approaches allow the description of the shape of an object in all of its biological complexity. However, when biological objects present only few anatomical landmarks, sliding semi-landmarks may provide good descriptors of shape. The sliding procedure, mandatory for sliding semi-landmarks, requires several steps that may be time-consuming. We here compare the time required by two different software packages (‘Edgewarp’ and ‘Morpho’) for the same sliding task, and investigate potential differences in the results and biological interpretation. ‘Morpho’ is much faster than ‘Edgewarp,’ notably as a result of the greater computational power of the ‘Morpho’ software routines and the complexity of the ‘Edgewarp’ workflow. Morphospaces obtained using both software packages are similar and provide a consistent description of the biological variability. The principal differences between the two software packages are observed in areas characterized by abrupt changes in the bone topography. In summary, both software packages perform equally well in terms of the description of biological structures, yet differ in the simplicity of the workflow and time needed to perform the analyses. creator: Léo Botton-Divet creator: Alexandra Houssaye creator: Anthony Herrel creator: Anne-Claire Fabre creator: Raphael Cornette uri: https://doi.org/10.7717/peerj.1417 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Botton-Divet et al. title: Testing the enemy release hypothesis in a native insect species with an expanding range link: https://peerj.com/articles/1415 last-modified: 2015-11-19 description: The enemy release hypothesis (ERH) predicts that the spread of (invasive) species will be facilitated by release from their enemies as they occupy new areas. However, the ERH is rarely tested on native (non-invasive, long established) species with expanding or shifting ranges. I tested the ERH for a native damselfly (Enallagma clausum) whose range has recently expanded in western Canada, with respect to its water mite and gregarine parasites. Parasitism levels (prevalence and intensity) were also compared between E. clausum and a closely related species, Enallagma boreale, which has long been established in the study region and whose range is not shifting. A total of 1,150 damselflies were collected at three ‘old’ sites for E. clausum in Saskatchewan, and three ‘new’ sites in Alberta. A little more than a quarter of the damselflies collected were parasitized with, on average, 18 water mite individuals, and 20% were parasitized by, on average, 10 gregarine individuals. I assessed whether the differences between levels of infection (prevalence and intensity) were due to site type or host species. The ERH was not supported: Enallagma clausum has higher or the same levels of parasitism in new sites than old sites. However, E. boreale seems to be benefitting from the recent range expansion of a native, closely related species through ecological release from its parasites because the parasites may be choosing to infest the novel, potentially naïve, host instead of the well-established host. creator: Julia J. Mlynarek uri: https://doi.org/10.7717/peerj.1415 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Mlynarek title: A new threat to bees? Entomopathogenic nematodes used in biological pest control cause rapid mortality in Bombus terrestris link: https://peerj.com/articles/1413 last-modified: 2015-11-19 description: There is currently a great deal of concern about population declines in pollinating insects. Many potential threats have been identified which may adversely affect the behaviour and health of both honey bees and bumble bees: these include pesticide exposure, and parasites and pathogens. Whether biological pest control agents adversely affect bees has been much less well studied: it is generally assumed that biological agents are safer for wildlife than chemical pesticides. The aim of this study was to test whether entomopathogenic nematodes sold as biological pest control products could potentially have adverse effects on the bumble bee Bombus terrestris. One product was a broad spectrum pest control agent containing both Heterorhabditis sp. and Steinernema sp., the other product was specifically for weevil control and contained only Steinernema kraussei. Both nematode products caused ≥80% mortality within the 96 h test period when bees were exposed to soil containing entomopathogenic nematodes at the recommended field concentration of 50 nematodes per cm2 soil. Of particular concern is the fact that nematodes from the broad spectrum product could proliferate in the carcasses of dead bees, and therefore potentially infect a whole bee colony or spread to the wider environment. creator: Alexandrea Dutka creator: Alison McNulty creator: Sally M. Williamson uri: https://doi.org/10.7717/peerj.1413 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Dutka et al. title: Trait correlates of distribution trends in the Odonata of Britain and Ireland link: https://peerj.com/articles/1410 last-modified: 2015-11-19 description: A major challenge in ecology is understanding why certain species persist, while others decline, in response to environmental change. Trait-based comparative analyses are useful in this regard as they can help identify the key drivers of decline, and highlight traits that promote resistance to change. Despite their popularity trait-based comparative analyses tend to focus on explaining variation in range shift and extinction risk, seldom being applied to actual measures of species decline. Furthermore they have tended to be taxonomically restricted to birds, mammals, plants and butterflies. Here we utilise a novel approach to estimate occurrence trends for the Odonata in Britain and Ireland, and examine trait correlates of these trends using a recently available trait dataset. We found the dragonfly fauna in Britain and Ireland has undergone considerable change between 1980 and 2012, with 22 and 53% of species declining and increasing, respectively. Distribution region, habitat specialism and range size were the key traits associated with these trends, where habitat generalists that occupy southern Britain tend to have increased in comparison to the declining narrow-ranged specialist species. In combination with previous evidence, we conclude that the lower trend estimates for the narrow-ranged specialists could be a sign of biotic homogenization with ecological specialists being replaced by warm-adapted generalists. creator: Gary D. Powney creator: Steve S.A. Cham creator: Dave Smallshire creator: Nick J.B. Isaac uri: https://doi.org/10.7717/peerj.1410 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Powney et al. title: Variation in partner benefits in a shrimp—sea anemone symbiosis link: https://peerj.com/articles/1409 last-modified: 2015-11-19 description: Symbiotic interactions, where two species occur in close physical proximity for the majority of the participants’ lifespans, may constrain the fitness of one or both of the participants. Host choice could result in lineage divergence in symbionts if fitness benefits vary across the interaction with hosts. Symbiotic interactions are common in the marine environment, particularly in the most diverse marine ecosystems: coral reefs. However, the variation in symbiotic interactions that may drive diversification is poorly understood in marine systems. We measured the fecundity of the symbiotic shrimp Periclimenes yucatanicus on two anemone hosts on coral reefs in Panama, and found that while fecundity varies among host species, this variation is explained largely by host size, not species. This suggests that shrimp on larger hosts may have higher fitness regardless of host species, which in turn could drive selection for host choice, a proposed driver of diversification in this group. creator: C. Seabird McKeon creator: James L. O’Donnell uri: https://doi.org/10.7717/peerj.1409 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McKeon and O’Donnell title: Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription link: https://peerj.com/articles/1403 last-modified: 2015-11-19 description: Hydrozoans display the most morphological diversity within the phylum Cnidaria. While recent molecular studies have provided some insights into their evolutionary history, sister group relationships remain mostly unresolved, particularly at mid-taxonomic levels. Specifically, within Hydroidolina, the most speciose hydrozoan subclass, the relationships and sometimes integrity of orders are highly unsettled. Here we obtained the near complete mitochondrial sequence of twenty-six hydroidolinan hydrozoan species from a range of sources (DNA and RNA-seq data, long-range PCR). Our analyses confirm previous inference of the evolution of mtDNA in Hydrozoa while introducing a novel genome organization. Using RNA-seq data, we propose a mechanism for the expression of mitochondrial mRNA in Hydroidolina that can be extrapolated to the other medusozoan taxa. Phylogenetic analyses using the full set of mitochondrial gene sequences provide some insights into the order-level relationships within Hydroidolina, including siphonophores as the first diverging clade, a well-supported clade comprised of Leptothecata-Filifera III–IV, and a second clade comprised of Aplanulata-Capitata s.s.-Filifera I–II. Finally, we describe our relatively inexpensive and accessible multiplexing strategy to sequence long-range PCR amplicons that can be adapted to most high-throughput sequencing platforms. creator: Ehsan Kayal creator: Bastian Bentlage creator: Paulyn Cartwright creator: Angel A. Yanagihara creator: Dhugal J. Lindsay creator: Russell R. Hopcroft creator: Allen G. Collins uri: https://doi.org/10.7717/peerj.1403 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Analysis of structural relationship among the occupational dysfunction on the psychological problem in healthcare workers: a study using structural equation modeling link: https://peerj.com/articles/1389 last-modified: 2015-11-19 description: Purpose. The purpose of this study is to demonstrate the hypothetical model based on structural relationship with the occupational dysfunction on psychological problems (stress response, burnout syndrome, and depression) in healthcare workers.Method. Three cross sectional studies were conducted to assess the following relations: (1) occupational dysfunction on stress response (n = 468), (2) occupational dysfunction on burnout syndrome (n = 1,142), and (3) occupational dysfunction on depression (n = 687). Personal characteristics were collected through a questionnaire (such as age, gender, and job category, opportunities for refreshment, time spent on leisure activities, and work relationships) as well as the Classification and Assessment of Occupational Dysfunction (CAOD). Furthermore, study 1 included the Stress Response Scale-18 (SRS-18), study 2 used the Japanese Burnout Scale (JBS), and study 3 employed the Center for Epidemiological Studies Depression Scale (CES-D). The Kolmogorov–Smirnov test, confirmatory factor analysis (CFA), exploratory factor analysis (EFA), and path analysis of structural equation modeling (SEM) analysis were used in all of the studies. EFA and CFA were used to measure structural validity of four assessments; CAOD, SRS-18, JBS, and CES-D. For examination of a potential covariate, we assessed the correlation of the total and factor score of CAOD and personal factors in all studies. Moreover, direct and indirect effects of occupational dysfunction on stress response (Study 1), burnout syndrome (Study 2), and depression (Study 3) were also analyzed.Results. In study 1, CAOD had 16 items and 4 factors. In Study 2 and 3, CAOD had 16 items and 5 factors. SRS-18 had 18 items and 3 factors, JBS had 17 items and 3 factors, and CES-D had 20 items and 4 factors. All studies found that there were significant correlations between the CAOD total score