title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2016-01 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Deficiencies of effectiveness of intervention studies in veterinary medicine: a cross-sectional survey of ten leading veterinary and medical journals link: https://peerj.com/articles/1649 last-modified: 2016-01-28 description: The validity of studies that assess the effectiveness of an intervention (EoI) depends on variables such as the type of study design, the quality of their methodology, and the participants enrolled. Five leading veterinary journals and 5 leading human medical journals were hand-searched for EoI studies for the year 2013. We assessed (1) the prevalence of randomized controlled trials (RCTs) among EoI studies, (2) the type of participants enrolled, and (3) the methodological quality of the selected studies. Of 1707 eligible articles, 590 were EoI articles and 435 RCTs. Random allocation to the intervention was performed in 52% (114/219; 95%CI:45.2–58.8%) of veterinary EoI articles, against 87% (321/371; 82.5–89.7%) of human EoI articles (adjusted OR:9.2; 3.4–24.8). Veterinary RCTs were smaller (median: 26 animals versus 465 humans) and less likely to enroll real patients, compared with human RCTs (OR:331; 45–2441). Only 2% of the veterinary RCTs, versus 77% of the human RCTs, reported power calculations, primary outcomes, random sequence generation, allocation concealment and estimation methods. Currently, internal and external validity of veterinary EoI studies is limited compared to human medical ones. To address these issues, veterinary interventional research needs to improve its methodology, increase the number of published RCTs and enroll real clinical patients. creator: Nicola Di Girolamo creator: Reint Meursinge Reynders uri: https://doi.org/10.7717/peerj.1649 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Di Girolamo & Meursinge Reynders title: AMAS: a fast tool for alignment manipulation and computing of summary statistics link: https://peerj.com/articles/1660 last-modified: 2016-01-28 description: The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python’s core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License. creator: Marek L. Borowiec uri: https://doi.org/10.7717/peerj.1660 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Borowiec title: An analysis of structural relationship among achievement motive on social participation, purpose in life, and role expectations among community dwelling elderly attending day services link: https://peerj.com/articles/1655 last-modified: 2016-01-28 description: Background. Achievement motive is defined as the intention to achieve one’s goals. Achievement motive is assumed to promote clients to choices and actions toward their valuable goal, so it is an important consideration in rehabilitation.Purpose. The purpose of this study is to demonstrate the structural relationship among achievement motive on purpose in life, social participation, and role expectation of community-dwelling elderly people.Methods. Participants were community-dwelling elderly people in day-service centers. A total of 281 participants (male: 127, female: 154) answered the self-administered questionnaire in cross-sectional research. The questionnaire was comprised of demographic data and scales that evaluated achievement motive, social participation, purpose in life, and role expectation. We studied the structural relationship established by our hypothesized model via a structural equation modeling approach.Results. We checked the standardized path coefficients and the modification indices; the modified model’s statistics were a good fit: CFI = 0.984, TLI = 0.983, RMSEA = 0.050, 90% CI [0.044–0.055]. Achievement motive had a significantly direct effect on purpose in life (direct effect = 0.445, p value < 0.001), a significantly indirect effect on purpose in life via social participation or role expectation (indirect effect = 0.170, p value < 0.001) and a total effect on purpose in life (total effect = 0.615).Discussion. This result suggests that enhancing the intention to achieve one’s goals enables participants to feel a spirit of challenge with a purpose and a sense of fulfillment in their daily lives. creator: Nobuyuki Sano creator: Makoto Kyougoku uri: https://doi.org/10.7717/peerj.1655 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sano and Kyougoku title: Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling link: https://peerj.com/articles/1645 last-modified: 2016-01-28 description: The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest. creator: Pawel Wasowicz creator: Maxime Pauwels creator: Andrzej Pasierbinski creator: Ewa M. Przedpelska-Wasowicz creator: Alicja A. Babst-Kostecka creator: Pierre Saumitou-Laprade creator: Adam Rostanski uri: https://doi.org/10.7717/peerj.1645 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wasowicz et al. title: Decadal comparison of a diminishing coral community: a study using demographics to advance inferences of community status link: https://peerj.com/articles/1643 last-modified: 2016-01-28 description: The most common coral monitoring methods estimate coral abundance as percent cover, either via in situ observations or derived from images. In recent years, growing interest and effort has focused on colony-based (demographic) data to assess the status of coral populations and communities. In this study, we relied on two separate data sets (photo-derived percent cover estimates, 2002–12, and opportunistic in situ demographic sampling, 2004 and 2012) to more fully infer decadal changes in coral communities at a small, uninhabited Caribbean island. Photo-derived percent cover documented drastic declines in coral abundance including disproportionate declines in Orbicella spp. While overall in situ estimates of total coral density were not different between years, densities of several rarer taxa were. Meandrina meandrites and Stephanocoenia intersepta increased while Leptoseris cucullata decreased significantly, changes that were not discernable from the photo-derived cover estimates. Demographic data also showed significant shifts to larger colony sizes (both increased mean colony sizes and increased negative skewness of size frequency distributions, but similar maximum colony sizes) for most taxa likely indicating reduced recruitment. Orbicella spp. differed from this general pattern, significantly shifting to smaller colony sizes due to partial mortality. Both approaches detected significant decadal changes in coral community structure at Navassa, though the demographic sampling provided better resolution of more subtle, taxon-specific changes. creator: Margaret Miller creator: Dana E. Williams creator: Brittany E. Huntington creator: Gregory A. Piniak creator: Mark J.A. Vermeij uri: https://doi.org/10.7717/peerj.1643 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Protective effects of the extracts of Barringtonia racemosa shoots against oxidative damage in HepG2 cells link: https://peerj.com/articles/1628 last-modified: 2016-01-28 description: Barringtonia racemosa is a tropical plant with medicinal values. In this study, the ability of the water extracts of the leaf (BLE) and stem (BSE) from the shoots to protect HepG2 cells against oxidative damage was studied. Five major polyphenolic compounds consisting of gallic acid, ellagic acid, protocatechuic acid, quercetin and kaempferol were identified using HPLC-DAD and ESI-MS. Cell viability assay revealed that BLE and BSE were non-cytotoxic (cell viabilities >80%) at concentration less than 250 µg/ml and 500 µg/ml, respectively. BLE and BSE improved cellular antioxidant status measured by FRAP assay and protected HepG2 cells against H2O2-induced cytotoxicity. The extracts also inhibited lipid peroxidation in HepG2 cells as well as the production of reactive oxygen species. BLE and BSE could also suppress the activities of superoxide dismutase and catalase during oxidative stress. The shoots of B. racemosa can be an alternative bioactive ingredient in the prevention of oxidative damage. creator: Kin Weng Kong creator: Sarni Mat-Junit creator: Norhaniza Aminudin creator: Fouad Abdulrahman Hassan creator: Amin Ismail creator: Azlina Abdul Aziz uri: https://doi.org/10.7717/peerj.1628 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kong et al. title: Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum link: https://peerj.com/articles/1607 last-modified: 2016-01-28 description: Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria. creator: Karthik Anantharaman creator: Christopher T. Brown creator: David Burstein creator: Cindy J. Castelle creator: Alexander J. Probst creator: Brian C. Thomas creator: Kenneth H. Williams creator: Jillian F. Banfield uri: https://doi.org/10.7717/peerj.1607 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Anantharaman et al. title: Evaluation of the global impacts of mitigation on persistent, bioaccumulative and toxic pollutants in marine fish link: https://peerj.com/articles/1573 last-modified: 2016-01-28 description: Although persistent, bioaccumulative and toxic pollutants (PBTs) are well-studied individually, their distribution and variability on a global scale are largely unknown, particularly in marine fish. Using 2,662 measurements collected from peer-reviewed literature spanning 1969–2012, we examined variability of five classes of PBTs, considering effects of geography, habitat, and trophic level on observed concentrations. While we see large-scale spatial patterning in some PBTs (chlordanes, polychlorinated biphenyls), habitat type and trophic level did not contribute to significant patterning, with the exception of mercury. We further examined patterns of change in PBT concentration as a function of sampling year. All PBTs showed significant declines in concentration levels through time, ranging from 15–30% reduction per decade across PBT groups. Despite consistent evidence of reductions, variation in pollutant concentration remains high, indicating ongoing consumer risk of exposure to fish with pollutant levels exceeding EPA screening values. The temporal trends indicate that mitigation programs are effective, but that global levels decline slowly. In order for monitoring efforts to provide more targeted assessments of risk to PBT exposure, these data highlight an urgent need for improved replication and standardization of pollutant monitoring protocols for marine finfish. creator: Lindsay T. Bonito creator: Amro Hamdoun creator: Stuart A. Sandin uri: https://doi.org/10.7717/peerj.1573 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bonito et al. title: A new species of Metopocetus (Cetacea, Mysticeti, Cetotheriidae) from the Late Miocene of the Netherlands link: https://peerj.com/articles/1572 last-modified: 2016-01-28 description: The family Cetotheriidae has played a major role in recent discussions of baleen whale phylogenetics. Within this group, the enigmatic, monotypic Metopocetus durinasus has been interpreted as transitional between herpetocetines and other members of the family, but so far has been restricted to a single, fragmentary cranium of uncertain provenance and age. Here, we expand the genus and shed new light on its phylogenetic affinities and functional morphology by describing Metopocetus hunteri sp. nov. from the Late Miocene of the Netherlands. Unlike the holotype of M. durinasus, the material described here is confidently dated and preserves both the tympanic bulla and additional details of the basicranium. M. hunteri closely resembles M. durinasus, differing primarily in its somewhat less distally expanded compound posterior process of the tympanoperiotic. Both species are characterised by the development of an unusually large fossa on the ventral surface of the paroccipital process, which extends anteriorly on to the compound posterior process and completely floors the facial sulcus. In life, this enlarged fossa may have housed the posterior sinus and/or the articulation of the stylohyal. Like other cetotheriids, Metopocetus also bears a well-developed, posteriorly-pointing dorsal infraorbital foramen near the base of the ascending process of the maxilla, the precise function of which remains unclear. creator: Felix Georg Marx creator: Mark E.J. Bosselaers creator: Stephen Louwye uri: https://doi.org/10.7717/peerj.1572 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Marx et al. title: Is Acropora palmata recovering? A case study in Los Roques National Park, Venezuela link: https://peerj.com/articles/1539 last-modified: 2016-01-28 description: Eight years ago (2007), the distribution and status of Acropora palmata was quantified throughout Los Roques archipelago in Venezuela. The aim was to produce a baseline study for this species which combined population genetics with demographic data. The results highlighted that A. palmata had the potential to recover in at least 6 out of 10 sites surveyed. Recovery potential was assumed to be high at sites with a relatively high abundance of the coral, low disease prevalence, high genetic diversity, and high rates of sexual reproduction. However, as noted, Zubillaga et al. (2008) realized recovery was still strongly dependent on local and regional stressors. In 2014 (this study), the status of A. palmata was re-evaluated at Los Roques. We increased the number of sites from 10 in the original baseline study to 106. This allowed us to assess the population status throughout the entirety of the MPA. Furthermore, we also identified local threats that may have hindered population recovery. Here, we show that A. palmata now has a relatively restricted distribution throughout the park, only occurring in 15% of the sites surveyed. Large stands of old dead colonies were common throughout the archipelago; a result which demonstrates that this species has lost almost 50% of its original distribution over the past decades. The majority of corals recorded were large adults (∼2 m height), suggesting that these older colonies might be less susceptible or more resilient to local and global threats. However, 45% of these surviving colonies showed evidence of partial mortality and degradation of living tissues. Interestingly, the greatest increase in partial mortality occurred at sites with the lowest levels of protection (${X}_{o}^{2}=5.4> {X}_{c}^{2}=4.5$Xo2=5.4>Xc2=4.5; df = 4, p < 0.05). This may suggest there is a positive role of small scale marine management in assisting reef recovery. We also recorded a significant reduction (${X}_{\mathrm{exp}}^{2}=126.8> {X}_{\mathrm{cri}}^{2}=15.5$Xexp2=126.8>Xcri2=15.5; df = 8; p < 0.05) in the density of A. palmata in sites that had previously been categorized as having a high potential for recovery. One explanation for this continued decline may be due to the fact that over the past 10 years, two massive bleaching events have occurred throughout the Caribbean with records showing that Los Roques has experienced unprecedented declines in overall coral cover. We therefore conclude that although local protection could promote recovery, the impacts from global threats such as ocean warming may hamper the recovery of this threatened species. creator: Aldo Croquer creator: Francoise Cavada-Blanco creator: Ainhoa L. Zubillaga creator: Esteban A. Agudo-Adriani creator: Michael Sweet uri: https://doi.org/10.7717/peerj.1539 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Croquer et al. title: The metabolomic profile of gamma-irradiated human hepatoma and muscle cells reveals metabolic changes consistent with the Warburg effect link: https://peerj.com/articles/1624 last-modified: 2016-01-26 description: The two human cell lines HepG2 from hepatoma and HMCL-7304 from striated muscle were γ-irradiated with doses between 0 and 4 Gy. Abundant γH2AX foci were observed at 4 Gy after 4 h of culture post-irradiation. Sham-irradiated cells showed no γH2AX foci and therefore no signs of radiation-induced double-strand DNA breaks. Flow cytometry indicated that 41.5% of HepG2 cells were in G2/M and this rose statistically significantly with increasing radiation dose reaching a plateau at ∼47%. Cell lysates from both cell lines were subjected to metabolomic analysis using Gas Chromatography-Mass Spectrometry (GCMS). A total of 46 metabolites could be identified by GCMS in HepG2 cell lysates and 29 in HMCL-7304 lysates, most of which occurred in HepG2 cells. Principal Components Analysis (PCA) showed a clear separation of sham, 1, 2 and 4 Gy doses. Orthogonal Projection to Latent Structures-Discriminant Analysis (OPLS-DA) revealed elevations in intracellular lactate, alanine, glucose, glucose 6-phosphate, fructose and 5-oxoproline, which were found by univariate statistics to be highly statistically significantly elevated at both 2 and 4 Gy compared with sham irradiated cells. These findings suggested upregulation of cytosolic aerobic glycolysis (the Warburg effect), with potential shunting of glucose through aldose reductase in the polyol pathway, and consumption of reduced Glutathione (GSH) due to γ-irradiation. In HMCL-7304 myotubes, a putative Warburg effect was also observed only at 2 Gy, albeit a lesser magnitude than in HepG2 cells. It is anticipated that these novel metabolic perturbations following γ-irradiation of cultured cells will lead to a fuller understanding of the mechanisms of tissue damage following ionizing radiation exposure. creator: Min Wang creator: Adrian Keogh creator: Susan Treves creator: Jeffrey R. Idle creator: Diren Beyoğlu uri: https://doi.org/10.7717/peerj.1624 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Wang et al. title: Systematics of the Rubidgeinae (Therapsida: Gorgonopsia) link: https://peerj.com/articles/1608 last-modified: 2016-01-26 description: The subfamily Rubidgeinae, containing the largest known African gorgonopsians, is thoroughly revised. Rubidgeinae is diagnosed by the absence of a blade-like parasphenoid rostrum and reduction or absence of the preparietal. Seven rubidgeine species from the Karoo Basin of South Africa are recognized as valid: Aelurognathus tigriceps, Clelandina rubidgei, Dinogorgon rubidgei, Leontosaurus vanderhorsti, Rubidgea atrox, Smilesaurus ferox, and Sycosaurus laticeps. Rubidgeines are also present in other African basins: A. tigriceps and S. laticeps occur in the Upper Madumabisa Mudstone Formation of Zambia, and D. rubidgei, R. atrox, and the endemic species Ruhuhucerberus haughtoni comb. nov. and Sycosaurus nowaki comb. nov. occur in the Usili Formation of Tanzania. Aelurognathus nyasaensis from the Chiweta Beds of Malawi also represents a rubidgeine, but of uncertain generic referral pending further preparation. No rubidgeine material is known outside of Africa: the purported Russian rubidgeine Leogorgon klimovensis is not clearly referable to this group and may not be diagnosable. Phylogenetic analysis of rubidgeines reveals strong support for a clade (Rubidgeini) of advanced rubidgeines including Clelandina, Dinogorgon, Leontosaurus, and Rubidgea. Support for Smilesaurus as a rubidgeine is weak; it may, as previous authors have suggested, represent an independent evolution of large body size from an Arctops-like ancestor. Temporally, rubidgeines are restricted to the Late Permian, first appearing in the Tropidostoma Assemblage Zone and reaching highest diversity in the Cistecephalus and Daptocephalus assemblage zones of the Beaufort Group. creator: Christian F. Kammerer uri: https://doi.org/10.7717/peerj.1608 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kammerer title: Genetic diversity in migratory bats: Results from RADseq data for three tree bat species at an Ohio windfarm link: https://peerj.com/articles/1647 last-modified: 2016-01-26 description: Genetic analyses can identify the scale at which wildlife species are impacted by human activities, and provide demographic information useful for management. Here, we use thousands of nuclear DNA genetic loci to assess whether genetic structure occurs within Lasiurus cinereus (Hoary Bat), L. borealis (Red Bat), and Lasionycteris noctivagans (Silver-Haired Bat) bats found at a wind turbine site in Ohio, and to also estimate demographic parameters in each of these three groups. Our specific goals are to: 1) demonstrate the feasibility of isolating RADseq loci from these tree bat species, 2) test for genetic structure within each species, including any structure that may be associated with time (migration period), and 3) use coalescent-based modeling approaches to estimate genetically-effective population sizes and patterns of population size changes over evolutionary timescales. Thousands of loci were successfully genotyped for each species, demonstrating the value of RADseq for generating polymorphic loci for population genetic analyses in these bats. There was no evidence for genetic differentiation between groups of samples collected at different times throughout spring and fall migration, suggesting that individuals from each species found at the wind facility are from single panmictic populations. Estimates of present-day effective population sizes varied across species, but were consistently large, on the order of 105–106. All populations show evidence of expansions that date to the Pleistocene. These results, along with recent work also suggesting limited genetic structure in bats across North America, argue that additional biomarker systems such as stable-isotopes or trace elements should be investigated as alternative and/or complementary approaches to genetics for sourcing individuals collected at single wind farm sites. creator: Michael G. Sovic creator: Bryan C. Carstens creator: H. Lisle Gibbs uri: https://doi.org/10.7717/peerj.1647 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sovic et al. title: Combined effect of 17β-estradiol and resveratrol against apoptosis induced by interleukin-1β in rat nucleus pulposus cells via PI3K/Akt/caspase-3 pathway link: https://peerj.com/articles/1640 last-modified: 2016-01-26 description: Background: In previous studies, both 17β-estradiol (E2) and resveratrol (RES) were reported to protect intervertebral disc cells against aberrant apoptosis. Given that E2 has a better anti-apoptotic effect with more cancer risk and RES has an anti-apoptotic effect with less cancer risk, the combined use of E2 with RES is promising in developing clinical therapies to treat apoptosis-related diseases such as intervertebral disc degeneration in the future. Objective: The purpose of this study was to explore the combined effect of E2 with RES on rat nucleus pulposus cells and the underlying mechanisms. Methods: TUNEL assay and FACS analysis were used to determine apoptotic incidence of nucleus pulposus cells. MTS assay was used to determine cell viability, and cellular binding assay was used to determine cell-ECM (extracellular matrix) ability. Real-time quantitative RT-PCR was to determine mRNA level of target genes. And Western blot was used to determine the protein level. Results: Both E2 and RES decreased apoptotic incidence when used singly; interestingly, they decreased apoptosis more efficiently when used combinedly. Meanwhile, E2 and RES combined together against the decrease of cell viability and binding ability resulting from IL-1β cytotoxicity. As well, activated caspase-3 was suppressed by the combined effect. Furthermore, IL-1β downregulated expression level of type II collagen and aggrecan (standing for anabolism), while upregulated MMP-3 and MMP-13 (standing for catabolism). However, the combined use of E2 with RES effectively abolished the above negative effects caused by IL-1β, better than either single use. Finally, it turned out to be that E2 and RES combined together against apoptosis via the activation of PI3K/Akt/caspase-3 pathway. Conclusion: This study presented that IL-1β induced aberrant apoptosis, which was efficiently resisted by the combined use of E2 with RES via PI3K/Akt/caspase-3 pathway. creator: Si-Dong Yang creator: Lei Ma creator: Da-Long Yang creator: Wen-Yuan Ding uri: https://doi.org/10.7717/peerj.1640 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Yang et al. title: Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB link: https://peerj.com/articles/1638 last-modified: 2016-01-26 description: Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1–2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility. creator: Leng-Feng Lee creator: Brian R. Umberger uri: https://doi.org/10.7717/peerj.1638 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Lee & Umberger title: The Tibetan medicine Zuotai influences clock gene expression in the liver of mice link: https://peerj.com/articles/1632 last-modified: 2016-01-26 description: Background. The circadian clock is involved in drug metabolism, efficacy and toxicity. Drugs could in turn affect the biological clock as a mechanism of their actions. Zuotai is an essential component of many popular Tibetan medicines for sedation, tranquil and “detoxification,” and is mainly composed of metacinnabar (β-HgS). The pharmacological and/or toxicological basis of its action is unknown. This study aimed to examine the effect of Zuotai on biological clock gene expression in the liver of mice. Materials and methods. Mice were orally given Zuotai (10 mg/kg, 1.5-fold of clinical dose) daily for 7 days, and livers were collected every 4 h during the 24 h period. Total RNA was extracted and subjected to real-time RT-PCR analysis of circadian clock gene expression. Results. Zuotai decreased the oscillation amplitude of the clock core gene Clock, neuronal PAS domain protein 2 (Npas2), Brain and muscle Arnt-like protein-1 (Bmal1) at 10:00. For the clock feedback negative control genes, Zuotai had no effect on the oscillation of the clock gene Cryptochrome (Cry1) and Period genes (Per1–3). For the clock-driven target genes, Zuotai increased the oscillation amplitude of the PAR-bZip family member D-box-binding protein (Dbp), decreased nuclear factor interleukin 3 (Nfil3) at 10:00, but had no effect on thyrotroph embryonic factor (Tef); Zuotai increased the expression of nuclear receptor Rev-Erbα (Nr1d1) at 18:00, but had little influence on the nuclear receptor Rev-Erbβ (Nr1d2) and RORα. Conclusion. The Tibetan medicine Zuotai could influence the expression of clock genes, which could contribute to pharmacological and/or toxicological effects of Zuotai. creator: Huan Li creator: Wen-Kai Li creator: Yuan-Fu Lu creator: Li-Xin Wei creator: Jie Liu uri: https://doi.org/10.7717/peerj.1632 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Li et al. title: A new Lower Triassic ichthyopterygian assemblage from Fossil Hill, Nevada link: https://peerj.com/articles/1626 last-modified: 2016-01-26 description: We report a new ichthyopterygian assemblage from Lower Triassic horizons of the Prida Formation at Fossil Hill in central Nevada. Although fragmentary, the specimens collected so far document a diverse fauna. One partial jaw exhibits isodont dentition with blunt tipped, mesiodistally compressed crowns and striated enamel. These features are shared with the Early Triassic genus Utatsusaurus known from coeval deposits in Japan and British Columbia. An additional specimen exhibits a different dentition characterized by relatively small, rounded posterior teeth resembling other Early Triassic ichthyopterygians, particularly Grippia. This Nevada assemblage marks a southward latitudinal extension for Early Triassic ichthyopterygians along the eastern margin of Panthalassa and indicates repeated trans-hemispheric dispersal events in Early Triassic ichthyopterygians. creator: Neil P. Kelley creator: Ryosuke Motani creator: Patrick Embree creator: Michael J. Orchard uri: https://doi.org/10.7717/peerj.1626 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kelley et al. title: Influence of isoflurane on the diastolic pressure-flow relationship and critical occlusion pressure during arterial CABG surgery: a randomized controlled trial link: https://peerj.com/articles/1619 last-modified: 2016-01-26 description: The effects of isoflurane on the determinants of blood flow during Coronary Artery Bypass Graft (CABG) surgery are not completely understood. This study characterized the influence of isoflurane on the diastolic Pressure-Flow (P-F) relationship and Critical Occlusion Pressure (COP) during CABG surgery. Twenty patients undergoing CABG surgery were studied. Patients were assigned to an isoflurane or control group. Hemodynamic and flow measurements during CABG surgery were performed twice (15 minutes after the discontinuation of extracorporeal circulation (T15) and again 15 minutes later (T30)). The zero flow pressure intercept (a measure of COP) was extrapolated from a linear regression analysis of the instantaneous diastolic P-F relationship. In the isoflurane group, the application of isoflurane significantly increased the slope of the diastolic P-F relationship by 215% indicating a mean reduction of Coronary Vascular Resistance (CVR) by 46%. Simultaneously, the Mean Diastolic Aortic Pressure (MDAP) decreased by 19% mainly due to a decrease in the systemic vascular resistance index by 21%. The COP, cardiac index, heart rate, Left Ventricular End-Diastolic Pressure (LVEDP) and Coronary Sinus Pressure (CSP) did not change significantly. In the control group, the parameters remained unchanged. In both groups, COP significantly exceeded the CSP and LVEDP at both time points. We conclude that short-term application of isoflurane at a sedative concentration markedly increases the slope of the instantaneous diastolic P-F relationship during CABG surgery implying a distinct decrease with CVR in patients undergoing CABG surgery. creator: José Hinz creator: Ashham Mansur creator: Gerd G. Hanekop creator: Andreas Weyland creator: Aron F. Popov creator: Jan D. Schmitto creator: Frank F. G. Grüne creator: Martin Bauer creator: Stephan Kazmaier uri: https://doi.org/10.7717/peerj.1619 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hinz et al. title: Sustained attention in skilled and novice martial arts athletes: a study of event-related potentials and current sources link: https://peerj.com/articles/1614 last-modified: 2016-01-26 description: Background. Research on sports has revealed that behavioral responses and event-related brain potentials (ERP) are better in expert than in novice athletes for sport-related tasks. Focused attention is essential for optimal athletic performance across different sports but mainly in combat disciplines. During combat, long periods of focused attention (i.e., sustained attention) are required for a good performance. Few investigations have reported effects of expertise on brain electrical activity and its neural generators during sport-unrelated attention tasks. The aim of the present study was to assess the effect of expertise (i.e., skilled and novice martial arts athletes) analyzing the ERP during a sustained attention task (Continuous Performance Task; CPT) and the cortical three-dimensional distribution of current density, using the sLORETA technique. Methods. CPT consisted in an oddball-type paradigm presentation of five stimuli (different pointing arrows) where only one of them (an arrow pointing up right) required a motor response (i.e., target). CPT was administered to skilled and novice