and the personal factor that included opportunities for refreshment, time spent on leisure activities, and work relationships (p < 0.01). The hypothesis model results suggest that the classification of occupational dysfunction had good fit on the stress response (RMSEA = 0.061, CFI = 0.947, and TLI = 0.943), burnout syndrome (RMSEA = 0.076, CFI = 0.919, and TLI = 0.913), and depression (RMSEA = 0.060, CFI = 0.922, TLI = 0.917). Moreover, the detected covariates include opportunities for refreshment, time spent on leisure activities, and work relationships on occupational dysfunction.Conclusion. Our findings indicate that psychological problems are associated with occupational dysfunction in healthcare workers. Reduction of occupational dysfunction might be a strategy of better preventive occupational therapies for healthcare workers with psychological problems. However, longitudinal studies will be needed to determine a causal relationship. creator: Mutsumi Teraoka creator: Makoto Kyougoku uri: https://doi.org/10.7717/peerj.1389 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Teraoka and Kyougoku title: An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64 link: https://peerj.com/articles/1401 last-modified: 2015-11-17 description: In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because of too specific computing platforms. This effect, known as ‘workflow decay’, can be diminished by using a standardized informatic infrastructure. Thus, we compiled an integrated platform, which contains ready-to-use tools and workflows for mass spectrometry data analysis. Apart from general unit operations, such as peak picking and identification of proteins and metabolites, we put a strong emphasis on the statistical validation of results and Data Mining. MASSyPup64 includes e.g., the OpenMS/TOPPAS framework, the Trans-Proteomic-Pipeline programs, the ProteoWizard tools, X!Tandem, Comet and SpiderMass. The statistical computing language R is installed with packages for MS data analyses, such as XCMS/metaXCMS and MetabR. The R package Rattle provides a user-friendly access to multiple Data Mining methods. Further, we added the non-conventional spreadsheet program teapot for editing large data sets and a command line tool for transposing large matrices. Individual programs, console commands and modules can be integrated using the Workflow Management System (WMS) taverna. We explain the useful combination of the tools by practical examples: (1) A workflow for protein identification and validation, with subsequent Association Analysis of peptides, (2) Cluster analysis and Data Mining in targeted Metabolomics, and (3) Raw data processing, Data Mining and identification of metabolites in untargeted Metabolomics. Association Analyses reveal relationships between variables across different sample sets. We present its application for finding co-occurring peptides, which can be used for target proteomics, the discovery of alternative biomarkers and protein–protein interactions. Data Mining derived models displayed a higher robustness and accuracy for classifying sample groups in targeted Metabolomics than cluster analyses. Random Forest models do not only provide predictive models, which can be deployed for new data sets, but also the variable importance. We demonstrate that the later is especially useful for tracking down significant signals and affected pathways in untargeted Metabolomics. Thus, Random Forest modeling supports the unbiased search for relevant biological features in Metabolomics. Our results clearly manifest the importance of Data Mining methods to disclose non-obvious information in biological mass spectrometry . The application of a Workflow Management System and the integration of all required programs and data in a consistent platform makes the presented data analyses strategies reproducible for non-expert users. The simple remastering process and the Open Source licenses of MASSyPup64 (http://www.bioprocess.org/massypup/) enable the continuous improvement of the system. creator: Robert Winkler uri: https://doi.org/10.7717/peerj.1401 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Winkler title: The apparent permeabilities of Caco-2 cells to marketed drugs: magnitude, and independence from both biophysical properties and endogenite similarities link: https://peerj.com/articles/1405 last-modified: 2015-11-17 description: We bring together fifteen, nonredundant, tabulated collections (amounting to 696 separate measurements) of the apparent permeability (Papp) of Caco-2 cells to marketed drugs. While in some cases there are some significant interlaboratory disparities, most are quite minor. Most drugs are not especially permeable through Caco-2 cells, with the median Papp value being some 16 ⋅ 10−6 cm s−1. This value is considerably lower than those (1,310 and 230 ⋅ 10−6 cm s−1) recently used in some simulations that purported to show that Papp values were too great to be transporter-mediated only. While these values are outliers, all values, and especially the comparatively low values normally observed, are entirely consistent with transporter-only mediated uptake, with no need to invoke phospholipid bilayer diffusion. The apparent permeability of Caco-2 cells to marketed drugs is poorly correlated with either simple biophysical properties, the extent of molecular similarity to endogenous metabolites (endogenites), or any specific substructural properties. In particular, the octanol:water partition coefficient, logP, shows negligible correlation with Caco-2 permeability. The data are best explained on the basis that most drugs enter (and exit) Caco-2 cells via a multiplicity of transporters of comparatively weak specificity. creator: Steve O’Hagan creator: Douglas B. Kell uri: https://doi.org/10.7717/peerj.1405 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 O’Hagan and Kell title: Ecological drivers and habitat associations of estuarine bivalves link: https://peerj.com/articles/1348 last-modified: 2015-11-12 description: Community composition of the infaunal bivalve fauna of the St. Lucie Estuary and southern Indian River Lagoon, eastern Florida was sampled quarterly for 10 years as part of a long-term benthic monitoring program. A total of 38,514 bivalves of 137 taxa were collected and identified. We utilized this data, along with sediment samples and environmental measurements gathered concurrently, to assess the community composition, distribution, and ecological drivers of the infaunal bivalves of this estuary system. Salinity had the strongest influence on bivalve assemblage across the 15 sites, superseding the influences of sediment type, water turbidity, temperature and other environmental parameters. The greatest diversity was found in higher salinity euhaline sites, while the greatest abundance of individual bivalves was found in medium salinity mixohaline sites, the lowest diversity and abundances were found in the low salinity oligohaline sites, demonstrating a strong positive association between salinity and diversity/abundance. Water management decisions for the estuary should incorporate understanding of the role of salinity on bivalve diversity, abundance, and ecosystem function. creator: C. Seabird McKeon creator: Björn G. Tunberg creator: Cora A. Johnston creator: Daniel J. Barshis uri: https://doi.org/10.7717/peerj.1348 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McKeon et al. title: New craniodental remains of Wakaleo alcootaensis (Diprotodontia: Thylacoleonidae) a carnivorous marsupial from the late Miocene Alcoota Local Fauna of the Northern Territory, Australia link: https://peerj.com/articles/1408 last-modified: 2015-11-12 description: New jaws and teeth referable to the rare thylacoleonid marsupial Wakaleo alcootaensis are figured and described. The species is the geologically youngest known member of the genus and is only known from the late Miocene Alcoota Local Fauna of the Northern Territory, Australia. A revised diagnosis of the species is presented which is found to be morphologically distinct from its congeners. W. alcootaensis can be distinguished from other species of Wakaleo by its greater size, deeply recessed masseteric fossa, more steeply angled I1, loss of P2, greater P3 to M1 ratio and loss of M3. Several characters of W. alcootaensis, including the increase in size, steeply angled I1, increase of the relative size of P3, and reduction of the molar row are present in at least some species of Thylacoleo. Phylogenetic analysis suggests that these character states are convergences and that there was parallel evolution in these two thylacoleonid lineages. creator: Adam M. Yates uri: https://doi.org/10.7717/peerj.1408 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Yates title: Demographic and genetic factors in the recovery or demise of ex situ populations following a severe bottleneck in fifteen species of Hawaiian tree snails link: https://peerj.com/articles/1406 last-modified: 2015-11-12 description: Wild populations of endangered Hawaiian tree snails have declined precipitously over the last century due to introduced predators and other human impacts. Life history traits, such as very low fecundity (<5 offspring per year across taxa) and maturity at approximately four years of age have made recovery difficult. Conservation efforts such as in situ predator-free enclosures may increase survival to maturity by protecting offspring from predation, but no long-term data existed prior to this study demonstrating the demographic and genetic parameters necessary to maintain populations within those enclosures. We evaluated over 20 years of evidence for the dynamics of survival and extinction in captive ex situ populations of Hawaiian tree snails established from wild-collected individuals. From 1991 to 2006, small numbers of snails (<15) from fifteen species were collected from the wild to initiate captive-reared populations as a hedge against extinction. This small number of founders resulted in a severe bottleneck in each of the captive-reared populations. We identified key demographic parameters that predicted population recovery from this bottleneck. Species with captive populations that produced between two and four offspring per adult per year and had 20–50% of those offspring survive to maturity recovered to numbers above 100 individuals, and maintained viable populations following a decline that occurred between 2009 and 2014. Those populations that had less than two offspring per adult per year and less than 20% survival to maturity did not reach 100 individuals in captivity, and many of these populations died out during the recent decline. We suggest that small reductions in fitness may contribute to extirpation in taxa with inherently low fecundity, by keeping populations below a threshold number essential to long-term recovery. Future ex situ populations should be founded with no less than 15 adults, and maintained in conditions closely approximating the temperature and humidity of source locations to optimize fitness. Permanent translocations of wild populations for conservation purposes will be more likely to succeed with greater than 100 adults, and should be limited to locations with a similar climate to source locations. creator: Melissa R. Price creator: David Sischo creator: Mark-Anthony Pascua creator: Michael G. Hadfield uri: https://doi.org/10.7717/peerj.1406 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Price et al. title: Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter link: https://peerj.com/articles/1400 last-modified: 2015-11-12 description: A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain CoronadoT falls within the Erythrobacteraceae family and the genus Porphyrobacter based on 16S rRNA phylogenetic analysis. This strain has Q-10 as the predominant respiratory lipoquinone, as do other members of the family. The fatty acid profile of this strain is similar to other Porphyrobacter, however CoronadoT contains predominately C18:1ω7cis and C16:0, a high percentage of the latter not being observed in any other Erythrobacteraceae. This strain is catalase-positive and oxidase-negative, can grow from 4 to 28 °C, at NaCl concentrations 0.1–1.5%, and at pH 6.0–8.0. On the basis of phenotypic and phylogenetic data presented in this study, strain CoronadoT represents a novel species in the Porphyrobacter genus for which the name Porphyrobacter mercurialis sp. nov. is proposed; the type strain is CoronadoT (=DSMZ 29971, =LMG 28700). creator: David A. Coil creator: Jennifer C. Flanagan creator: Andrew Stump creator: Alexandra Alexiev creator: Jenna M. Lang creator: Jonathan A. Eisen uri: https://doi.org/10.7717/peerj.1400 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Coil et al. title: Factors affecting the identification of individual mountain bongo antelope link: https://peerj.com/articles/1303 last-modified: 2015-11-12 description: The recognition of individuals forms the basis of many endangered species monitoring protocols. This process typically relies on manual recognition techniques. This study aimed to calculate a measure of the error rates inherent within the manual technique and also sought to identify visual traits that aid identification, using the critically endangered mountain bongo, Tragelaphus eurycerus isaaci, as a model system. Identification accuracy was assessed with a matching task that required same/different decisions to side-by-side pairings of individual bongos. Error rates were lowest when only the flanks of bongos were shown, suggesting that the inclusion of other visual traits confounded accuracy. Accuracy was also higher for photographs of captive animals than camera-trap images, and in observers experienced in working with mountain bongos, than those unfamiliar with the sub-species. These results suggest that the removal of non-essential morphological traits from photographs of bongos, the use of high-quality images, and relevant expertise all help increase identification accuracy. Finally, given the rise in automated identification and the use of citizen science, something our results would suggest is applicable within the context of the mountain bongo, this study provides a framework for assessing their accuracy in individual as well as species identification. creator: Gwili E.M. Gibbon creator: Markus Bindemann creator: David L. Roberts uri: https://doi.org/10.7717/peerj.1303 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gibbon et al. title: Can we measure beauty? Computational evaluation of coral reef aesthetics link: https://peerj.com/articles/1390 last-modified: 2015-11-10 description: The natural beauty of coral reefs attracts millions of tourists worldwide resulting in substantial revenues for the adjoining economies. Although their visual appearance is a pivotal factor attracting humans to coral reefs current monitoring protocols exclusively target biogeochemical parameters, neglecting changes in their aesthetic appearance. Here we introduce a standardized computational approach to assess coral reef environments based on 109 visual features designed to evaluate the aesthetic appearance of art. The main feature groups include color intensity and diversity of the image, relative size, color, and distribution of discernable objects within the image, and texture. Specific coral reef aesthetic values combining all 109 features were calibrated against an established biogeochemical assessment (NCEAS) using machine learning algorithms. These values were generated for ∼2,100 random photographic images collected from 9 coral reef locations exposed to varying levels of anthropogenic influence across 2 ocean systems. Aesthetic values proved accurate predictors of the NCEAS scores (root mean square error < 5 for N ≥ 3) and significantly correlated to microbial abundance at each site. This shows that mathematical approaches designed to assess the aesthetic appearance of photographic images can be used as an inexpensive monitoring tool for coral reef ecosystems. It further suggests that human perception of aesthetics is not purely subjective but influenced by inherent reactions towards measurable visual cues. By quantifying aesthetic features of coral reef systems this method provides a cost efficient monitoring tool that targets one of the most important socioeconomic values of coral reefs directly tied to revenue for its local population. creator: Andreas F. Haas creator: Marine Guibert creator: Anja Foerschner creator: Tim Co creator: Sandi Calhoun creator: Emma George creator: Mark Hatay creator: Elizabeth Dinsdale creator: Stuart A. Sandin creator: Jennifer E. Smith creator: Mark J.A. Vermeij creator: Ben Felts creator: Phillip Dustan creator: Peter Salamon creator: Forest Rohwer uri: https://doi.org/10.7717/peerj.1390 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Haas et al. title: Effects of sex and site on amino acid metabolism enzyme gene expression and activity in rat white adipose tissue link: https://peerj.com/articles/1399 last-modified: 2015-11-10 description: Background and Objectives. White adipose tissue (WAT) shows marked sex- and diet-dependent differences. However, our metabolic knowledge of WAT, especially on amino acid metabolism, is considerably limited. In the present study, we compared the influence of sex on the amino acid metabolism profile of the four main WAT sites, focused on the paths related to ammonium handling and the urea cycle, as a way to estimate the extent of WAT implication on body amino-nitrogen metabolism.Experimental Design. Adult female and male rats were maintained, undisturbed, under standard conditions for one month. After killing them under isoflurane anesthesia. WAT sites were dissected and weighed. Subcutaneous, perigonadal, retroperitoneal and mesenteric WAT were analyzed for amino acid metabolism gene expression and enzyme activities.Results. There was a considerable stability of the urea cycle activities and expressions, irrespective of sex, and with only limited influence of site. Urea cycle was more resilient to change than other site-specialized metabolic pathways. The control of WAT urea cycle was probably related to the provision of arginine/citrulline, as deduced from the enzyme activity profiles. These data support a generalized role of WAT in overall amino-N handling. In contrast, sex markedly affected WAT ammonium-centered amino acid metabolism in a site-related way, with relatively higher emphasis in males’ subcutaneous WAT.Conclusions. We found that WAT has an active amino acid metabolism. Its gene expressions were lower than those of glucose-lipid interactions, but the differences were quantitatively less important than usually reported. The effects of sex on urea cycle enzymes expression and activity were limited, in contrast with the wider variations observed in other metabolic pathways. The results agree with a centralized control of urea cycle operation affecting the adipose organ as a whole. creator: Sofía Arriarán creator: Silvia Agnelli creator: Xavier Remesar creator: José Antonio Fernández-López creator: Marià Alemany uri: https://doi.org/10.7717/peerj.1399 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Arriarán et al. title: Homeotic transformations and number changes in the vertebral column of Triturus newts link: https://peerj.com/articles/1397 last-modified: 2015-11-10 description: We explored intraspecific variation in vertebral formulae, more specifically the variation in the number of thoracic vertebrae and frequencies of transitional sacral vertebrae in Triturus newts (Caudata: Salamandridae). Within salamandrid salamanders this monophyletic group shows the highest disparity in the number of thoracic vertebrae and considerable intraspecific variation in the number of thoracic vertebrae. Triturus species also differ in their ecological preferences, from predominantly terrestrial to largely aquatic. Following Geoffroy St. Hilaire’s and Darwin’s rule which states that structures with a large number of serially homologous repetitive elements are more variable than structures with smaller numbers, we hypothesized that the variation in vertebral formulae increases in more elongated species with a larger number of thoracic vertebrae. We furthermore hypothesized that the frequency of transitional vertebrae will be correlated with the variation in the number of thoracic vertebrae within the species. We also investigated potential effects of species hybridization on the vertebral formula. The proportion of individuals with a number of thoracic vertebrae different from the modal number and the range of variation in number of vertebrae significantly increased in species with a larger number of thoracic vertebrae. Contrary to our expectation, the frequencies of transitional vertebrae were not correlated with frequencies of change in the complete vertebrae number. The frequency of transitional sacral vertebra in hybrids did not significantly differ from that of the parental species. Such a pattern could be a result of selection pressure against transitional vertebrae and/or a bias towards the development of full vertebrae numbers. Although our data indicate relaxed selection for vertebral count changes in more elongated, aquatic species, more data on different selective pressures in species with different numbers of vertebrae in the two contrasting, terrestrial and aquatic environments are needed to test for causality. creator: Maja Slijepčević creator: Frietson Galis creator: Jan W. Arntzen creator: Ana Ivanović uri: https://doi.org/10.7717/peerj.1397 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Slijepčević et al. title: Current nutrition promotion, beliefs and barriers among cancer nurses in Australia and New Zealand link: https://peerj.com/articles/1396 last-modified: 2015-11-10 description: Rationale. Many cancer patients and survivors do not meet nutritional and physical activity guidelines, thus healthier eating and greater levels of physical activity could have considerable benefits for these individuals. While research has investigated cancer survivors’ perspective on their challenges in meeting the nutrition and physical guidelines, little research has examined how health professionals may assist their patients meet these guidelines. Cancer nurses are ideally placed to promote healthy behaviours to their patients, especially if access to dieticians or dietary resources is limited. However, little is known about cancer nurses’ healthy eating promotion practices to their patients. The primary aim of this study was to examine current healthy eating promotion practices, beliefs and barriers of cancer nurses in Australia and New Zealand. A secondary aim was to gain insight into whether these practices, beliefs and barriers were influenced by the nurses’ hospital or years of work experience.Patients and Methods. An online questionnaire was used to obtain data. Sub-group cancer nurse comparisons were performed on hospital location (metropolitan vs regional and rural) and years of experience (<25 or ≥25 years) using ANOVA and chi square analysis for continuous and categorical data respectively.Results. A total of 123 Australasian cancer nurses responded to the survey. Cancer nurses believed they were often the major provider of nutritional advice to their cancer patients (32.5%), a value marginally less than dieticians (35.9%) but substantially higher than oncologists (3.3%). The majority promoted healthy eating prior (62.6%), during (74.8%) and post treatment (64.2%). Most cancer nurses felt that healthy eating had positive effects on the cancer patients’ quality of life (85.4%), weight management (82.9%), mental health (80.5%), activities of daily living (79.7%) and risk of other chronic diseases (79.7%), although only 75.5% agreed or strongly agreed that this is due to a strong evidence base. Lack of time (25.8%), adequate