martial arts athletes while EEG were recorded. Amplitude ERP data from target and non-target stimuli were compared between groups. Subsequently, current source analysis for each ERP component was performed on each subject. sLORETA images were compared by condition and group using Statistical Non-Parametric Mapping analysis. Results. Skilled athletes showed significant amplitude differences between target and non-target conditions in early ERP components (P100 and P200) as opposed to the novice group; however, skilled athletes showed no significant effect of condition in N200 but novices did show a significant effect. Current source analysis showed greater differences in activations in skilled compared with novice athletes between conditions in the frontal (mainly in the Superior Frontal Gyrus and Medial Frontal Gyrus) and limbic (mainly in the Anterior Cingulate Gyrus) lobes. Discussion. These results are supported by previous findings regarding activation of neural structures that underlie sustained attention. Our findings may indicate a better-controlled attention in skilled athletes, which suggests that expertise can improve effectiveness in allocation of attentional resources during the first stages of cognitive processing during combat. creator: Javier Sanchez-Lopez creator: Juan Silva-Pereyra creator: Thalia Fernandez uri: https://doi.org/10.7717/peerj.1614 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sanchez-Lopez et al. title: A method for histopathological study of the multifocal nature of spinal cord lesions in murine experimental autoimmune encephalomyelitis link: https://peerj.com/articles/1600 last-modified: 2016-01-26 description: Experimental autoimmune encephalomyelitis (EAE) is a well-established mouse model for multiple sclerosis and is characterized by infiltration of mononuclear cells and demyelination within the central nervous system along with the clinical symptoms of paralysis. EAE is a multifocal and random disease, which sometimes makes histopathologic analysis of lesions difficult as it may not be possible to predict where lesions will occur, especially when evaluating cross sections of spinal cord. Consequently, lesions may be easily missed due to limited sampling in traditional approaches. To evaluate the entire length of the spinal cord while maintaining anatomic integrity, we have developed a method to section the cord within the decalcified spinal column, which allows for the study of the multifocal nature of this disease and also minimizes handling artifact. HE and Luxol fast blue staining of these spinal cord sections revealed a paucity of lesions in some areas, while others showed marked inflammation and demyelination. The percentage of spinal cord affected by EAE was evaluated at four separate areas of longitudinally sectioned cord and it varied greatly within each animal. Immunohistochemical staining of in situ spinal cords which had undergone decalcification was successful for key immuno-markers used in EAE research including CD3 for T cells, B220 for B cells and F4/80 for murine macrophages. This method will allow investigators to look at the entire spinal cord on a single slide and evaluate the spinal cord with and without classic EAE lesions. creator: Katherine N. Gibson-Corley creator: Alexander W. Boyden creator: Mariah R. Leidinger creator: Allyn M. Lambertz creator: Georgina Ofori-Amanfo creator: Paul W. Naumann creator: J. Adam Goeken creator: Nitin J. Karandikar uri: https://doi.org/10.7717/peerj.1600 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Gibson-Corley et al. title: First insights into the diversity of gill monogeneans of ‘Gnathochromis’ and Limnochromis (Teleostei, Cichlidae) in Burundi: do the parasites mirror host ecology and phylogenetic history? link: https://peerj.com/articles/1629 last-modified: 2016-01-25 description: Monogenea is one of the most species-rich groups of parasitic flatworms worldwide, with many species described only recently, which is particularly true for African monogeneans. For example, Cichlidogyrus, a genus mostly occurring on African cichlids, comprises more than 100 nominal species. Twenty-two of these have been described from Lake Tanganyika, a famous biodiversity hotspot in which many vertebrate and invertebrate taxa, including monogeneans, underwent unique and spectacular radiations. Given their often high degrees of host specificity, parasitic monogeneans were also used as a potential tool to uncover host species relationships. This study presents the first investigation of the monogenean fauna occurring on the gills of endemic ‘Gnathochromis’ species along the Burundese coastline of Lake Tanganyika. We test whether their monogenean fauna reflects the different phylogenetic position and ecological niche of ‘Gnathochromis’ pfefferi and Gnathochromis permaxillaris. Worms collected from specimens of Limnochromis auritus, a cichlid belonging to the same cichlid tribe as G. permaxillaris, were used for comparison. Morphological as well as genetic characterisation was used for parasite identification. In total, all 73 Cichlidogyrus individuals collected from ‘G.’ pfefferi were identified as C. irenae. This is the only representative of Cichlidogyrus previously described from ‘G.’ pfefferi, its type host. Gnathochromis permaxillaris is infected by a species of Cichlidogyrus morphologically very similar to C. gillardinae. The monogenean species collected from L. auritus is considered as new for science, but sample size was insufficient for a formal description. Our results confirm previous suggestions that ‘G.’ pfefferi as a good disperser is infected by a single monogenean species across the entire Lake Tanganyika. Although G. permaxillaris and L. auritus are placed in the same tribe, Cichlidogyrus sp. occurring on G. permaxillaris is morphologically more similar to C. irenae from ‘G.’ pfefferi, than to the Cichlidogyrus species found on L. auritus. Various evolutionary processes, such as host-switching or duplication events, might underlie the pattern observed in this particular parasite-host system. Additional samples for the Cichlidogyrus species occuring on G. permaxillaris and L. auritus are needed to unravel their evolutionary history by means of (co-)phylogenetic analyses. creator: Nikol Kmentová creator: Milan Gelnar creator: Stephan Koblmüller creator: Maarten P.M. Vanhove uri: https://doi.org/10.7717/peerj.1629 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kmentová et al. title: Age-related changes of dental pulp tissue after experimental tooth movement in rats link: https://peerj.com/articles/1625 last-modified: 2016-01-25 description: It is generally accepted that the effect of orthodontic tooth movement on the dental pulp in adolescents is reversible and that it has no long-lasting effect on pulpal physiology. However, it is not clear yet if the same conclusion is also valid for adult subjects. Thus, in two groups of rats, aged 6 and 40 weeks respectively, 3 molars at one side of the maxilla were moved together in a mesial direction with a standardized orthodontic appliance delivering a force of 10 cN. The contralateral side served as a control. Parasagittal histological sections were prepared after tooth movement for 1, 2, 4, 8, and 12 weeks. The pulp tissue was characterized for the different groups, with special emphasis on cell density, inflammatory cells, vascularity, and odontoblasts. Dimensions of dentin and the pulpal horns was determined and related with the duration of orthodontic force application and age ware evaluated. We found that neither in young nor in adult rats, force application led to long-lasting or irreversible changes in pulpal tissues. Dimensional variables showed significant age-related changes. In conclusion, orthodontic tooth movement per se has no long-lasting or irreversible effect on pulpal tissues, neither in the young nor in the adult animals. creator: Martina Von Böhl creator: Yijin Ren creator: Anne M. Kuijpers-Jagtman creator: Piotr S. Fudalej creator: Jaap C. Maltha uri: https://doi.org/10.7717/peerj.1625 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Von Böhl et al. title: An explicit solution for calculating optimum spawning stock size from Ricker’s stock recruitment model link: https://peerj.com/articles/1623 last-modified: 2016-01-25 description: Stock-recruitment models have been used for decades in fisheries management as a means of formalizing the expected number of offspring that recruit to a fishery based on the number of parents. In particular, Ricker’s stock recruitment model is widely used due to its flexibility and ease with which the parameters can be estimated. After model fitting, the spawning stock size that produces the maximum sustainable yield (SMSY) to a fishery, and the harvest corresponding to it (UMSY), are two of the most common biological reference points of interest to fisheries managers. However, to date there has been no explicit solution for either reference point because of the transcendental nature of the equation needed to solve for them. Therefore, numerical or statistical approximations have been used for more than 30 years. Here I provide explicit formulae for calculating both SMSY and UMSY in terms of the productivity and density-dependent parameters of Ricker’s model. creator: Mark D. Scheuerell uri: https://doi.org/10.7717/peerj.1623 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Scheuerell title: Molecular evidence for sediment nitrogen fixation in a temperate New England estuary link: https://peerj.com/articles/1615 last-modified: 2016-01-25 description: Primary production in coastal waters is generally nitrogen (N) limited with denitrification outpacing nitrogen fixation (N2-fixation). However, recent work suggests that we have potentially underestimated the importance of heterotrophic sediment N2-fixation in marine ecosystems. We used clone libraries to examine transcript diversity of nifH (a gene associated with N2-fixation) in sediments at three sites in a temperate New England estuary (Waquoit Bay, Massachusetts, USA) and compared our results to net sediment N2 fluxes previously measured at these sites. We observed nifH expression at all sites, including a site heavily impacted by anthropogenic N. At this N impacted site, we also observed mean net sediment N2-fixation, linking the geochemical rate measurement with nifH expression. This same site also had the lowest diversity (non-parametric Shannon = 2.75). At the two other sites, we also detected nifH transcripts, however, the mean N2 flux indicated net denitrification. These results suggest that N2-fixation and denitrification co-occur in these sediments. Of the unique sequences in this study, 67% were most closely related to uncultured bacteria from various marine environments, 17% to Cluster III, 15% to Cluster I, and only 1% to Cluster II. These data add to the growing body of literature that sediment heterotrophic N2-fixation, even under high inorganic nitrogen concentrations, may be an important yet overlooked source of N in coastal systems. creator: Silvia E. Newell creator: Kaitlyn R. Pritchard creator: Sarah Q. Foster creator: Robinson W. Fulweiler uri: https://doi.org/10.7717/peerj.1615 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Newell et al. title: Immunohistochemistry for the detection of neural and inflammatory cells in equine brain tissue link: https://peerj.com/articles/1601 last-modified: 2016-01-25 description: Phenotypic characterization of cellular responses in equine infectious encephalitides has had limited description of both peripheral and resident cell populations in central nervous system (CNS) tissues due to limited species-specific reagents that react with formalin-fixed, paraffin embedded tissue (FFPE). This study identified a set of antibodies for investigating the immunopathology of infectious CNS diseases in horses. Multiple commercially available staining reagents and antibodies derived from antigens of various species for manual immunohistochemistry (IHC) were screened. Several techniques and reagents for heat-induced antigen retrieval, non-specific protein blocking, endogenous peroxidase blocking, and visualization-detection systems were tested during IHC protocol development. Boiling of slides in a low pH, citrate-based buffer solution in a double-boiler system was most consistent for epitope retrieval. Pressure-cooking, microwaving, high pH buffers, and proteinase K solutions often resulted in tissue disruption or no reactivity. Optimal blocking reagents and concentrations of each working antibody were determined. Ultimately, a set of monoclonal (mAb) and polyclonal antibodies (pAb) were identified for CD3+ (pAb A0452, Dako) T-lymphocytes, CD79αcy+ B-lymphocytes (mAb HM57, Dako), macrophages (mAb MAC387, Leica), NF-H+ neurons (mAb NAP4, EnCor Biotechnology), microglia/macrophage (pAb Iba-1, Wako), and GFAP+ astrocytes (mAb 5C10, EnCor Biotechnology). In paraffin embedded tissues, mAbs and pAbs derived from human and swine antigens were very successful at binding equine tissue targets. Individual, optimized protocols are provided for each positively reactive antibody for analyzing equine neuroinflammatory disease histopathology. creator: Gretchen H. Delcambre creator: Junjie Liu creator: Jenna M. Herrington creator: Kelsey Vallario creator: Maureen T. Long uri: https://doi.org/10.7717/peerj.1601 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Delcambre et al. title: The feasibility and radiological features of sacral alar iliac fixation in an adult population: a 3D imaging study link: https://peerj.com/articles/1587 last-modified: 2016-01-25 description: Background: Surgical treatments for adult spinal deformities often include pelvic fixation, and the feasibility of sacral-2 alar iliac (S2AI) screw fixation has been shown previously. However, sometimes S2AI screw fixation cannot be applied due to the presence of an osteolytic lesion or trauma or because the biomechanical properties of only an S2AI screw is insufficient. Therefore, we questioned the feasibility of using sacral AI screws in other segments and determined whether S3AI and S4AI screws have the potential to be used for sacral fractures. The aim of this study was to investigate the feasibility and radiological features of sacral AI fixation in S1–S4 in an adult population using 3D imaging techniques. Methods: Computed tomography (CT) scans were taken of 45 patients and were imported into Mimics (Version 10.01, Materialise, Belgium) software to reconstruct the 3D digital images. Next, a cylinder (radius of 3.5 mm) was drawn to imitate the screw trajectory of a S1–4 AI screw, and every imitated screw in each segment was adjusted to a maximum upward and downward angle to acquire the feasible region. The parameters of the S1–4AI screw trajectories were measured. Results: Sacral AI screws could be successfully imitated using 3D digital imaging. The S4AI screw trajectory could be obtained in 19 of 45 patient images (42.2%), while the feasibility rates of S1AI, S2AI, and S3AI screw fixation were 100%, 100%, and 91.1% (41/45), respectively. The feasible regions of S1AI, S2AI, and S3AI screw trajectories were wide enough, while the adjustable angle of S4AI screws was very small. Conclusion: It is feasible to place S1–2AI screws in the entire adult population and S3–4AI screws in some of the adult population. Furthermore, our study suggested that 3D digital images are suitable to study the feasibility of new screw fixation. creator: Ai-Min Wu creator: Yong-Long Chi creator: Wen-Fei Ni creator: Yi-Xing Huang uri: https://doi.org/10.7717/peerj.1587 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Wu