support structures (17.3%) nutrition expertise (12.2%) were cited by the cancer nurses as the most common barriers to promoting healthy eating to their patients. Comparisons based on their hospital location and years of experience, revealed very few significant differences, indicating that cancer nurses’ healthy eating promotion practices, beliefs and barriers were largely unaffected by hospital location or years of experience.Conclusion. Australasian cancer nurses have favourable attitudes towards promoting healthy eating to their cancer patients across multiple treatment stages and believe that healthy eating has many benefits for their patients. Unfortunately, several barriers to healthy eating promotion were reported. If these barriers can be overcome, nurses may be able to work more effectively with dieticians to improve the outcomes for cancer patients. creator: Petra G. Puhringer creator: Alicia Olsen creator: Mike Climstein creator: Sally Sargeant creator: Lynnette M. Jones creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.1396 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Puhringer et al. title: Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment link: https://peerj.com/articles/1395 last-modified: 2015-11-10 description: Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates’ phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes. creator: Michael W. Henson creator: Jorge W. Santo Domingo creator: Peter S. Kourtev creator: Roderick V. Jensen creator: James A. Dunn creator: Deric R. Learman uri: https://doi.org/10.7717/peerj.1395 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Henson et al. title: Detection of diabetic macular oedema: validation of optical coherence tomography using both foveal thickness and intraretinal fluid link: https://peerj.com/articles/1394 last-modified: 2015-11-10 description: No studies have yet evaluated jointly central foveal thickness (CFT) and the presence of intraretinal fluid (PIF) to diagnose diabetic macular oedema (DMO) using optic coherence tomography (OCT). We performed a cross-sectional observational study to validate OCT for the diagnosis of DMO using both CFT and PIF assessed by OCT (3D OCT-1 Maestro). A sample of 277 eyes from primary care diabetic patients was assessed in a Spanish region in 2014. Outcome: DMO diagnosed by stereoscopic mydriatic fundoscopy. OCT was used to measure CFT and PIF. A binary logistic regression model was constructed to predict the outcome using CFT and PIF. The area under the ROC curve (AUC) of the model was calculated and non-linear equations used to determine which CFT values had a high probability of the outcome (positive test), distinguishing between the presence or absence of PIF. Calculations were made of the sensitivity, specificity, and the positive (PLR) and negative (NLR) likelihood ratios. The model was validated using bootstrapping methodology. A total of 37 eyes had DMO. AUC: 0.88. Positive test: CFT ≥90 µm plus PIF (≥310 µm if no PIF). Clinical parameters: sensitivity, 0.83; specificity, 0.89; PLR, 7.34; NLR, 0.19. The parameters in the validation were similar. In conclusion, combining PIF and CFT provided a tool to very precisely discriminate the presence of DMO. Similar studies are needed to provide greater scientific evidence for the use of PIF in the diagnosis of DMO. creator: Carmen Hernández-Martínez creator: Antonio Palazón-Bru creator: Cesar Azrak creator: Aída Navarro-Navarro creator: Manuel Vicente Baeza-Díaz creator: José Juan Martínez-Toldos creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.1394 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hernández-Martínez et al. title: Ketoreductase TpdE from Rhodococcus jostii TMP1: characterization and application in the synthesis of chiral alcohols link: https://peerj.com/articles/1387 last-modified: 2015-11-10 description: Background. Production of highly pure enantiomers of vicinal diols is desirable, but difficult to achieve. Enantiomerically pure diols and acyloins are valuable bulk chemicals, promising synthones and potential building blocks for chiral polymers. Enzymatic reduction of ketones is a useful technique for the synthesis of the desired enantiomeric alcohols. Here, we report on the characterization of a ketoreductase TpdE from Rhodococcus jostii TMP1 that is a prospective tool for the synthesis of such compounds.Results. In this study, NADPH-dependent short-chain dehydrogenase/reductase TpdE from Rhodococcus jostii TMP1 was characterized. The enzyme exhibited broad substrate specificity towards aliphatic 2,3-diketones, butan-3-one-2-yl alkanoates, as well as acetoin and its acylated derivatives. TpdE stereospecifically reduced α-diketones to the corresponding diols. The GC-MS analysis of the reduction products of 2,3- and 3,4-diketones indicated that TpdE is capable of reducing both keto groups in its substrate leading to the formation of two new chiral atoms in the product molecule. Bioconversions of diketones to corresponding diols occurred using either purified enzyme or a whole-cell Escherichia coli BL21 (DE3) biocatalyst harbouring recombinant TpdE. The optimum temperature and pH were determined to be 30–35 °C and 7.5, respectively.Conclusions. The broad substrate specificity and stereoselectivity of TpdE from Rhodococcus jostii TMP1 make it a promising biocatalyst for the production of enantiomerically pure diols that are difficult to obtain by chemical routes. creator: Jonita Stankevičiūtė creator: Simonas Kutanovas creator: Rasa Rutkienė creator: Daiva Tauraitė creator: Romualdas Striela creator: Rolandas Meškys uri: https://doi.org/10.7717/peerj.1387 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Stankevičiūtė et al. title: Chemotaxis and degradation of organophosphate compound by a novel moderately thermo-halo tolerant Pseudomonas sp. strain BUR11: evidence for possible existence of two pathways for degradation link: https://peerj.com/articles/1378 last-modified: 2015-11-10 description: An organophosphate (OP) degrading chemotactic bacterial strain BUR11 isolated from an agricultural field was identified as a member of Pseudomonas genus on the basis of its 16S rRNA gene sequence. The strain could utilize parathion, chlorpyrifos and their major hydrolytic intermediates as sole source of carbon for its growth and exhibited positive chemotactic response towards most of them. Optimum concentration of parathion for its growth was recorded to be 200 ppm and 62% of which was degraded within 96 h at 37 °C. Growth studies indicated the strain to be moderately thermo-halo tolerant in nature. Investigation based on identification of intermediates of parathion degradation by thin layer chromatography (TLC), high performance liquid chromatography (HPLC), gas chromatography (GC) and liquid chromatography mass spectrometry (LC-MS/MS) provided evidence for possible existence of two pathways. The first pathway proceeds via 4-nitrophenol (4-NP) while the second proceeds through formation of 4-aminoparathion (4-APar), 4-aminophenol (4-AP) and parabenzoquinone (PBQ). This is the first report of chemotaxis towards organophosphate compound by a thermo-halo tolerant bacterium. creator: Santanu Pailan creator: Pradipta Saha uri: https://doi.org/10.7717/peerj.1378 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pailan and Saha title: Lung ultrasound in the diagnosis of pneumonia in children: proposal for a new diagnostic algorithm link: https://peerj.com/articles/1374 last-modified: 2015-11-10 description: Background. Despite guideline recommendations, chest radiography (CR) for the diagnosis of community-acquired pneumonia (CAP) in children is commonly used also in mild and/or uncomplicated cases. The aim of this study is to assess the reliability of lung ultrasonography (LUS) as an alternative test in these cases and suggest a new diagnostic algorithm.Methods. We reviewed the medical records of all patients admitted to the pediatric ward from February 1, 2013 to December 31, 2014 with respiratory signs and symptoms. We selected only cases with mild/uncomplicated clinical course and in which CR and LUS were performed within 24 h of each other. The LUS was not part of the required exams recorded in medical records but performed independently. The discharge diagnosis, made only on the basis of history and physical examination, laboratory and instrumental tests, including CR (without LUS), was used as a reference test to compare CR and LUS findings.Results. Of 52 selected medical records CAP diagnosis was confirmed in 29 (55.7%). CR was positive in 25 cases, whereas LUS detected pneumonia in 28 cases. Four patients with negative CR were positive in ultrasound findings. Instead, one patient with negative LUS was positive in radiographic findings. The LUS sensitivity was 96.5% (95% CI [82.2%–99.9%]), specificity of 95.6% (95% CI [78.0%–99.9%]), positive likelihood ratio of 22.2 (95% CI [3.2–151.2]), and negative likelihood ratio of 0.04 (95% CI [0.01–0.25]) for diagnosing pneumonia.Conclusion. LUS can be considered as a valid alternative diagnostic tool of CAP in children and its use must be promoted as a first approach in accordance with our new diagnostic algorithm. creator: Giulio Iorio creator: Maria Capasso creator: Giuseppe De Luca creator: Salvatore Prisco creator: Carlo Mancusi creator: Bruno Laganà creator: Vincenzo Comune uri: https://doi.org/10.7717/peerj.1374 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Iorio et al. title: Multiphasic strain differentiation of atypical mycobacteria from elephant trunk wash link: https://peerj.com/articles/1367 last-modified: 2015-11-10 description: Background. Two non-tuberculous mycobacterial strains, UM_3 and UM_11, were isolated from the trunk wash of captive elephants in Malaysia. As they appeared to be identical phenotypes, they were investigated further by conventional and whole genome sequence-based methods of strain differentiation.Methods. Multiphasic investigations on the isolates included species identification with hsp65 PCR-sequencing, conventional biochemical tests, rapid biochemical profiling using API strips and the Biolog Phenotype Microarray analysis, protein profiling with liquid chromatography-mass spectrometry, repetitive sequence-based PCR typing and whole genome sequencing followed by phylogenomic analyses.Results. The isolates were shown to be possibly novel slow-growing schotochromogens with highly similar biological and genotypic characteristics. Both strains have a genome size of 5.2 Mbp, G+C content of 68.8%, one rRNA operon and 52 tRNAs each. They qualified for classification into the same species with their average nucleotide identity of 99.98% and tetranucleotide correlation coefficient of 0.99999. At the subspecies level, both strains showed 98.8% band similarity in the Diversilab automated repetitive sequence-based PCR typing system, 96.2% similarity in protein profiles obtained by liquid chromatography mass spectrometry, and a genomic distance that is close to zero in the phylogenomic tree constructed with conserved orthologs. Detailed epidemiological tracking revealed that the elephants shared a common habitat eight years apart, thus, strengthening the possibility of a clonal relationship between the two strains. creator: Kok-Gan Chan creator: Mun Fai Loke creator: Bee Lee Ong creator: Yan Ling Wong creator: Kar Wai Hong creator: Kian Hin Tan creator: Sargit Kaur creator: Hien Fuh Ng creator: MFA Abdul Razak creator: Yun Fong Ngeow uri: https://doi.org/10.7717/peerj.1367 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Chan et al. title: The Bulimulidae (Mollusca: Pulmonata) from the Región de Atacama, northern Chile link: https://peerj.com/articles/1383 last-modified: 2015-11-05 description: The bulimulid genus BostryxTroschel, 1847 is the most species-rich genus of land snails found in Chile, with the majority of its species found only in the northern part of the country, usually in arid coastal zones. This genus has been sparsely studied in Chile and there is little information on their distribution, diversity or ecology. Here, for the first time, a formal analysis of the diversity of bulimulids in the Región de Atacama, northern Chile, is reported. Of the seventeen species recorded for the area, most of them were efectively found in the field collections and one record was based on literature. Five taxa are described as new: Bostryx ancavilorum sp. nov., Bostryx breurei sp. nov., Bostryx calderaensis sp. nov., Bostryx ireneae sp. nov. and Bostryx valdovinosi sp. nov., and the known geographic distribution of seven species is extended. Results reveal that the Región de Atacama is the richest region in terrestrial snails in Chile, after the Juan Fernández Archipelago. All of the terrestrial molluscan species occurring in the area are endemic to Chile, most of them with restricted geographic distributions along the coastal zones, and none of them are currently protected by law. Further sampling in northern Chile will probably reveal more snail species to be discovered and described. creator: Juan Francisco Araya uri: https://doi.org/10.7717/peerj.1383 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Araya title: Overexpression of centromere protein K (CENPK) in ovarian cancer is correlated with poor patient survival and associated with predictive and prognostic relevance link: https://peerj.com/articles/1386 last-modified: 2015-11-05 description: Ovarian cancer has a poor prognosis. Most patients are diagnosed with ovarian cancer when the disease has reached an advanced stage and cure rates are generally under 30%. Hence, early diagnosis of ovarian cancer is the best means to control the disease in the long term and abate mortality. So far, cancer antigen 125 (CA125) and human epididymis protein 4 (HE4) are the gold-standard tumor markers for ovarian cancer; however, these two markers can be elevated in a number of conditions unrelated to ovarian cancer, resulting in decreased specifically and positive predictive value. Therefore, it is urgent to identify novel biomarkers with high reliability and sensitivity for ovarian cancer. In this study for the first time, we identified a member of the centromere protein (CENP) family, CENPK, which was specifically upregulated in ovarian cancer tissues and cell lines and the overexpression of which was associated with poor prognoses in patients with ovarian cancer. In addition, the presence of CENPK significantly improved the sensitivity of CA125 or HE4 for predicting clinical outcomes of ovarian cancer patients. In conclusion, we identified that CENPK was specifically upregulated in ovarian cancer cells and can be used as a novel tumor marker of ovarian cancer. creator: Yi-Chao Lee creator: Chi-Chen Huang creator: Ding-Yen Lin creator: Wen-Chang Chang creator: Kuen-Haur Lee uri: https://doi.org/10.7717/peerj.1386 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lee et al. title: Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama link: https://peerj.com/articles/1385 last-modified: 2015-11-05 description: Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama. We surveyed sponge communities at each site using belt transects and differences between two sites were compared using the following variables: (1) sponge species richness, Shannon diversity, and inverse Simpson’s diversity; (2) phylogenetic diversity; (3) taxonomic and phylogenetic beta diversity; (4) trait diversity and dissimilarity; and (5) phylogenetic and trait patterns in community structure. We observed significantly higher sponge diversity at Punta Caracol, the site most distant from human development (∼5 km). Although phylogenetic diversity was lower at Saigon Bay, the site adjacent to a large village including many houses, businesses, and an airport, the sites did not exhibit significantly different patterns of phylogenetic relatedness in species composition. However, each site had a distinct taxonomic and phylogenetic composition (beta diversity). In addition, the sponge community at Saigon included a higher relative abundance of sponges with high microbial abundance and high chlorophyll a concentration, whereas the community at Punta Caracol had a more even distribution of these traits, yielding a significant difference in functional trait diversity between sites. These results suggest that lower diversity and potentially altered community function might be associated with proximity to human populations. This study highlights the importance of evaluating functional traits and phylogenetic diversity in addition to common diversity metrics when assessing potential environmental impacts on benthic communities. creator: Cole G. Easson creator: Kenan O. Matterson creator: Christopher J. Freeman creator: Stephanie K. Archer creator: Robert W. Thacker uri: https://doi.org/10.7717/peerj.1385 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Easson et al. title: Kisspeptin receptor agonist (FTM080) increased plasma concentrations of luteinizing hormone in anestrous ewes link: https://peerj.com/articles/1382 last-modified: 2015-11-05 description: Kisspeptin receptor (KISS1R) agonists with increased half-life and similar efficacy to kisspeptin in vitro may provide beneficial applications in breeding management of many species. However, many of these agonists have not been tested in vivo. These studies were designed to test and compare the effects of a KISS1R agonist (FTM080) and kisspeptin on luteinizing hormone (LH) in vivo. In experiment 1 (pilot study), sheep were treated with FTM080 (500 pmol/kg BW) or sterile water (VEH) intravenosuly. Blood was collected every 15 min before (1 h) and after (1 h) treatment. In experiment 2, sheep were treated with KP-10 (human Metastin 45-54; 500 pmol/kg BW), one of three dosages of FTM080 (500 (FTM080:500), 2500 (FTM080:2500), or 5000 (FTM080:5000) pmol/kg BW), or VEH intravenously. Blood was collected every 15 min before (1 h) and after (4 h) treatment. In experiment 1, FTM080:500 increased (P < 0.05) plasma LH concentrations when compared to VEH. The area under the curve (AUC) of LH following FTM080:500 treatment was also increased (P < 0.05). In experiment 2, plasma LH concentrations increased (P < 0.05) following treatment with KP-10 and FTM080:5000 when compared to VEH and FTM080:500. The AUC of LH following KP-10 was greater than (P < 0.05) all other treatments and the AUC of LH following FTM080:5000 was greater than (P < 0.05) all treatments except KP-10. These data provide evidence to suggest that FTM080 stimulates the gonadotropic axis of ruminants in vivo. Any increased half-life and comparable efficacy of FTM080 to KP-10 in vitro does not appear to translate to in vivo in sheep. creator: Brian K. Whitlock creator: Joseph A. Daniel creator: Lisa L. Amelse creator: Valeria M. Tanco creator: Kelly A. Chameroy creator: F. Neal Schrick uri: https://doi.org/10.7717/peerj.1382 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Whitlock et al. title: Characterization of the salivary microbiome in patients with pancreatic cancer link: https://peerj.com/articles/1373 last-modified: 2015-11-05 description: Clinical manifestations of pancreatic cancer often do not occur until the cancer has undergone metastasis, resulting in a very low survival rate. In this study, we investigated whether salivary bacterial profiles might provide useful biomarkers for early detection of pancreatic cancer. Using high-throughput sequencing of bacterial small subunit ribosomal RNA (16S rRNA) gene, we characterized the salivary microbiota of patients with pancreatic cancer and compared them to healthy patients and patients with other diseases, including pancreatic disease, non-pancreatic digestive disease/cancer and non-digestive disease/cancer. A total of 146 patients were enrolled at the UCSD Moores Cancer Center where saliva and demographic data were collected from each patient. Of these, we analyzed the salivary microbiome of 108 patients: 8 had been diagnosed with pancreatic cancer, 78 with other diseases and 22 were classified as non-diseased (healthy) controls. Bacterial 16S rRNA sequences were amplified directly from salivary DNA extractions and subjected to high-throughput sequencing (HTS). Several bacterial genera differed in abundance in patients with pancreatic cancer. We found a significantly higher ratio of Leptotrichia to Porphyromonas in the saliva of patients with pancreatic cancer than in the saliva of healthy patients or those with other disease (Kruskal–Wallis Test; P < 0.001). Leptotrichia abundances were confirmed using real-time qPCR with Leptotrichia specific primers. Similar to previous studies, we found lower relative abundances of Neisseria and Aggregatibacter in the saliva of pancreatic cancer patients, though these results were not significant at the P < 0.05 level (K–W Test; P = 0.07 and P = 0.09 respectively). However, the relative abundances of other previously identified bacterial biomarkers, e.g., Streptococcus mitis and Granulicatella adiacens, were not significantly different in the saliva of pancreatic cancer patients. Overall, this study supports the hypothesis that bacteria abundance profiles in saliva are useful biomarkers for pancreatic cancer though much larger patient studies are needed to verify their predictive utility. creator: Pedro J. Torres creator: Erin M. Fletcher creator: Sean M. Gibbons creator: Michael Bouvet creator: Kelly S. Doran creator: Scott T. Kelley uri: https://doi.org/10.7717/peerj.1373 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Torres et al. title: Malaria prevalence and incidence in an isolated, meso-endemic area of Mozambique link: https://peerj.com/articles/1370 last-modified: 2015-11-05 description: Isolated areas, such as the 2 × 7 km peninsula of Linga Linga in Mozambique, are the places where malaria might be most easily eliminated. Currently available control strategies include long-lasting insecticidal bednets impregnated with pyrethroid insecticides (LLINs), rapid diagnostic tests (RDTs) for diagnosis and artemisinin based combination therapy (ACT) for treatment and these were applied on the peninsula. In 2007, following a census of the population and mapping of 500 households, five annual all-age prevalence surveys were conducted. Information on LLIN use, house construction, and animal ownership was obtained. A spatially structured generalized additive model indicated that malaria risk was greatest towards the northern end of the peninsula and that people living in houses with grass or thatch roofs had a greater risk of malaria than those living in houses with corrugated iron roofs. Incidence peaked nine weeks after rainfall (r2 = 0.34, p = 0.0002). From 2009 incidence was measured at a centrally based project clinic. The proportion of under nine-year-old resident attendees diagnosed with malaria decreased significantly from 48% in 2009, to 35% in 2010 and 25% in 2011. At the same time, there was a shift in the peak age of cases from 1–4 year olds to 5–9 year olds. Nevertheless, in order to further reduce malaria transmission in an area such as Linga Linga, additional vector control measures need to be considered. creator: Jacques Derek Charlwood creator: Erzelia V.E. Tomás creator: Mauro Bragança creator: Nelson Cuamba creator: Michael Alifrangis creator: Michelle Stanton uri: https://doi.org/10.7717/peerj.1370 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Charlwood et al. title: The diagnostic and prognostic importance of oxidative stress biomarkers and acute phase proteins in Urinary Tract Infection (UTI) in camels link: https://peerj.com/articles/1363 last-modified: 2015-11-05 description: The present study aimed to investigate the diagnostic and prognostic importance of oxidative stress biomarkers and acute phase proteins in urinary tract infection (UTI) in camels. We describe the clinical, bacteriological and biochemical findings in 89 