et al. title: Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus) link: https://peerj.com/articles/1566 last-modified: 2016-01-25 description: Social insects use odors as cues for a variety of behavioral responses, including nestmate recognition. Past research on nestmate recognition indicates cuticular hydrocarbons are important nestmate discriminators for social insects, but other factors are likely to contribute to colony-specific odors. Here we experimentally tested whether external microbes contribute to nestmate recognition in red harvester ants (Pogonomyrmex barbatus). We changed the external microbiome of ants through topical application of either antibiotics or microbial cultures. We then observed behavior of nestmates when treated ants were returned to the nest. Ants whose external microbiome was augmented with microbial cultures were much more likely to be rejected than controls, but ants treated with antibiotics were not. This result is consistent with the possibility that external microbes are used for nestmate recognition. creator: Andy Dosmann creator: Nassim Bahet creator: Deborah M. Gordon uri: https://doi.org/10.7717/peerj.1566 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dosmann et al. title: Structural strength of cancellous specimens from bovine femur under cyclic compression link: https://peerj.com/articles/1562 last-modified: 2016-01-25 description: The incidence of osteoporotic fractures was estimated as nine million worldwide in 2000, with particular occurrence at the proximity of joints rich in cancellous bone. Although most of these fractures spontaneously heal, some fractures progressively collapse during the early post-fracture period. Prediction of bone fragility during progressive collapse following initial fracture is clinically important. However, the mechanism of collapse, especially the gradual loss of the height in the cancellous bone region, is not clearly proved. The strength of cancellous bone after yield stress is difficult to predict since structural and mechanical strength cannot be determined a priori. The purpose of this study was to identify whether the baseline structure and volume of cancellous bone contributed to the change in cancellous bone strength under cyclic loading. A total of fifteen cubic cancellous bone specimens were obtained from two 2-year-old bovines and divided into three groups by collection regions: femoral head, neck, and proximal metaphysis. Structural indices of each 5-mm cubic specimen were determined using micro-computed tomography. Specimens were then subjected to five cycles of uniaxial compressive loading at 0.05 mm/min with initial 20 N loading, 0.3 mm displacement, and then unloading to 0.2 mm with 0.1 mm displacement for five successive cycles. Elastic modulus and yield stress of cancellous bone decreased exponentially during five loading cycles. The decrease ratio of yield stress from baseline to fifth cycle was strongly correlated with bone volume fraction (BV/TV, r = 0.96, p < 0.01) and structural model index (SMI, r = − 0.81, p < 0.01). The decrease ratio of elastic modulus from baseline to fifth cycle was also correlated with BV/TV (r = 0.80, p < 0.01) and SMI (r = − 0.78, p < 0.01). These data indicate that structural deterioration of cancellous bone is associated with bone strength after yield stress. This study suggests that baseline cancellous bone structure estimated from adjacent non-fractured bone contributes to the cancellous bone strength during collapse. creator: Kaori Endo creator: Satoshi Yamada creator: Masahiro Todoh creator: Masahiko Takahata creator: Norimasa Iwasaki creator: Shigeru Tadano uri: https://doi.org/10.7717/peerj.1562 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Endo et al. title: Isolation and characterization of eight polymorphic microsatellites for the spotted spiny lobster, Panulirus guttatus link: https://peerj.com/articles/1467 last-modified: 2016-01-25 description: Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%). These eight microsatellites provide novel molecular markers for future conservation genetics research of P. guttatus. creator: Nathan Truelove creator: Donald C. Behringer creator: Mark J. Butler IV creator: Richard F. Preziosi uri: https://doi.org/10.7717/peerj.1467 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Truelove et al. title: Cross-platform normalization of microarray and RNA-seq data for machine learning applications link: https://peerj.com/articles/1621 last-modified: 2016-01-21 description: Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language. creator: Jeffrey A. Thompson creator: Jie Tan creator: Casey S. Greene uri: https://doi.org/10.7717/peerj.1621 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Thompson et al. title: Microscopical and elemental FESEM and Phenom ProX-SEM-EDS analysis of osteocyte- and blood vessel-like microstructures obtained from fossil vertebrates of the Eocene Messel Pit, Germany link: https://peerj.com/articles/1618 last-modified: 2016-01-21 description: The Eocene (∾48 Ma) Messel Pit in Germany is a UNESCO World Heritage Site because of its exceptionally preserved fossils, including vertebrates, invertebrates, and plants. Messel fossil vertebrates are typically characterized by their articulated state, and in some cases the skin, hair, feathers, scales and stomach contents are also preserved. Despite the exceptional macroscopic preservation of Messel fossil vertebrates, the microstructural aspect of these fossils has been poorly explored. In particular, soft tissue structures such as hair or feathers have not been chemically analyzed, nor have bone microstructures. I report here the preservation and recovery of osteocyte-like and blood vessel-like microstructures from the bone of Messel Pit specimens, including the turtles Allaeochelys crassesculpta and Neochelys franzeni, the crocodile Diplocynodon darwini, and the pangolin Eomanis krebsi. I used a Field Emission Scanning Electron Microscope (FESEM) and a Phenom ProX desktop scanning electron microscope (LOT-QuantumDesign) equipped with a thermionic CeB6 source and a high sensitivity multi-mode backscatter electron (BSE) for microscopical and elemental characterization of these bone microstructures. Osteocyte-like and blood vessel-like microstructures are constituted by a thin layer (∾50 nm thickness), external and internal mottled texture with slightly marked striations. Circular to linear marks are common on the external surface of the osteocyte-like microstructures and are interpreted as microbial troughs. Iron (Fe) is the most abundant element found in the osteocyte-like and blood vessel-like microstructures, but not in the bone matrix or collagen fibril-like microstructures. The occurrence of well-preserved soft-tissue elements (at least their physical form) establishes a promising background for future studies on preservation of biomolecules (proteins or DNA) in Messel Pit fossils. creator: Edwin Cadena uri: https://doi.org/10.7717/peerj.1618 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cadena title: The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content link: https://peerj.com/articles/1612 last-modified: 2016-01-21 description: Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis. creator: Zachery T. Lewis creator: Jasmine C.C. Davis creator: Jennifer T. Smilowitz creator: J. Bruce German creator: Carlito B. Lebrilla creator: David A. Mills uri: https://doi.org/10.7717/peerj.1612 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lewis et al. title: Chronic unpredicted mild stress-induced depression alter saxagliptin pharmacokinetics and CYP450 activity in GK rats link: https://peerj.com/articles/1611 last-modified: 2016-01-21 description: Background. This study was to explore the pharmacokinetics of saxagliptin (Sax) in Goto–Kakizaki (GK) rats complicated with depression induced by chronic unpredicted mild stress (CUMS). The comorbidity of diabetic patients with depression is becoming more and more epidemic. Whether depression mental disorder alters the pharmacokinetics of hypoglycemic drugs in diabetes patients is not clear.Methods. Five-week-old male GK rats were kept in the cage for 7 weeks in a specific pathogen free (SPF)-grade lab until the emergence of diabetes and were then divided into two groups: control group and depression model group. Rats in the CUMS-induced depression group were exposed to a series of stressors for 8 weeks. Plasma serotonin and dopamine levels and behavior of open-field test were used to confirm the establishment of the depression model. All rats were given 0.5 mg/kg Sax orally after 8 weeks and blood samples were collected at different time points. The Sax concentration was assayed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The CYP450 activity of the liver microsomes was determined by using cocktails of probe drugs in which the activities of CYP enzymes were assessed through the determination of the production of the probe drugs.Results. Statistically significant differences in Sax pharmacokinetics were observed for area under curve, clearance, peak concentration, peak time and mean residence time between the depression rats and the control rats, while no statistical differences were observed for half-time and distribution volume by HPLC-MS/MS analysis. The CYP450 activity had different changes in the depression group.Conclusions. These results indicated that CUMS-induced depression alters the drug metabolic process of Sax and CYP450 activity of the liver microsomal enzymes in GK rats. creator: Zhengchao Xia creator: Hongyan Wei creator: Jingjing Duan creator: Ting Zhou creator: Zhen Yang creator: Feng Xu uri: https://doi.org/10.7717/peerj.1611 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Xia et al. title: Molecular diversity of bacteria in commercially available “Spirulina” food supplements link: https://peerj.com/articles/1610 last-modified: 2016-01-21 description: The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes. creator: Elisabeth Vardaka creator: Konstantinos A. Kormas creator: Matina Katsiapi creator: Savvas Genitsaris creator: Maria Moustaka-Gouni uri: https://doi.org/10.7717/peerj.1610 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Vardaka et al. title: Bust economics: foragers choose high quality habitats in lean times link: https://peerj.com/articles/1609 last-modified: 2016-01-21 description: In environments where food resources are spatially variable and temporarily impoverished, consumers that encounter habitat patches with different food density should focus their foraging initially where food density is highest before they move to patches where food density is lower. Increasing missed opportunity costs should drive individuals progressively to patches with lower food density as resources in the initially high food density patches deplete. To test these expectations, we assessed the foraging decisions of two species of dasyurid marsupials (dunnarts: Sminthopsis hirtipes and S. youngsoni) during a deep drought, or bust period, in the Simpson Desert of central Australia. Dunnarts were allowed access to three patches containing different food densities using an interview chamber experiment. Both species exhibited clear preference for the high density over the lower food density patches as measured in total harvested resources. Similarly, when measuring the proportion of resources harvested within the patches, we observed a marginal preference for patches with initially high densities. Models analyzing behavioral choices at the population level found no differences in behavior between the two species, but models analyzing choices at the individual level uncovered some variation. We conclude that dunnarts can distinguish between habitat patches with different densities of food and preferentially exploit the most valuable. As our observations were made during bust conditions, experiments should be repeated during boom times to assess the foraging economics of dunnarts when environmental resources are high. creator: Sonny S. Bleicher creator: Christopher R. Dickman uri: https://doi.org/10.7717/peerj.1609 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bleicher and Dickman title: Comparative morphology of the mouthparts of the megadiverse South African monkey beetles (Scarabaeidae: Hopliini): feeding adaptations and guild structure link: https://peerj.com/articles/1597 last-modified: 2016-01-21 description: Although anthophilous Coleoptera are regarded to be unspecialised flower-visiting insects, monkey beetles (Scarabaeidae: Hopliini) represent one of the most important groups of pollinating insects in South Africa’s floristic hotspot of the Greater Cape Region. South African monkey beetles are known to feed on floral tissue; however, some species seem to specialise on pollen and/or nectar. The present study examined the mouthpart morphology and gut content of various hopliine species to draw conclusions on their feeding preferences. According to the specialisations of their mouthparts, the investigated species were classified into different feeding groups. Adaptations to pollen-feeding included a well-developed, toothed molar and a lobe-like, setose lacinia mobilis on the mandible as well as curled hairs or sclerotized teeth on the galea of the maxillae. Furthermore, elongated mouthparts were interpreted as adaptations for nectar feeding. Floral- and folial-tissue feeding species showed sclerotized teeth on the maxilla, but the lacinia was mostly found to be reduced to a sclerotized ledge. While species could clearly be identified as floral or folial tissue feeding, several species showed intermediate traits suggesting both pollen and nectar feeding adaptations. Mismatches found between mouthpart morphology and previously reported flower visiting behaviours across different genera and species requires alternative explanations, not necessarily associated with feeding preferences. Although detailed examinations of the mouthparts allowed conclusions about the feeding preference and flower-visiting behaviour, additional morphological and behavioural investigations, combined with greater taxon sampling and phylogenetic data, are still necessary to fully understand hopliine host plant relationships, related to monkey beetle diversity. creator: Florian Karolyi creator: Teresa Hansal creator: Harald W. Krenn creator: Jonathan F. Colville uri: https://doi.org/10.7717/peerj.1597 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Karolyi et al. title: Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage link: https://peerj.com/articles/1584 last-modified: 2016-01-21 description: The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths. creator: Chodon Sass creator: William J.D. Iles creator: Craig F. Barrett creator: Selena Y. Smith creator: Chelsea D. Specht uri: https://doi.org/10.7717/peerj.1584 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sass et al. title: Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets link: https://peerj.com/articles/1583 last-modified: 2016-01-21 description: Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now contains Neoaetosauroides engaeus and several taxa that were previously referred to the genus Stagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related to Desmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures. creator: William G. Parker uri: https://doi.org/10.7717/peerj.1583 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Parker title: Rat liver regeneration following ablation with irreversible electroporation link: https://peerj.com/articles/1571 last-modified: 2016-01-21 description: During the past