camels. Blood and urine samples from diseased (n = 74) and control camels (n = 15) were submitted to laboratory investigations. The urine analysis revealed high number of RBCS and pus cells. The concentrations of serum and erythrocytic malondialdehyde (sMDA & eMDA), Haptoglobin (Hp), serum amyloid A (SAA), Ceruloplasmin (Cp), fibrinogen (Fb), albumin, globulin and interleukin 6 (IL-6) were higher in diseased camels when compared to healthy ones. Catalase, super oxide dismutase and glutathione levels were lower in diseased camels when compared with control group. Forty one of 74 camels with UTI were successfully treated. The levels of malondialdehyde, catalase, super oxide dismutase, glutathione, Hp, SAA, Fb, total protein, globulin and IL-6 were associated with the odds of treatment failure. The MDA showed a great sensitivity (Se) and specificity (Sp) in predicting treatment failure (Se 85%/Sp 100%) as well as the SAA (Se 92%/Sp 87%) and globulin levels (Se 85%/Sp 100%) when using the cutoffs that maximizes the sum of Se + Sp. Multivariate logistic regression analysis revealed that two models had a high accuracy to predict failure with the first model including sex, sMDA and Hp as covariates (area under the receiver operating characteristic curve (AUC) = 0.92) and a second model using sex, SAA and Hp (AUC = 0.89). Conclusively, the oxidative stress biomarkers and acute phase proteins could be used as diagnostic and prognostic biomarkers in camel UTI management. Efforts should be forced to investigate such biomarkers in other species with UTI. creator: Wael M. El-Deeb creator: Sébastien Buczinski uri: https://doi.org/10.7717/peerj.1363 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 El-Deeb et al. title: Use of video surveillance to measure the influences of habitat management and landscape composition on pollinator visitation and pollen deposition in pumpkin (Cucurbita pepo) agroecosystems link: https://peerj.com/articles/1342 last-modified: 2015-11-05 description: Pumpkin (Cucurbita pepo) production relies on insect-mediated pollination, which is provided by managed and wild pollinators. The goals of this study were to measure the visitation frequency, longevity and temporal activity patterns of pumpkin pollinators and to determine if local habitat management and landscape composition affected this pollination service. We used video surveillance to monitor bee acitivty within male and female pumpkin flowers in 2011 and 2012 across a pollination window of 0600–1200 h. We also quantified the amount of pollen deposited in female flowers across this time period. In 2011, A. mellifera made significantly more floral visits than other bees, and in 2012 Bombus spp. was the dominant pumpkin pollinator. We found variation in visitation among male and female pumpkin flowers, with A. mellifera visiting female flowers more often and spending longer per visit within them than male flowers in both 2011 and 2012. The squash bee P. pruinosa visited male flowers more frequently in 2012, but individuals spent equal time in both flower sexes. We did not find variation in the timing of flower visitation among species across the observed pollination window. In both 2011 and 2012 we found that the majority of pollen deposition occurred within the first two hours (0600–0800 h) of observation; there was no difference between the pollen deposited during this two-hour period and full pollination window (0600–1200 h). Local additions of sweet alyssum floral strips or a field buffer strip of native wildflowers did not have an effect on the foraging activity of bees or pollen deposition. However, semi-natural and urban habitats in the surrounding landscape were positively correlated with the frequency of flower visitation by wild pollinators and the amount of pollen deposited within female flowers. creator: Benjamin W. Phillips creator: Mary M. Gardiner uri: https://doi.org/10.7717/peerj.1342 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Phillips and Gardiner title: First description of underwater acoustic diversity in three temperate ponds link: https://peerj.com/articles/1393 last-modified: 2015-11-05 description: The past decade has produced an increased ecological interest in sonic environments, or soundscapes. However, despite this rise in interest and technological improvements that allow for long-term acoustic surveys in various environments, some habitats’ soundscapes remain to be explored. Ponds, and more generally freshwater habitats, are one of these acoustically unexplored environments. Here we undertook the first long term acoustic monitoring of three temperate ponds in France. By aural and visual inspection of a selection of recordings, we identified 48 different sound types, and according to the rarefaction curves we calculated, more sound types are likely present in one of the three ponds. The richness of sound types varied significantly across ponds. Surprisingly, there was no pond-to-pond daily consistency of sound type richness variation; each pond had its own daily patterns of activity. We also explored the possibility of using six acoustic diversity indices to conduct rapid biodiversity assessments in temperate ponds. We found that all indices were sensitive to the background noise as estimated through correlations with the signal-to-noise ratio (SNR). However, we determined that the AR index could be a good candidate to measure acoustic diversities using partial correlations with the SNR as a control variable. Yet, research is still required to automatically compute the SNR in order to apply this index on a large data set of recordings. The results showed that these three temperate ponds host a high level of acoustic diversity in which the soundscapes were variable not only between but also within the ponds. The sources producing this diversity of sounds and the drivers of difference in daily song type richness variation both require further investigation. Such research would yield insights into the biodiversity and ecology of temperate ponds. creator: Camille Desjonquères creator: Fanny Rybak creator: Marion Depraetere creator: Amandine Gasc creator: Isabelle Le Viol creator: Sandrine Pavoine creator: Jérôme Sueur uri: https://doi.org/10.7717/peerj.1393 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Desjonquères et al. title: Age, growth, and recruitment patterns of juvenile ladyfish (Elops sp) from the east coast of Florida (USA) link: https://peerj.com/articles/1392 last-modified: 2015-11-03 description: Ladyfish (Elops sp) are a common and economically valuable coastal nearshore species found along coastal beaches, bays, and estuaries of the southeastern United States, and subtropical and tropical regions worldwide. Previously, ladyfish were a substantial bycatch in Florida’s commercial fisheries, but changes in regulations significantly reduced commercial landings. Today, ladyfish are still taken in commercial fisheries in Florida, but many are also taken by recreational anglers. Life-history information and research interest in ladyfish is almost non-existent, especially information on age and growth. Thus, the overarching purpose of this study was to expand our understanding of ladyfish age and growth characteristics. The specific objectives were to describe, for the first time, age, growth, and recruitment patterns of juvenile ladyfish from the east coast of Florida (USA). In the Indian River Lagoon (IRL), annual monthly length-frequency distributions were confounded because a few small individuals recruited throughout the year; monthly length-frequency data generally demonstrated a cyclical pattern. The smallest were collected in September and the largest in May. Post-hoc analysis showed no significant difference in length between August and May, or among the other months. In Volusia County (VC), annual monthly length-frequency distribution demonstrated growth generally occurred from late-winter and spring to summer. The smallest ladyfish were collected in February and the largest in August. On average, the absolute growth rate in the IRL was 36.3 mm in 60 days or 0.605 mm day−1. Cohort-specific daily growth rates, elevations, and coincidentals were similar among sampling years. Cohort-specific growth rates ranged from 1.807 in 1993 to 1.811 mm day−1 in 1994. Overall, growth was best (i.e., goodness of fit) described by exponential regression. On average, the absolute growth rate in VC was 28 mm in 150 days or 0.1866 mm day−1. Cohort-specific daily growth rates were significantly different among sampling years; however, the elevations and coincidentals were similar. Cohort-specific growth rates ranged from 1.741 in 1994 to 1.933 mm day−1 in 1993. Mean ladyfish growth was best described by linear regression; however, natural growth was explained better by exponential regression. In the IRL, the corrected exponential growth equation yielded a size-at-age 1 of 156.0 mm SL, which corresponded to an estimated growth rate of 0.4356 mm day−1. In VC, the corrected exponential growth equation yielded a size-at-age 1 of 80 mm SL corresponding to an estimated growth rate of 0.2361 mm day−1. creator: Juan C. Levesque uri: https://doi.org/10.7717/peerj.1392 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Levesque title: Baseline coral disease surveys within three marine parks in Sabah, Borneo link: https://peerj.com/articles/1391 last-modified: 2015-11-03 description: Two of the most significant threats to coral reefs worldwide are bleaching and disease. However, there has been a scarcity of research on coral disease in South-East Asia, despite the high biodiversity and the strong dependence of local communities on the reefs in the region. This study provides baseline data on coral disease frequencies within three national parks in Sabah, Borneo, which exhibit different levels of human impacts and management histories. High mean coral cover (55%) and variable disease frequency (mean 0.25 diseased colonies m−2) were found across the three sites. Highest disease frequency (0.44 diseased colonies per m2) was seen at the site closest to coastal population centres. Bleaching and pigmentation responses were actually higher at Sipadan, the more remote, offshore site, whereas none of the other coral diseases detected in the other two parks were detected in Sipadan. Results of this study offer a baseline dataset of disease in these parks and indicate the need for continued monitoring, and suggest that coral colonies in parks under higher anthropogenic stressors and with lower coral cover may be more susceptible to contracting disease. creator: Jennifer Miller creator: Michael J. Sweet creator: Elizabeth Wood creator: John Bythell uri: https://doi.org/10.7717/peerj.1391 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Miller et al. title: Alpine endemic spiders shed light on the origin and evolution of subterranean species link: https://peerj.com/articles/1384 last-modified: 2015-11-03 description: We designed a comparative study to unravel the phylogeography of two Alpine endemic spiders characterized by a different degree of adaptation to subterranean life: Troglohyphantes vignai (Araneae, Linyphiidae) and Pimoa rupicola (Araneae, Pimoidae), the latter showing minor adaptation to hypogean life. We sampled populations of the model species in caves and other subterranean habitats across their known geographical range in the Western Alps. By combining phylogeographic inferences and Ecological Niche Modeling techniques, we inferred the biogeographic scenario that led to the present day population structure of the two species. According to our divergent time estimates and relative uncertainties, the isolation of T. vignai and P. rupicola from their northern sister groups was tracked back to Middle–Late Miocene. Furthermore, the fingerprint left by Pleistocene glaciations on the population structure revealed by the genetic data, led to the hypothesis that a progressive adaptation