decade, irreversible electroporation (IRE) ablation has emerged as a promising tool for the treatment of multiple diseases including hepatic cancer. However, the mechanisms behind the tissue regeneration following IRE ablation have not been investigated. Our results indicate that IRE treatment immediately kills the cells at the treatment site preserving the extracellular architecture, in effect causing in vivo decellularization. Over the course of 4 weeks, progenitor cell differentiation, through YAP and notch pathways, together with hepatocyte expansion led to almost complete regeneration of the ablated liver leading to the formation of hepatocyte like cells at the ablated zone. We did not observe significant scarring or tumor formation at the regenerated areas 6 months post IRE. Our study suggests a new model to study the regeneration of liver when the naïve extracellular matrix is decellularized in vivo with completely preserved extracellular architecture. creator: Alexander Golberg creator: Bote G. Bruinsma creator: Maria Jaramillo creator: Martin L. Yarmush creator: Basak E. Uygun uri: https://doi.org/10.7717/peerj.1571 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Golberg et al. title: Potential impact of co-payment at point of care to influence emergency department utilization link: https://peerj.com/articles/1544 last-modified: 2016-01-21 description: Background. Many proponents for healthcare reform suggest increased cost-sharing by patients as a method to reduce overall expenditures. Prior studies on the effects of co-payments for ED visits have generally not been directed toward understanding patient attitudes/behavior at point of care.Objectives. We conducted a survey at point of care to test our hypothesis that a significant number of patients with urgent chief complaints might have avoided the ED if asked to provide a co-payment.Methods. Cross-sectional study design. Stable, oriented, consenting patients at an inner-city, academic ED were consecutively enrolled at hours in which trained research associates were available to assist with data collection. Enrolled patients completed a written survey providing demographic/chief complaint information, and then were asked whether 13 interval amounts of co-payment ranging from 0 to >500 would have impacted their decision to visit the ED. Categorical data are presented as frequency of occurrence and analyzed by chi-square; continuous data presented as means ± standard deviation, analyzed by t-tests. ORs and 95% confidence intervals provided. Primary outcome parameter was the % of patients who would have avoided the ED if asked to pay any co-payment for several urgent chief complaints: chest pain, SOB, and abdominal pain.Results. A total of 581 patients were enrolled; 63.1% female, mean age 42.4 ± 15.1 years, 65% Hispanic, 71.2% income less than 20,000, 28.6% less than high school graduate, 81.3% had primary care physician, 57.6% had 2 or more ED visits/past year. Overall, 30.2% of patients chose 0 as the maximum they would have been willing to pay if it was required to be seen in the ED. 16/58 (28%; 95% CI [18–40%]) of chest pain patients, 9/43 (20.9%; 95% CI [11–35%]) of SOB patients, and 24/127 (26.8%; 95% CI [13–27%]) of abdominal pain patients would have been unwilling to pay a co-pay. Patients with income >20,000 were more willing to pay a co-payment (OR = 2.55; 95% CI [1.59–4.10]). No significant relationship was identified between willingness to pay for: gender, race, education, established primary care provider, and frequency of ED visits.Conclusion. Overall, 30.2% of our patients would not have accepted a co-pay in order to be seen, including more than 20% of the patients with chest pain, shortness of breath, and abdominal pain respectively. creator: Zachary Baum creator: Michael R. Simmons creator: Jose H. Guardiola creator: Cynthia Smith creator: Lynn Carrasco creator: Joann Ha creator: Peter Richman uri: https://doi.org/10.7717/peerj.1544 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baum et al. title: Arthropods of the great indoors: characterizing diversity inside urban and suburban homes link: https://peerj.com/articles/1582 last-modified: 2016-01-19 description: Although humans and arthropods have been living and evolving together for all of our history, we know very little about the arthropods we share our homes with apart from major pest groups. Here we surveyed, for the first time, the complete arthropod fauna of the indoor biome in 50 houses (located in and around Raleigh, North Carolina, USA). We discovered high diversity, with a conservative estimate range of 32–211 morphospecies, and 24–128 distinct arthropod families per house. The majority of this indoor diversity (73%) was made up of true flies (Diptera), spiders (Araneae), beetles (Coleoptera), and wasps and kin (Hymenoptera, especially ants: Formicidae). Much of the arthropod diversity within houses did not consist of synanthropic species, but instead included arthropods that were filtered from the surrounding landscape. As such, common pest species were found less frequently than benign species. Some of the most frequently found arthropods in houses, such as gall midges (Cecidomyiidae) and book lice (Liposcelididae), are unfamiliar to the general public despite their ubiquity. These findings present a new understanding of the diversity, prevalence, and distribution of the arthropods in our daily lives. Considering their impact as household pests, disease vectors, generators of allergens, and facilitators of the indoor microbiome, advancing our knowledge of the ecology and evolution of arthropods in homes has major economic and human health implications. creator: Matthew A. Bertone creator: Misha Leong creator: Keith M. Bayless creator: Tara L.F. Malow creator: Robert R. Dunn creator: Michelle D. Trautwein uri: https://doi.org/10.7717/peerj.1582 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bertone et al. title: Association of trait and specific hopes: cross sectional study on students and workers of health professions in Split, Croatia link: https://peerj.com/articles/1604 last-modified: 2016-01-19 description: Introduction. Hope (hoping) is most commonly assessed as a dispositional trait and associated with quality of life, self-care agency and non-attempts of suicide. However, little research has been conducted on hoping for specific events.Materials and Methods. We distributed a survey consisting of Integrative Hope Scale (IHS) and visual analogue scales on which respondents could declare their levels (intensity) of hope for specific events, to all first year health students enrolled at the University Department of Health Studies, Split, Croatia in 2011/2012, as well as to working health professionals attending a nursing conference in April 2012.Results. A total of 161 (89.4%) students and 88 (89.8%) working health professionals returned the completed questionnaires. We found high trait hope scores of students and working health professionals (Md = 111, 95% CI [109–113] vs. Md = 115, 95% CI [112–119]; U = 5,353, P = 0.065), and weak to moderate correlations of trait and specific hopes (r = 0.18–0.48, Spearman’s rank correlation coefficient). Students and workers reported 31 different things they hoped for most in life, of which the most prevalent were being healthy and happy. There was very little agreement between participants’ reported influence of the four factors compromising the trait hope (self-confidence, ambition, optimism, and social support) on their specific hopes.Conclusions. Our findings, while strengthening the validity of hope as a trait, indicate that specific hopes of individuals are moderated by factors not captured by the IHS trait scale. Further research should explore specific hoping in detail, as well as the effectiveness of interventions aimed at increasing specific or generalized hoping. creator: Mario Malički creator: Domagoj Marković creator: Matko Marušić uri: https://doi.org/10.7717/peerj.1604 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Malički et al. title: Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene link: https://peerj.com/articles/1602 last-modified: 2016-01-19 description: Background. It is widely assumed that the uterine cavity in non-pregnant women is physiologically sterile, also as a premise to the long-held view that human infants develop in a sterile uterine environment, though likely reflecting under-appraisal of the extent of the human bacterial metacommunity. In an exploratory study, we aimed to investigate the putative presence of a uterine microbiome in a selected series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene.Methods. Nineteen women with various reproductive conditions, including subfertility, scheduled for hysteroscopy and not showing uterine anomalies were recruited. Subjects were highly diverse with regard to demographic and medical history and included nulliparous and parous women. Endometrial tissue and mucus harvesting was performed by use of a transcervical device designed to obtain endometrial biopsy, while avoiding cervicovaginal contamination. Bacteria were targeted by use of a barcoded Illumina MiSeq paired-end sequencing method targeting the 16S rRNA gene V1-2 region, yielding an average of 41,194 reads per sample after quality filtering. Taxonomic annotation was pursued by comparison with sequences available through the Ribosomal Database Project and the NCBI database.Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 phylotypes were present in all samples. In some 90% of the women included, community architecture was fairly similar inasmuch B. xylanisolvens, B. thetaiotaomicron, B. fragilis and an undetermined Pelomonas taxon constituted over one third of the endometrial bacterial community. On the singular phylotype level, six women showed predominance of L. crispatus or L. iners in the presence of the Bacteroides core. Two endometrial communities were highly dissimilar, largely lacking the Bacteroides core, one dominated by L. crispatus and another consisting of a highly diverse community, including Prevotella spp., Atopobium vaginae, and Mobiluncus curtisii.Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiota dominated by Bacteroides residing on the endometrium of the human non-pregnant uterus. The transcervical sampling approach may be influenced to an unknown extent by endocervical microbiota, which remain uncharacterised, and therefore warrants further validation. Nonetheless, consistent with our understanding of the human microbiome, the uterine microbiota are likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease. creator: Hans Verstraelen creator: Ramiro Vilchez-Vargas creator: Fabian Desimpel creator: Ruy Jauregui creator: Nele Vankeirsbilck creator: Steven Weyers creator: Rita Verhelst creator: Petra De Sutter creator: Dietmar H. Pieper creator: Tom Van De Wiele uri: https://doi.org/10.7717/peerj.1602 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Verstraelen et al. title: Low regeneration of lesions produced by coring in Orbicella faveolata link: https://peerj.com/articles/1596 last-modified: 2016-01-19 description: The extraction of tissue-skeleton cores from coral colonies is a common procedure to study diverse aspects of their biology, water quality or to obtain environmental proxies. Coral species preferred for such studies in Caribbean reefs belong to the genera Orbicella. The long term effects of coring in the coral colony are seldom evaluated and in many Caribbean countries this practice is not regulated. We monitored 50 lesions produced on Orbicella faveolata colonies by the extraction of two centimeter-diameter cores to determine if they were able to heal after a four year period. At the end of the study 4% of the lesions underwent full regeneration, 52% underwent partial regeneration, 14% suffered additional tissue loss but remained surrounded by live tissue, and 30% merged with dead areas of the colonies. Given the low capacity of Orbicella faveolata to regenerate tissue-skeleton lesions, studies that use coring should be regulated and mitigation actions, such as using less destructive techniques and remediation measures after extraction, should be conducted to facilitate tissue regeneration. creator: Rosa E. Rodríguez-Martínez creator: Adán Guillermo Jordán-Garza creator: Eric Jordán-Dahlgren uri: https://doi.org/10.7717/peerj.1596 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rodríguez-Martínez et al. title: Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments link: https://peerj.com/articles/1593 last-modified: 2016-01-19 description: Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning. creator: Petter Thureborn creator: Andrea Franzetti creator: Daniel Lundin creator: Sara Sjöling uri: https://doi.org/10.7717/peerj.1593 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Thureborn et al. title: Not so sluggish: the success of the Felimare picta complex (Gastropoda, Nudibranchia) crossing Atlantic biogeographic barriers link: https://peerj.com/articles/1561 last-modified: 2016-01-19 description: The molecular phylogeny of the Atlanto-Mediterranean species of the genus Felimare, particularly those attributed to the species F. picta, was inferred using two mitochondrial markers (16S and COI). A recent revision of the Chromodorididae clarified the taxonomic relationships at the family level redefining the genus Felimare. However, conflicting taxonomic classifications have been proposed for a restrict group of taxa with overlapping morphological characteristics and geographical distributions designated here as the Felimare picta complex. Three major groups were identified: one Mediterranean and amphi-Atlantic group; a western Atlantic group and a tropical eastern Atlantic group. F. picta forms a paraphyletic group since some subspecies are more closely related with taxa traditionaly classified as independent species (e.g. F. zebra) than with other subspecies with allopatric distributions (e.g. F. picta picta and F. picta tema). Usually, nudibranchs have adhesive demersal eggs, short planktonic larval phases and low mobility as adults unless rafting on floating materials occurs. Surprisingly however, the phylogeny of the F. picta complex suggests that they successfully cross main Atlantic biogeographic barriers including the mid-Atlantic barrier. This ability to cross different biogeographic barriers may be related to F. picta’s distinct life history and ecological traits. Compared to other Chromodorididae F. picta has larger eggs and planktotrophic larvae which could be related to a longer planktonic phase. creator: Frederico Almada creator: André Levy creator: Joana I. Robalo uri: https://doi.org/10.7717/peerj.1561 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Almada et al. title: Mining integrated semantic networks for drug repositioning opportunities link: https://peerj.com/articles/1558 last-modified: 2016-01-19 description: Current research and development approaches to drug discovery have become less fruitful and more costly. One alternative paradigm is that of drug repositioning. Many marketed examples of repositioned drugs have been identified through serendipitous or rational observations, highlighting the need for more systematic methodologies to tackle the problem. Systems level approaches have the potential to enable the development of novel methods to understand the action of therapeutic compounds, but requires an integrative approach to biological data. Integrated networks can facilitate systems level analyses by combining multiple sources of evidence to provide a rich description of drugs, their targets and their interactions. Classically, such networks can be mined manually where a skilled person is able to identify portions of the graph (semantic subgraphs) that are indicative of relationships between drugs and highlight possible repositioning opportunities. However, this approach is not scalable. Automated approaches are required to systematically mine integrated networks for these subgraphs and bring them to the attention of the user. We introduce a formal framework for the definition of integrated networks and their associated semantic subgraphs for drug interaction analysis and describe DReSMin, an algorithm for mining semantically-rich networks for occurrences of a given semantic subgraph. This algorithm allows instances of complex semantic subgraphs that contain data about putative drug repositioning opportunities to be identified in a computationally tractable fashion, scaling close to linearly with network data. We demonstrate the utility of our approach by mining an integrated drug interaction network built from 11 sources. This work identified and ranked 9,643,061 putative drug-target interactions, showing a strong correlation between highly scored associations and those supported by literature. We discuss the 20 top ranked associations in more detail, of which 14 are novel and 6 are supported by the literature. We also show that our approach better prioritizes known drug-target interactions, than other state-of-the art approaches for predicting such interactions. creator: Joseph Mullen creator: Simon J. Cockell creator: Hannah Tipney creator: Peter M. Woollard creator: Anil Wipat uri: https://doi.org/10.7717/peerj.1558 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mullen et al. title: Unravelling the potential of nitric acid as a surface modifier for improving the hemocompatibility of metallocene polyethylene for blood contacting devices link: https://peerj.com/articles/1388 last-modified: 2016-01-19 description: Design of blood compatible surfaces is obligatory to minimize platelet surface interactions and improve the thromboresistance of foreign surfaces when they are utilized as biomaterials particularly for blood contacting devices. Pure metallocene polyethylene (mPE) and nitric acid (HNO3) treated mPE antithrombogenicity and hydrophilicity were investigated. The contact angle of the mPE treated with HNO3 decreased. Surface of mPE and HNO3 treated mPE investigated with FTIR revealed no major changes in its functional groups. 3D Hirox digital microscopy, SEM and AFM images show increased porosity and surface roughness. Blood coagulation assays prothrombin time (PT) and activated partial thromboplastin time (APTT) were delayed significantly (P < 0.05) for HNO3 treated mPE. Hemolysis assay and platelet adhesion of the treated surface resulted in the lysis of red blood cells and platelet adherence, respectively indicating improved hemocompatibility of HNO3 treated mPE. To determine that HNO3 does not deteriorate elastic modulus of mPE, the elastic modulus of mPE and HNO3 treated mPE was compared and the result shows no significant difference. Hence, the overall observation suggests that the novel HNO3 treated mPE may hold great promises to be exploited for blood contacting devices like grafts, catheters, and etc. creator: Muthu Vignesh Vellayappan creator: Saravana Kumar Jaganathan creator: Ida Idayu Muhamad uri: https://doi.org/10.7717/peerj.1388 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Vellayappan et al. title: Pharmacophagy in green lacewings (Neuroptera: Chrysopidae: Chrysopa spp.)? link: https://peerj.com/articles/1564 last-modified: 2016-01-18 description: Green lacewings (Neuroptera: Chrysopidae) are voracious predators of aphids and other small, soft-bodied insects and mites. Earlier, we identified (1R,2S,5R,8R)-iridodial from wild males of the goldeneyed lacewing, Chrysopa oculata Say, which is released from thousands of microscopic dermal glands on the abdominal sterna. Iridodial-baited traps attract C. oculata and other Chrysopa spp. males into traps, while females come to the vicinity of, but do not usually enter traps. Despite their healthy appearance and normal fertility, laboratory-reared C. oculata males do not produce iridodial. Surprisingly, goldeneyed lacewing males caught alive in iridodial-baited traps attempt to eat the lure and, in Asia, males of other Chrysopa species reportedly eat the native plant, Actinidia polygama (Siebold & Zucc.) Maxim. (Actinidiaceae) to obtain the monoterpenoid, neomatatabiol. These observations suggest that Chrysopa males must sequester exogenous natural iridoids in order to produce iridodial; we investigated this phenomenon in laboratory feeding studies. Lacewing adult males fed various monoterpenes reduced carbonyls to alcohols and saturated double bonds, but did not convert these compounds to iridodial. Only males fed the common aphid sex pheromone component, (1R,4aS,7S,7aR)-nepetalactol, produced (1R,2S,5R,8R)-iridodial. Furthermore, although C. oculata males fed the second common aphid sex pheromone component, (4aS,7S,7aR)-nepetalactone, did not produce iridodial, they did convert ∼75% of this compound to the corresponding dihydronepetalactone, and wild C. oculata males collected in early spring contained traces of this dihydronepetalactone. These findings are consistent with the hypothesis that Chrysopa males feed on oviparae (the late-season pheromone producing stage of aphids) to obtain nepetalactol as a precursor to iridodial. In the spring, however, wild C. oculata males produce less iridodial than do males collected later in the season. Therefore, we further hypothesize that Asian Chrysopa eat A. polygama to obtain iridoid precursors in order to make their pheromone, and that other iridoid-producing plants elsewhere in the world must be similarly usurped by male Chrysopa species to sequester pheromone precursors. creator: Jeffrey R. Aldrich creator: Kamal Chauhan creator: Qing-He Zhang uri: https://doi.org/10.7717/peerj.1564 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Aldrich et al. title: Expression patterns of cysteine peptidase genes across the Tribolium castaneum life cycle provide clues to biological function link: https://peerj.com/articles/1581 last-modified: 2016-01-18 description: The red flour beetle, Tribolium castaneum, is a major agricultural pest responsible for considerable loss of stored grain and cereal products worldwide. T. castaneum larvae have a highly compartmentalized gut, with cysteine peptidases mostly in the acidic anterior part of the midgut that are critical to the early stages of food digestion. In previous studies, we described 26 putative cysteine peptidase genes in T. castaneum (types B, L, O, F, and K) located mostly on chromosomes 3, 7, 8, and 10. In the present study, we hypothesized that specific cysteine peptidase genes could be associated with digestive functions for food processing based on comparison of gene expression profiles in different developmental stages, feeding and non-feeding. RNA-Seq was used to determine the relative expression of cysteine peptidase genes among four major developmental stages (egg, larvae, pupae, and adult) of T. castaneum. We also compared cysteine peptidase genes in T. castaneum to those in other model insects and coleopteran pests. By combining transcriptome expression, phylogenetic comparisons, response to dietary inhibitors, and other existing data, we identified key cysteine peptidases that T. castaneum larvae and adults use for food digestion, and thus new potential targets for biologically-based control products. creator: Lindsey Perkin creator: Elena N. Elpidina creator: Brenda Oppert uri: https://doi.org/10.7717/peerj.1581 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: The role of geography and host abundance in the distribution of parasitoids of an alien pest link: https://peerj.com/articles/1592 last-modified: 2016-01-18 description: Chalcid wasps (Hymenoptera: Chalcidoidea) are probably the most effective and abundant parasitoids of the horse chestnut leaf miner (Cameraria ohridella), an alien pest in Europe that lacks specialized enemies. We studied how the species richness and abundance of chalcids are influenced by altitude, direction of an alien spread and host abundance of C. ohridella. We quantified the numbers and species richness of chalcid wasps and the numbers of C. ohridella that emerged from horse chestnut (Aesculus hippocastanum) leaf litter samples collected from 35 sites in the Czech Republic. Species richness of chalcids, which was considered an indicator of the possible adaptation of parasitoids to this alien host, was unrelated to C. ohridella abundance, direction of spread, or altitude. Chalcid abundance, which was considered an indicator of parasitism of the alien host, was strongly and positively related to C. ohridella abundance. Chalcid abundance was negatively related to direction of spread and positively related, although in a non-linear manner, to altitude. The relationship of chalcid abundance with direction of spread and altitude was weaker than that with C. ohridella abundance. The results provide evidence that biological control of the alien pest C. ohridella by natural enemies might develop in the future. creator: Petra Nováková creator: Jaroslav Holuša creator: Jakub Horák uri: https://doi.org/10.7717/peerj.1592 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nováková et al. title: The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission link: https://peerj.com/articles/1591 last-modified: 2016-01-18 description: Sacbrood virus (SBV) and Deformed wing virus (DWV) are evolutionarily related positive-strand RNA viruses, members of the Iflavirus group. They both infect the honeybee Apis mellifera but have strikingly different levels of virulence when transmitted orally. Honeybee larvae orally infected with SBV usually accumulate high levels of the virus, which halts larval development and causes insect death. In contrast, oral DWV infection at the larval stage usually causes asymptomatic infection with low levels of the virus, although high doses of ingested DWV could lead to DWV replicating to high levels. We investigated effects of DWV and SBV infection on the transcriptome of honeybee larvae and pupae using global RNA-Seq and real-time PCR analysis. This showed that high levels of SBV replication resulted in down-regulation of the genes involved in cuticle and muscle development, together with changes in expression of putative immune-related genes. In particular, honeybee larvae with high levels of SBV replication, with and without high levels of DWV replication, showed concerted up-regulated expression of antimicrobial peptides (AMPs), and down-regulated expression of the prophenoloxidase activating enzyme (PPAE) together with up-regulation of the expression of a putative serpin, which could lead to the suppression of the melanisation pathway. The effects of high SBV levels on expression of these immune genes were unlikely to be a consequence of SBV-induced developmental changes, because similar effects were observed in honeybee pupae infected by injection. In the orally infected larvae with high levels of DWV replication alone we observed no changes of AMPs or of gene expression in the melanisation pathway. In the injected pupae, high levels of DWV alone did not alter expression of the tested melanisation pathway genes, but resulted in up-regulation of the AMPs, which could be attributed to the effect of DWV on the regulation of AMP expression in response to wounding. We propose that the difference in expression of the honeybee immune genes induced by SBV and DWV may be an evolutionary adaptation to the different predominant transmission routes used by these viruses. creator: Eugene V. Ryabov creator: Jessica M. Fannon creator: Jonathan D. Moore creator: Graham R. Wood creator: David J. Evans uri: https://doi.org/10.7717/peerj.1591 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ryabov et al. title: Non-invasive cortisol measurements as indicators of physiological stress responses in guinea pigs link: https://peerj.com/articles/1590 last-modified: 2016-01-18 description: Non-invasive measurements of glucocorticoid (GC) concentrations, including cortisol and corticosterone, serve as reliable indicators of adrenocortical activities and physiological stress loads in a variety of species. As an alternative to invasive analyses based on plasma, GC concentrations in saliva still represent single-point-of-time measurements, suitable for studying short-term or acute stress responses, whereas fecal GC metabolites (FGMs) reflect overall stress loads and stress responses after a species-specific time frame in the long-term. In our study species, the domestic guinea pig, GC measurements are commonly used to indicate stress responses to different environmental conditions, but the biological relevance of non-invasive measurements is widely unknown. We therefore established an experimental protocol based on the animals’ natural stress responses to different environmental conditions and compared GC levels in plasma, saliva, and fecal samples during non-stressful social isolations and stressful two-hour social confrontations with unfamiliar individuals. Plasma and saliva cortisol concentrations were significantly increased directly after the social confrontations, and plasma and saliva cortisol levels were strongly correlated. This demonstrates a high biological relevance of GC measurements in saliva. FGM levels measured 20 h afterwards, representing the reported mean gut passage time based on physiological validations, revealed that the overall stress load was not affected by the confrontations, but also no relations to plasma cortisol levels were detected. We therefore measured FGMs in two-hour intervals for 24 h after another social confrontation and detected significantly increased levels after four to twelve hours, reaching peak concentrations already after six hours. Our findings confirm that non-invasive GC measurements in guinea pigs are highly biologically relevant in indicating physiological stress responses compared to circulating levels in plasma in the short- and long-term. Our approach also underlines the importance of detailed investigations on how to use and interpret non-invasive measurements, including the determination of appropriate time points for sample collections. creator: Matthias Nemeth creator: Elisabeth Pschernig creator: Bernard Wallner creator: Eva Millesi uri: https://doi.org/10.7717/peerj.1590 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nemeth et al. title: Cranial ontogenetic variation in early saurischians and the role of heterochrony in the diversification of predatory dinosaurs link: https://peerj.com/articles/1589 last-modified: 2016-01-18 description: Non-avian saurischian skulls underwent at least 165 million years of evolution and shapes varied from elongated skulls, such as in the theropod Coelophysis, to short and box-shaped skulls, such as in the sauropod Camarasaurus. A number of factors have long been considered to drive skull shape, including phylogeny, dietary preferences and functional constraints. However, heterochrony is increasingly being recognized as an important factor in dinosaur evolution. In order to quantitatively analyse the impact of heterochrony on saurischian skull shape, we analysed five ontogenetic trajectories using two-dimensional geometric morphometrics in a phylogenetic framework. This allowed for the comparative investigation of main ontogenetic shape changes and the evaluation of how heterochrony affected skull shape through both ontogenetic and phylogenetic trajectories. Using