to subterranean habitats occurred in T. vignai, followed by strong population isolation. On the other hand, P. rupicola underwent a remarkable genetic bottleneck during the Pleistocene glaciations, that shaped its present population structure. It seems likely that such shallow population structure is both the result of the minor degree of specialization to hypogean life and the higher dispersal ability characterizing this species. The simultaneous study of overlapping spider species showing different levels of adaptation to hypogean life, disclosed a new way to clarify patterns of biological diversification and to understand the effects of past climatic shift on the subterranean biodiversity. creator: Stefano Mammola creator: Marco Isaia creator: Miquel A. Arnedo uri: https://doi.org/10.7717/peerj.1384 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Mammola et al. title: Effects of acute levodopa challenge on resting cerebral blood flow in Parkinson’s Disease patients assessed using pseudo-continuous arterial spin labeling link: https://peerj.com/articles/1381 last-modified: 2015-11-03 description: Introduction. Levodopa is the gold-standard for treatment of Parkinson’s disease (PD) related motor symptoms. In this study, we used pseudo-continuous arterial spin labeling (pCASL) to quantify changes in cerebral blood flow (CBF) after acute oral administration of levodopa in PD patients.Materials and Methods. Thirteen patients (3 females, age 66.2 ± 8.7 years) with moderately advanced PD (Hoehn and Yahr stage >2 (median 2.5), disease duration >3 years) were scanned on a 3T Siemens MR scanner before and after oral levodopa administration. Statistical parametric mapping was used to detect drug-induced changes in CBF and its correlation to clinical severity scales. Images were normalized and flipped in order to examine effects on the more affected (left) and less affected (right) cerebral hemispheres across the cohort.Results. Levodopa did not change global CBF but increased regional CBF in dorsal midbrain, precuneus/cuneus, more affected inferior frontal pars opercularis and triangularis, bilateral pre- and postcentral gyri, more affected inferior parietal areas, as well as less affected putamen/globus pallidus by 27–74% (p < 0.05, FWE corrected for multiple comparisons). CBF change was negatively correlated with improvement in bradykinesia UPDRS-III subscore in the more affected precentral gyrus, and total predrug UPDRS-III score in the mid-cingulate region. Drug-induced CBF change in a widespread network of regions including parietal and postcentral areas was also negatively correlated with the predrug rigidity UPDRS-III subscore.Conclusion. These findings are in line with prior reports of abnormal activity in the nigrostriatal pathway of PD patients and demonstrate the feasibility of pCASL as a neuroimaging tool for investigating in vivo physiological effects of acute drug administration in PD. creator: Yufen Chen creator: Peter Pressman creator: Tanya Simuni creator: Todd B. Parrish creator: Darren R. Gitelman uri: https://doi.org/10.7717/peerj.1381 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Chen et al. title: The herbaceous landlord: integrating the effects of symbiont consortia within a single host link: https://peerj.com/articles/1379 last-modified: 2015-11-03 description: Plants are typically infected by a consortium of internal fungal associates, including endophytes in their leaves, as well as arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) in their roots. It is logical that these organisms will interact with each other and the abiotic environment in addition to their host, but there has been little work to date examining the interactions of multiple symbionts within single plant hosts, or how the relationships among symbionts and their host change across environmental conditions. We examined the grass Agrostis capillaris in the context of a climate manipulation experiment in prairies in the Pacific Northwest, USA. Each plant was tested for presence of foliar endophytes in the genus Epichloë, and we measured percent root length colonized (PRLC) by AMF and DSE. We hypothesized that the symbionts in our system would be in competition for host resources, that the outcome of that competition could be driven by the benefit to the host, and that the host plants would be able to allocate carbon to the symbionts in such a way as to maximize fitness benefit within a particular environmental context. We found a correlation between DSE and AMF PRLC across climatic conditions; we also found a fitness cost to increasing DSE colonization, which was negated by presence of Epichloë endophytes. These results suggest that selective pressure on the host is likely to favor host/symbiont relationships that structure the community of symbionts in the most beneficial way possible for the host, not necessarily favoring the individual symbiont that is most beneficial to the host in isolation. These results highlight the need for a more integrative, systems approach to the study of host/symbiont consortia. creator: Roo Vandegrift creator: Bitty A. Roy creator: Laurel Pfeifer-Meister creator: Bart R. Johnson creator: Scott D. Bridgham uri: https://doi.org/10.7717/peerj.1379 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Vandegrift et al. title: Rapid loss of phosphorus during early pedogenesis along a glacier retreat choronosequence, Gongga Mountain (SW China) link: https://peerj.com/articles/1377 last-modified: 2015-11-03 description: The loss of phosphorus (P) during the early pedogenesis stage is important at the ecosystem level, and it also plays an important role in the global P cycle. The seasonal variation of total P (Pt) and its fractions along a young soil chronosequence (Hailuogou chronosequence) on the eastern slope of Gongga Mountain, SW China, was investigated based on the modified Hedley fractionation technique to understand P loss during the early pedogenesis stage. The results showed that the mineral P (mainly apatite) was the dominant fraction of Pt in the C horizon of the soil, and the seasonal difference in Pt and its fractions was insignificant. In the A horizon, Pt concentrations decreased markedly compared with those in the C horizon, and as the age of the soil increased, the inorganic P (Pi) significantly decreased and the organic P (Po) prominently increased. Seasonally, the P fractions exhibited various distributions in the A horizon. The variation of Pt and its fractions revealed that the P loss was rapid along the 120-year soil chronosequence. The P stocks in soils (0–30 cm) started to decrease at the 52 year site. And the P stock depletion reached almost 17.6% at the 120-year site. The loss of P from the soil of the Hailuogou chronosequence was mainly attributed to weathering, plant uptake, and transport by runoff. About 36% P loss was transported into plant biomass P at the 120 year site. The data obtained indicated that the glacier retreat chronosequence could be used to elucidate the fast rate of P loss during the early pedogenic stage. creator: Yanhong Wu creator: Jun Zhou creator: Haijian Bing creator: Hongyang Sun creator: Jipeng Wang uri: https://doi.org/10.7717/peerj.1377 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wu et al. title: Development and application of molecular biomarkers for characterizing Caribbean Yellow Band Disease in Orbicella faveolata link: https://peerj.com/articles/1371 last-modified: 2015-11-03 description: Molecular stress responses associated with coral diseases represent an under-studied area of cnidarian transcriptome investigations. Caribbean Yellow Band Disease (CYBD) is considered a disease of Symbiodinium within the tissues of the coral host Orbicella faveolata. There is a paucity of diagnostic tools to assist in the early detection and characterization of coral diseases. The validity of a diagnostic test is determined by its ability to distinguish host organisms that have the disease from those that do not. The ability to detect and identify disease-affected tissue before visible signs of the disease are evident would then be a useful diagnostic tool for monitoring and managing disease outbreaks. Representational Difference Analysis (RDA) was utilized to isolate differentially expressed genes in O. faveolata exhibiting CYBD. Preliminary screening of RDA products identified a small number of genes of interest (GOI) which included an early growth response factor and ubiquitin ligase from the coral host as well as cytochrome oxidase from the algal symbiont. To further characterize the specificity of response, quantitative real-time PCR (qPCR) was utilized to compare the expression profiles of these GOIs within diseased tissues (visible lesions), tissues that precede visible lesions by 2–4 cm (transition area), and tissues from healthy-looking colonies with no signs of disease. Results show there are distinctive differences in the expression profiles of these three GOIs within each tissue examined. Collectively, this small suite of GOIs can provide a molecular “finger print” which is capable of differentiating between infected and uninfected colonies on reefs where CYBD is known to occur. creator: Michael Morgan creator: Kylia Goodner creator: James Ross creator: Angela Z. Poole creator: Elizabeth Stepp creator: Christopher H. Stuart creator: Cydney Wilbanks creator: Ernesto Weil uri: https://doi.org/10.7717/peerj.1371 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Morgan et al. title: Laboratory and clinical trials of cocamide diethanolamine lotion against head lice link: https://peerj.com/articles/1368 last-modified: 2015-11-03 description: Context. During the late 1990s, insecticide resistance had rendered a number of treatment products ineffective; some companies saw this as an opportunity to develop alternative types of treatment. We investigated the possibility that a surfactant-based lotion containing 10% cocamide diethanolamine (cocamide DEA) was effective to eliminate head louse infestation.Settings and Design. Initial in vitro testing of the lotion formulation versus laboratory reared body/clothing lice, followed by two randomised, controlled, community-based, assessor blinded, clinical studies.Materials and Methods. Preliminary laboratory tests were performed by exposing lice or louse eggs to the product using a method that mimicked the intended use. Clinical Study 1: Children and adults with confirmed head louse infestation were treated by investigators using a single application of aqueous 10% cocamide DEA lotion applied for 60 min followed by shampooing or a single 1% permethrin creme rinse treatment applied to pre-washed hair for 10 min. Clinical Study 2: Compared two treatment regimens using 10% cocamide DEA lotion that was concentrated by hair drying. A single application left on for 8 h/overnight was compared with two applications 7 days apart of 2 h duration, followed by a shampoo wash.Results. The initial laboratory tests showed a pediculicidal effect for a 60 min application but limited ovicidal effect. A longer application time of 8 h or overnight was found capable of killing all eggs but this differed between batches of test material. Clinical Study 1: Both treatments performed badly with only 3/23 (13%) successful treatments using cocamide DEA and 5/25 (23.8%) using permethrin. Clinical Study 2: The single overnight application of cocamide DEA concentrated by hair drying gave 10/56 (17.9%) successes compared with 19/56 (33.9%) for the 2 h application regimen repeated after 1 week. Intention to treat analysis showed no significant difference (p = 0.0523) between the treatments. Over the two studies, there were 18 adverse events possibly or probably associated with treatment, most of which were increased pruritus after treatment.Conclusions. Cocamide DEA 10% lotion, even when concentrated by hair drying, showed limited activity to eliminate head louse infestation. creator: Ian F. Burgess creator: Elizabeth R. Brunton creator: Christine M. Brown uri: https://doi.org/10.7717/peerj.1368 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Burgess et al. title: Suberoylanilide hydroxamic acid suppresses hepatic stellate cells activation by HMGB1 dependent reduction of NF-κB1 link: https://peerj.com/articles/1362 last-modified: 2015-11-03 description: Hepatic stellate cells (HSCs) activation is essential to the pathogenesis of liver fibrosis. Exploring drugs targeting HSC activation is a promising anti-fibrotic strategy. In the present study, we found suberoylanilide hydroxamic acid (SAHA), a histone deacetylase inhibitor, prominently suppressed the activation phenotype of a human hepatic stellate cell line—LX2. The production of collagen type I and α-smooth muscle actin (α-SMA) as well as the proliferation and migration of LX2 cells were significantly reduced by SAHA treatment. To determine the molecular mechanisms underlying this suppression, genome wild gene regulation by SAHA was determined by Affymetrix 1.0 human cDNA array. Upon SAHA treatment, the abundance of 331 genes was up-regulated and 173 genes was down-regulated in LX2 cells. Bioinformatic analyses of these altered genes highlighted the high mobility group box 1 (HMGB1) pathway was one of the most relevant pathways that contributed to SAHA induced suppression of HSCs activation. Further studies demonstrated the increased acetylation of intracellular HMGB1 in SAHA treated HSCs, and this increasing is most likely to be responsible for SAHA induced down-regulation of nuclear factor kappa B1 (NF-κB1) and is one of the main underlying mechanisms for the therapeutic effect of SAHA for liver fibrosis. creator: Wenwen Wang creator: Min Yan creator: Qiuhong Ji creator: Jinbiao Lu creator: Yuhua Ji creator: Juling Ji uri: https://doi.org/10.7717/peerj.1362 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wang et al. title: Removal of concentrated sulfamethazine by acclimatized aerobic sludge and possible metabolic products link: https://peerj.com/articles/1359 last-modified: 2015-11-03 description: This article examined the biological removal of high concentrated sulfamethazine (SMZ) antibiotics by the acclimatized activated sludge in lab-scale SBRs system. The removal of SMZ was characterized by a quick adsorption and a slow process of biodegradation. The adsorption capacity of activated sludge for SMZ was 44 and 47 µg SMZ/g SS, respectively, with the initial SMZ concentrations of 1 and 2 mg/L. The adsorption process fitted pseudo-second-order kinetic model. In a series of batch studies, with the increase of initial SMZ concentration that were 1, 2, 3, 5, 7 and 9 mg/L, 56.0%, 51.3%, 42.2%, 29.5%, 25.0% and 20.8% of influent SMZ were biodegraded within 24 h of biological reaction, respectively. The Monod equation applied to simulate SMZ biodegradation had a good coefficient of determination (R2 > 0.99). Furthermore, the results of HPLC demonstrated that the SMZ was not completely removed by the acclimatized activated sludge. From the analysis of LC-MS, 4 intermediates of SMZ biodegradation were identified: Sulfanilic Acid, 4-amino-N-(4,6-dimethyl-2 pyrimidin) benzene sulfonamide, N-(4,6-dimethyl-2-pyrimidin)-4-N-(benzene sulfonamide) benzene sulfonamide, N-(4,6-dimethyl-2-pyrimidin)-4-N-(4,6-dimethyl pyrimidine) benzene sulfonamide, and N-(4,6-dimethyl-2-pyrimidin)-4-N-(3-dimethyl-4-N sodium benzene sulfonamide) benzene sulfonamide. creator: Na Yang creator: Junfeng Wan creator: Shiju Zhao creator: Yan Wang uri: https://doi.org/10.7717/peerj.1359 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Yang et al. title: Chewed out: an experimental link between food material properties and repetitive loading of the masticatory apparatus in mammals link: https://peerj.com/articles/1345 last-modified: 2015-11-03 description: Using a model organism (rabbits) that resembles a number of mammalian herbivores in key aspects of its chewing behaviors, we examined how variation in dietary mechanical properties affects food breakdown during mastication. Such data have implications for understanding phenotypic variation in the mammalian feeding apparatus, particularly with respect to linking jaw form to diet-induced repetitive loading. Results indicate that chewing frequency (chews/s) is independent of food properties, whereas chewing investment (chews/g) and chewing duration(s), which are proportional to repetitive loading of the jaws, are positively related to food stiffness and toughness. In comparisons of displacement-limited and stress-limited fragmentation indices, which respectively characterize the intraoral breakdown of tough and stiff foods, increases in chewing investment and duration are linked solely to stiffness. This suggests that stiffer foods engender higher peak loads and increased cyclical loading. Our findings challenge conventional wisdom by demonstrating that toughness does not, by itself, underlie increases in cyclical loading and loading duration. Instead, tough foods may be associated with such jaw-loading patterns because they must be processed in greater volumes owing to their lower nutritive quality and for longer periods of time to increase oral exposure to salivary chemicals. creator: Matthew J. Ravosa creator: Jeremiah E. Scott creator: Kevin R. McAbee creator: Anna J. Veit creator: Annika L. Fling uri: https://doi.org/10.7717/peerj.1345 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ravosa et al. title: Overcoming pain thresholds with multilevel models—an example using quantitative sensory testing (QST) data link: https://peerj.com/articles/1335 last-modified: 2015-11-03 description: The assessment of somatosensory function is a cornerstone of research and clinical practice in neurology. Recent initiatives have developed novel protocols for quantitative sensory testing (QST). Application of these methods led to intriguing findings, such as the presence lower pain-thresholds in healthy children compared to healthy adolescents. In this article, we (re-) introduce the basic concepts of signal detection theory (SDT) as a method to investigate such differences in somatosensory function in detail. SDT describes participants’ responses according to two parameters, sensitivity and response-bias. Sensitivity refers to individuals’ ability to discriminate between painful and non-painful stimulations. Response-bias refers to individuals’ criterion for giving a “painful” response. We describe how multilevel models can be used to estimate these parameters and to overcome central critiques of these methods. To provide an example we apply these methods to data from the mechanical pain sensitivity test of the QST protocol. The results show that adolescents are more sensitive to mechanical pain and contradict the idea that younger children simply use more lenient criteria to report pain. Overall, we hope that the wider use of multilevel modeling to describe somatosensory functioning may advance neurology research and practice. creator: Gerrit Hirschfeld creator: Markus R. Blankenburg creator: Moritz Süß creator: Boris Zernikow uri: https://doi.org/10.7717/peerj.1335 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hirschfeld et al. title: Relationship of central incisor implant placement to the ridge configuration anterior to the nasopalatine canal in dentate and partially edentulous individuals: a comparative study link: https://peerj.com/articles/1315 last-modified: 2015-11-03 description: Background. The aims of this study were to investigate the ridge contour anterior to the nasopalatine canal, and the difference between the incidences of the nasopalatine canal perforation in dentate and partially edentulous patients by cone-beam computed tomography.Methods. Cone-beam computed tomography scan images from 72 patients were selected from database and divided into dentate and partially edentulous groups. The configuration of the ridge anterior to the canal including palatal concavity depth, palatal concavity height, palatal concavity angle, bone height coronal to the incisive foramen, and bone width anterior to the canal was measured. A virtual implant placement procedure was used, and the incidences of perforation were evaluated after implant placement in the cingulum position with the long axis along with the designed crown.Results. Comparing with variable values from dentate patients, the palatal concavity depth and angle were greater by 0.9 mm and 4°, and bone height was shorter by 1.1 mm in partially edentulous patients, respectively. Bone width in edentulous patients was narrower than in dentate patients by 1.2 mm at incisive foramen level and 0.9 mm at 8 mm subcrestal level, respectively. After 72 virtual cylindrical implants (4.1 × 12 mm) were placed, a total of 12 sites (16.7%) showed a perforation and three-fourths occurred in partially edentulous patients. After replacing with 72 tapered implants (4.3 × 13 mm), only 6 implants (8.3%) broke into the canal in the partially edentulous patient group.Conclusions. The nasopalatine canal may get close to the implant site and the bone width anterior to the canal decreases after the central incisor extraction. The incidence of nasopalatine canal perforation may occur more commonly during delayed implant placement in central incisor missing patients. creator: Xueting Jia creator: Wenjie Hu creator: Huanxin Meng uri: https://doi.org/10.7717/peerj.1315 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Jia et al. title: Successful survival, growth, and reproductive potential of quagga mussels in low calcium lake water: is there uncertainty of establishment risk? link: https://peerj.com/articles/1276 last-modified: 2015-11-03 description: The risk of quagga mussel (Dreissena rostriformis bugensis Andrusov 1897) establishment into water-bodies of the western US has expanded the geographic concern regarding the ecological and economic impacts this species will have in aquatic ecosystems. Thresholds based on calcium concentrations, an element critical for mussel growth and physiology, have been used as a primary predictor of quagga mussel establishment success to aid management decisions. We evaluated the invasion potential of quagga mussels in low calcium waters using laboratory experiments to compare the survival, growth and reproductive potential of adult mussels held for 90 days at low (9 and 12 ppm), moderate (15 to 32 ppm) and high (72 ppm) calcium water concentrations. In conjunction with adult experiments, veliger stage survival, growth and settlement were evaluated under similar low, moderate, and high calcium water treatments. Adult mussels survived, grew and showed reproductive potential in low calcium water (12 ppm). Veligers were also able to survive, grow and settle in low calcium water. Higher levels of natural seston biomass appeared to improve adult mussel life history performance in low calcium water. Survival curve analysis predicted that 99% adult mortality could occur in <170 days at 9 ppm and 12 ppm, however water with >15 ppm could have adults surviving more than a year. The results from these bioassays provide further evidence that quagga mussels have higher risk of establishment in low calcium lakes if habitats exist that have slightly elevated calcium. These results should help emphasize the vulnerability of water-body in the 12 to 15 ppm calcium range that could potentially be at risk of establishing sustainable quagga mussel populations. Furthermore, these results provide insights into the uncertainty of using a single parameter in assigning establishment risk given the complexity of variables in specific water-bodies that influence life history performance of introduced species. creator: Clinton J. Davis creator: Emma K. Ruhmann creator: Kumud Acharya creator: Sudeep Chandra creator: Christopher L. Jerde uri: https://doi.org/10.7717/peerj.1276 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Davis et al.