principal component analyses and multivariate regressions, it was possible to quantify different ontogenetic trajectories and evaluate them for evidence of heterochronic events allowing testing of previous hypotheses on cranial heterochrony in saurischians. We found that the skull shape of the hypothetical ancestor of Saurischia likely led to basal Sauropodomorpha through paedomorphosis, and to basal Theropoda mainly through peramorphosis. Paedomorphosis then led from Orionides to Avetheropoda, indicating that the paedomorphic trend found by previous authors in advanced coelurosaurs may extend back into the early evolution of Avetheropoda. Not only are changes in saurischian skull shape complex due to the large number of factors that affected it, but heterochrony itself is complex, with a number of possible reversals throughout non-avian saurischian evolution. In general, the sampling of complete ontogenetic trajectories including early juveniles is considerably lower than the sampling of single adult or subadult individuals, which is a major impediment to the study of heterochrony on non-avian dinosaurs. Thus, the current work represents an exploratory analysis. To better understand the cranial ontogeny and the impact of heterochrony on skull evolution in saurischians, the data set that we present here must be expanded and complemented with further sampling from future fossil discoveries, especially of juvenile individuals. creator: Christian Foth creator: Brandon P. Hedrick creator: Martin D. Ezcurra uri: https://doi.org/10.7717/peerj.1589 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Foth et al. title: The association between maternal psychological stress and inflammatory cytokines in allergic young children link: https://peerj.com/articles/1585 last-modified: 2016-01-18 description: Background. Previous studies have shown that psychological stress is linked to asthma prevalence. Parental psychological stress may potentially influence inflammatory responses in their allergic children. The purpose of this study is to clarify the association between maternal psychological status and inflammatory response of allergic young children.Methods. The study subjects were 152 young allergic children (median age: 13 months) who had not shown any allergic symptoms in the past one month. mRNA expression levels of the inflammatory response genes IL-6, IL-8, IL-10 and IL-22 were quantified by qRT-PCR. Maternal psychological status was assessed by standardized questionnaires: the Centre for Epidemiological Studies Depression Scale (CES-D) for depression and the Japanese Perceived Stress Scale (JPSS) for perceived stress.Results. A significant positive association was observed between maternal CES-D scores and IL-6 mRNA expression in the children with asthma. The JPSS scores were also positively associated with IL-8 mRNA expression in asthmatic children and IL-6 mRNA expression in children with allergic rhinitis. Similar trends were observed among children positive for house dust mite-specific IgE, but these associations were not significant.Conclusion. This study supports the hypothesis that maternal psychological stress affects the inflammatory response in their allergic children. creator: Mayumi Tsuji creator: Chihaya Koriyama creator: Megumi Yamamoto creator: Ayumi Anan creator: Eiji Shibata creator: Toshihiro Kawamoto uri: https://doi.org/10.7717/peerj.1585 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tsuji et al. title: Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region link: https://peerj.com/articles/1474 last-modified: 2016-01-18 description: Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species. creator: Julio Peñas creator: Sara Barrios creator: Javier Bobo-Pinilla creator: Juan Lorite creator: M. Montserrat Martínez-Ortega uri: https://doi.org/10.7717/peerj.1474 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Peñas et al. title: Normal distal pulmonary vein anatomy link: https://peerj.com/articles/1579 last-modified: 2016-01-14 description: Background. It is well known that the pulmonary veins (PVs), especially their myocardial sleeves play a critical role in the initiation and maintenance of atrial fibrillation. Understanding the PV anatomy is crucial for the safety and efficacy of all procedures performed on PVs. The aim of this study was to present normal distal PV anatomy and to create a juxtaposition of all PV ostium variants.Methods. A total of 130 randomly selected autopsied adult human hearts (Caucasian) were examined. The number of PVs ostia was evaluated and their diameter was measured. The ostium-to-last-tributary distance and macroscopic presence of myocardial sleeves were also evaluated.Results. Five hundred forty-one PV ostia were identified. Four classical PV ostia patterns (two left and two right PVs) were observed in 70.8% of all cases. The most common variant was the classical pattern with additional middle right PV (19.2%), followed by the common ostium for the left superior and the inferior PVs (4.44%). Mean diameters of PV ostia (for the classical pattern) were: left superior = 13.8 ± 2.9 mm; left inferior = 13.3 ± 3.4 mm; right superior = 14.3 ± 2.9 mm; right inferior = 13.7 ± 3.3 mm. When present, the additional middle right PV ostium had the smallest PV ostium diameter in the heart (8.2 ± 4.1 mm). The mean ostium-to-last-tributary (closest to the atrium) distances were: left superior = 15.1 ± 4.6 mm; left inferior = 13.5 ± 4.0 mm; right superior = 11.8 ± 4.0 mm; right inferior = 11.0 ± 3.7 mm. There were no statistically significant differences between sexes in ostia diameters and ostium-to-last-tributary distances.Conclusion. Only 71% of the cases have four standard pulmonary veins. The middle right pulmonary vein is present in almost 20% of patients. Presented data can provide useful information for the clinicians during interventional procedures or radiologic examinations of PVs. creator: Wiesława Klimek-Piotrowska creator: Mateusz K. Hołda creator: Katarzyna Piątek creator: Mateusz Koziej creator: Jakub Hołda uri: https://doi.org/10.7717/peerj.1579 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Klimek-Piotrowska et al. title: Effects of temperature and host stage on the parasitization rate and offspring sex ratio of Aenasius bambawalei Hayat in Phenacoccus solenopsis Tinsley link: https://peerj.com/articles/1586 last-modified: 2016-01-14 description: Temperature and host stage are important factors that determine the successful development of parasitoids. Aenasius bambawalei Hayat (Hymenoptera: Encyrtidae) is a primary parasitoid of the newly invasive mealybug, Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae). The effects of temperature on the parasitic characteristics of A. bambawalei have seldom been investigated. In the study, we explored the effects of temperature, exposure time, and host stage on the parasitization rate and offspring sex ratio (female to male) of A. bambawalei under laboratory conditions. The laboratory results showed that the successful parasitization rate of A. bambawalei increased with higher temperatures and older host stages. When the parasitoids were exposed to 36 °C for 24 h, the parasitization rate of female adults (52%) was nearly two times that of 3rd instar nymphs. Additionally, heat stress duration and host stage resulted in an increase in the offspring sex ratio of A. bambawalei. When A. bambawalei was exposed to 36 °C for 24 h, the offspring sex ratio increased dramatically to 81.78% compared with those exposed for 12 h, and it increased to 45.34% compared with those exposed for 16 h. The offspring sex ratio was clearly higher when the host stage was an adult female mealybug Our findings provide important guidance for the mass rearing and field releases of A. bambawalei for the management of P. solenopsis in the future. creator: Juan Zhang creator: Jun Huang creator: Yaobin Lu creator: Tianfeng Xia uri: https://doi.org/10.7717/peerj.1586 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhang et al. title: Trophic ecology of sea urchins in coral-rocky reef systems, Ecuador link: https://peerj.com/articles/1578 last-modified: 2016-01-14 description: Sea urchins are important grazers and influence reef development in the Eastern Tropical Pacific (ETP). Diadema mexicanum and Eucidaris thouarsii are the most important sea urchins on the Ecuadorian coastal reefs. This study provided a trophic scenario for these two species of echinoids in the coral-rocky reef bottoms of the Ecuadorian coast, using stable isotopes. We evaluated the relative proportion of algal resources assimilated, and trophic niche of the two sea urchins in the most southern coral-rocky reefs of the ETP in two sites with different disturbance level. Bayesian models were used to estimate the contribution of algal sources, niche breadth, and trophic overlap between the two species. The sea urchins behaved as opportunistic feeders, although they showed differential resource assimilation. Eucidaris thouarsii is the dominant species in disturbed environments; likewise, their niche amplitude was broader than that of D. mexicanum when conditions were not optimal. However, there was no niche overlap between the species. The Stable Isotope Analysis in R (SIAR) indicated that both sea urchins shared limiting resources in the disturbed area, mainly Dictyota spp. (contributions of up to 85% for D. mexicanum and up to 75% for E. thouarsii). The Stable Isotope Bayesian Ellipses in R (SIBER) analysis results indicated less interspecific competition in the undisturbed site. Our results suggested a trophic niche partitioning between sympatric sea urchin species in coastal areas of the ETP, but the limitation of resources could lead to trophic overlap and stronger habitat degradation. creator: Nancy Cabanillas-Terán creator: Peggy Loor-Andrade creator: Ruber Rodríguez-Barreras creator: Jorge Cortés uri: https://doi.org/10.7717/peerj.1578 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cabanillas-Terán et al. title: The effect of repeated laser stimuli to ink-marked skin on skin temperature—recommendations for a safe experimental protocol in humans link: https://peerj.com/articles/1577 last-modified: 2016-01-14 description: Background. Nd:YAP laser is widely used to investigate the nociceptive and pain systems, generating perpetual and laser-evoked neurophysiological responses. A major procedural concern for the use of Nd:YAP laser stimuli in experimental research is the risk of skin damage. The absorption of Nd:YAP laser stimuli is greater in darker skin, or in pale skin that has been darkened with ink, prompting some ethics boards to refuse approval to experimenters wishing to track stimulus location by marking the skin with ink. Some research questions, however, require laser stimuli to be delivered at particular locations or within particular zones, a requirement that is very difficult to achieve if marking the skin is not possible. We thoroughly searched the literature for experimental evidence and protocol recommendations for safe delivery of Nd:YAP laser stimuli over marked skin, but found nothing.Methods. We designed an experimental protocol to define safe parameters for the use of Nd:YAP laser stimuli over skin that has been marked with black dots, and used thermal imaging to assess the safety of the procedure at the forearm and the back.Results. Using thermal imaging and repeated laser stimulation to ink-marked skin, we demonstrated that skin temperature did not increase progressively across the course of the experiment, and that the small change in temperature seen at the forearm was reversed during the rest periods between blocks. Furthermore, no participant experienced skin damage due to the procedure.Conclusion. This protocol offers parameters for safe, confident and effective experimentation using repeated Nd:YAP laser on skin marked with ink, thus paving the way for investigations that depend on it. creator: Victoria J. Madden creator: Mark J. Catley creator: Luzia Grabherr creator: Francesca Mazzola creator: Mohammad Shohag creator: G. Lorimer Moseley uri: https://doi.org/10.7717/peerj.1577 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Madden et al. title: Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system link: https://peerj.com/articles/1576 last-modified: 2016-01-14 description: Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals. creator: Jordan D. Satler creator: Amanda J. Zellmer creator: Bryan C. Carstens uri: https://doi.org/10.7717/peerj.1576 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Satler et al. title: Faces in commonly experienced configurations enter awareness faster due to their curvature relative to fixation link: https://peerj.com/articles/1565 last-modified: 2016-01-14 description: The extent to which perceptually suppressed face stimuli are still processed has been extensively studied using the continuous flash suppression paradigm (CFS). Studies that rely on breaking CFS (b-CFS), in which the time it takes for an initially suppressed stimulus to become detectable is measured, have provided evidence for relatively complex processing of invisible face stimuli. In contrast, adaptation and neuroimaging studies have shown that perceptually suppressed faces are only processed for a limited set of features, such as its general shape. In this study, we asked whether perceptually suppressed face stimuli presented in their commonly experienced configuration would break suppression faster than when presented in an uncommonly experienced configuration. This study was motivated by a recent neuroimaging study showing that commonly experienced face configurations are more strongly represented in the fusiform face area. Our findings revealed that faces presented in commonly experienced configurations indeed broke suppression faster, yet this effect did not interact with face inversion suggesting that, in a b-CFS context, perceptually suppressed faces are potentially not processed by specialized (high-level) face processing mechanisms. Rather, our pattern of results is consistent with an interpretation based on the processing of more basic visual properties such as convexity. creator: Pieter Moors creator: Johan Wagemans creator: Lee de-Wit uri: https://doi.org/10.7717/peerj.1565 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Moors et al. title: A prospective randomized trial examining health care utilization in individuals using multiple smartphone-enabled biosensors link: https://peerj.com/articles/1554 last-modified: 2016-01-14 description: Background. Mobile health and digital medicine technologies are becoming increasingly used by individuals with common, chronic diseases to monitor their health. Numerous devices, sensors, and apps are available to patients and consumers–some of which have been shown to lead to improved health management and health outcomes. However, no randomized controlled trials have been conducted which examine health care costs, and most have failed to provide study participants with a truly comprehensive monitoring system. Methods. We conducted a prospective randomized controlled trial of adults who had submitted a 2012 health insurance claim associated with hypertension, diabetes, and/or cardiac arrhythmia. The intervention involved receipt of one or more mobile devices that corresponded to their condition(s) (hypertension: Withings Blood Pressure Monitor; diabetes: Sanofi iBGStar Blood Glucose Meter; arrhythmia: AliveCor Mobile ECG) and an iPhone with linked tracking applications for a period of 6 months; the control group received a standard disease management program. Moreover, intervention study participants received access to an online health management system which provided participants detailed device tracking information over the course of the study. This was a monitoring system designed by leveraging collaborations with device manufacturers, a connected health leader, health care provider, and employee wellness program–making it both unique and inclusive. We hypothesized that health resource utilization with respect to health insurance claims may be influenced by the monitoring intervention. We also examined health-self management. Results & Conclusions. There was little evidence of differences in health care costs or utilization as a result of the intervention. Furthermore, we found evidence that the control and intervention groups were equivalent with respect to most health care utilization outcomes. This result suggests there are not large short-term increases or decreases in health care costs or utilization associated with monitoring chronic health conditions using mobile health or digital medicine technologies. Among secondary outcomes there was some evidence of improvement in health self-management which was characterized by a decrease in the propensity to view health status as due to chance factors in the intervention group. creator: Cinnamon S. Bloss creator: Nathan E. Wineinger creator: Melissa Peters creator: Debra L. Boeldt creator: Lauren Ariniello creator: Ju Young Kim creator: Judith Sheard creator: Ravi Komatireddy creator: Paddy Barrett creator: Eric J. Topol uri: https://doi.org/10.7717/peerj.1554 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bloss et al. title: Residual mitochondrial transmembrane potential decreases unsaturated fatty acid level in sake yeast during alcoholic fermentation link: https://peerj.com/articles/1552 last-modified: 2016-01-14 description: Oxygen, a key nutrient in alcoholic fermentation, is rapidly depleted during this process. Several pathways of oxygen utilization have been reported in the yeast Saccharomyces cerevisiae during alcoholic fermentation, namely synthesis of unsaturated fatty acid, sterols and heme, and the mitochondrial electron transport chain. However, the interaction between these pathways has not been investigated. In this study, we showed that the major proportion of unsaturated fatty acids of ester-linked lipids in sake fermentation mash is derived from the sake yeast rather than from rice or koji (rice fermented with Aspergillus). Additionally, during alcoholic fermentation, inhibition of the residual mitochondrial activity of sake yeast increases the levels of unsaturated fatty acids of ester-linked lipids. These findings indicate that the residual activity of the mitochondrial electron transport chain reduces molecular oxygen levels and decreases the synthesis of unsaturated fatty acids, thereby increasing the synthesis of estery flavors by sake yeast. This is the first report of a novel link between residual mitochondrial transmembrane potential and the synthesis of unsaturated fatty acids by the brewery yeast during alcoholic fermentation. creator: Kazutaka Sawada creator: Hiroshi Kitagaki uri: https://doi.org/10.7717/peerj.1552 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sawada & Kitagaki title: The impact of land reform on the status of large carnivores in Zimbabwe link: https://peerj.com/articles/1537 last-modified: 2016-01-14 description: Large carnivores are decreasing in number due to growing pressure from an expanding human population. It is increasingly recognised that state-protected conservation areas are unlikely to be sufficient to protect viable populations of large carnivores, and that private land will be central to conservation efforts. In 2000, a fast-track land reform programme (FTLRP) was initiated in Zimbabwe, ostensibly to redress the racial imbalance in land ownership, but which also had the potential to break up large areas of carnivore habitat on private land. To date, research has focused on the impact of the FTLRP process on the different human communities, while impacts on wildlife have been overlooked. Here we provide the first systematic assessment of the impact of the FTLRP on the status of large carnivores. Spoor counts were conducted across private, resettled and communal land use types in order to estimate the abundance of large carnivores, and to determine how this had been affected by land reform. The density of carnivore spoor differed significantly between land use types, and was lower on resettlement land than on private land, suggesting that the resettlement process has resulted in a substantial decline in carnivore abundance. Habitat loss and high levels of poaching in and around resettlement areas are the most likely causes. The FTLRP resulted in the large-scale conversion of land that was used sustainably and productively for wildlife into unsustainable, unproductive agricultural land uses. We recommended that models of land reform should consider the type of land available, that existing expertise in land management should be retained where possible, and that resettlement programmes should be carefully planned in order to minimise the impacts on wildlife and on people. creator: Samual T. Williams creator: Kathryn S. Williams creator: Christoffel J. Joubert creator: Russell A. Hill uri: https://doi.org/10.7717/peerj.1537 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Williams et al. title: Probable impact of age and hypoxia on proliferation and microRNA expression profile of bone marrow-derived human mesenchymal stem cells link: https://peerj.com/articles/1536 last-modified: 2016-01-14 description: Decline in the therapeutic potential of bone marrow-derived mesenchymal stem cells (MSC) is often seen with older donors as compared to young. Although hypoxia is known as an approach to improve the therapeutic potential of MSC in term of cell proliferation and differentiation capacity, its effects on MSC from aged donors have not been well studied. To evaluate the influence of hypoxia on different age groups, MSC from young (<30 years) and aged (>60 years) donors were expanded under hypoxic (5% O2) and normal (20% O2) culture conditions. MSC from old donors exhibited a reduction in proliferation rate and differentiation potential together with the accumulation of senescence features compared to that of young donors. However, MSC cultured under hypoxic condition showed enhanced self-renewing and proliferation capacity in both age groups as compared to normal condition. Bioinformatic analysis of the gene ontology (GO) and KEGG pathway under hypoxic culture condition identified hypoxia-inducible miRNAs that were found to target transcriptional activity leading to enhanced cell proliferation, migration as well as decrease in growth arrest and apoptosis through the activation of multiple signaling pathways. Overall, differentially expressed miRNA provided additional information to describe the biological changes of young and aged MSCs expansion under hypoxic culture condition at the molecular level. Based on our findings, the therapeutic potential hierarchy of MSC according to donor’s age group and culture conditions can be categorized in the following order: young (hypoxia) > young (normoxia) > old aged (hypoxia) > old aged (normoxia). creator: Norlaily Mohd Ali creator: Lily Boo creator: Swee Keong Yeap creator: Huynh Ky creator: Dilan A. Satharasinghe creator: Woan Charn Liew creator: Han Kiat Ong creator: Soon Keng Cheong creator: Tunku Kamarul uri: https://doi.org/10.7717/peerj.1536 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mohd Ali et al. title: Preoperative CT versus diffusion weighted magnetic resonance imaging of the liver in patients with rectal cancer; a prospective randomized trial link: https://peerj.com/articles/1532 last-modified: 2016-01-14 description: Introduction. Colorectal cancer is one of the most frequent cancers in the world and liver metastases are seen in up to 19% of patients with colorectal cancers. Detection of liver metastases is not only vital for sufficient treatment and survival, but also for a better estimation of prognosis. The aim of this study was to evaluate the feasibility of diffusion weighted MRI of the liver as part of a combined MR evaluation of patients with rectal cancers and compare it with the standard preoperative evaluation of the liver with CT.Methods. Consecutive patients diagnosed with rectal cancers were asked to participate in the study. Preoperative CT and diffusion weighted MR (DWMR) were compared to contrast enhanced laparoscopic ultrasound (CELUS).Results. A total of 35 patients were included, 15 patients in Group-1 having the standard CT evaluation of the liver and 20 patients in Group-2 having the standard CT evaluation of the liver and DWMR of the liver. Compared with CELUS, the per-patient sensitivity/specificity was 50/100% for CT, and for DWMR: 100/94% and 100/100% for Reader 1 and 2, respectively. The per-lesion sensitivity of CT and DWMR were 17% and 89%, respectively compared with CELUS. Furthermore, one patient had non-resectable metastases after DWMR despite being diagnosed with resectable metastases after CT. Another patient was diagnosed with multiple liver metastases during CELUS, despite a negative CT-scan.Discussion. DWMR is feasible for preoperative evaluation of liver metastases. The current standard preoperative evaluation with CT-scan results in disadvantages like missed metastases and futile operations. We recommend that patients with rectal cancer, who are scheduled for MR of the rectum, should have a DWMR of the liver performed at the same time. creator: Michael P. Achiam creator: Vibeke B. Løgager creator: Bjørn Skjoldbye creator: Jakob M. Møller creator: Torben Lorenzen creator: Vera L. Rasmussen creator: Henrik S. Thomsen creator: Talie H. Mollerup creator: Cecilie Okholm creator: Jacob Rosenberg uri: https://doi.org/10.7717/peerj.1532 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Achiam et al. title: Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus link: https://peerj.com/articles/1522 last-modified: 2016-01-14 description: Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages. creator: Felipe Coutinho creator: Diogo Antonio Tschoeke creator: Fabiano Thompson creator: Cristiane Thompson uri: https://doi.org/10.7717/peerj.1522 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Coutinho et al. title: Acute hypothalamic suppression significantly affects trabecular bone but not cortical bone following recovery and ovariectomy surgery in a rat model link: https://peerj.com/articles/1575 last-modified: 2016-01-12 description: Background. Osteoporosis is “a pediatric disease with geriatric consequences.” Bone morphology and tissue quality co-adapt during ontogeny for sufficient bone stiffness. Altered bone morphology from hypothalamic amenorrhea, a risk factor for low bone mass in women, may affect bone strength later in life. Our purpose was to determine if altered morphology following hypothalamic suppression during development affects cortical bone strength and trabecular bone volume (BV/TV) at maturity.Methods. Female rats (25 days old) were assigned to a control (C) group (n = 45) that received saline injections (.2 cc) or an experimental group (GnRH-a) (n = 45) that received gonadotropin releasing hormone antagonist injections (.24 mg per dose) for 25 days. Fifteen animals from each group were sacrificed immediately after the injection protocol at Day 50 (C, GnRH-a). The remaining animals recovered for 135 days and a subset of each group was sacrificed at Day 185 ((C-R) (n = 15) and (G-R) (n = 15)). The remaining animals had an ovariectomy surgery (OVX) at 185 days of age and were sacrificed 40 days later (C-OVX) (n = 15) and (G-OVX) (n = 15). After sacrifice femurs were mechanically tested and scanned using micro CT. Serum C-terminal telopeptides (CTX) and insulin-like growth factor 1 (IGF-1) were measured. Two-way ANOVA (2 groups (GnRH-a and Control) X 3 time points (Injection Protocol, Recovery, post-OVX)) was computed.Results. GnRH-a injections suppressed uterine weights (72%) and increased CTX levels by 59%. Bone stiffness was greater in the GnRH-a groups compared to C. Ash content and cortical bone area were similar between groups at all time points. Polar moment of inertia, a measure of bone architecture, was 15% larger in the GnRH-a group and remained larger than C (19%) following recovery. Both the polar moment of inertia and cortical area increased linearly with the increases in body weight. Following the injection protocol, trabecular BV/TV was 31% lower in the GnRH-a group compared to C, a similar deficit in BV/TV was also measured following recovery and post-OVX. The trabecular number and thickness were lower in the GnRH-a group compared to control.Conclusion. These data suggest that following a transient delay in pubertal onset, trabecular bone volume was significantly lower and no restoration of bone volume occurred following recovery or post-OVX surgery. However, cortical bone strength was maintained through architectural adaptations in the cortical bone envelope. An increase in the polar moment of inertia offset increased bone resorption. The current data are the first to suppress trabecular bone during growth, and then add an OVX protocol at maturity. Trabecular bone and cortical bone differed in their response to hypothalamic suppression during development; trabecular bone was more sensitive to the negative effects of hypothalamic suppression. creator: Vanessa R. Yingling creator: Kathryn A. Mitchell creator: Megan Lunny uri: https://doi.org/10.7717/peerj.1575 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yingling et al. title: The identification of immune genes in the milk transcriptome of the Tasmanian devil (Sarcophilus harrisii) link: https://peerj.com/articles/1569 last-modified: 2016-01-12 description: Tasmanian devil (Sarcophilus harrisii) pouch young, like other marsupials, are born underdeveloped and immunologically naïve, and are unable to mount an adaptive immune response. The mother’s milk provides nutrients for growth and development as well as providing passive immunity. To better understand immune response in this endangered species, we set out to characterise the genes involved in passive immunity by sequencing and annotating the transcriptome of a devil milk sample collected during mid-lactation. At mid-lactation we expect the young to have heightened immune responses, as they have emerged from the pouch, encountering new pathogens. A total of 233,660 transcripts were identified, including approximately 17,827 unique protein-coding genes and 846 immune genes. The most highly expressed transcripts were dominated by milk protein genes such as those encoding early lactation protein, late lactation proteins, α-lactalbumin, α-casein and β-casein. There were numerous highly expressed immune genes including lysozyme, whey acidic protein, ferritin and major histocompatibility complex I and II. Genes encoding immunoglobulins, antimicrobial peptides, chemokines and immune cell receptors were also identified. The array of immune genes identified in this study reflects the importance of the milk in providing immune protection to Tasmanian devil young and provides the first insight into Tasmanian devil milk. creator: Rehana V. Hewavisenti creator: Katrina M. Morris creator: Denis O’Meally creator: Yuanyuan Cheng creator: Anthony T. Papenfuss creator: Katherine Belov uri: https://doi.org/10.7717/peerj.1569 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hewavisenti et al. title: The influence of mature oak stands and spruce plantations on soil-dwelling click beetles in lowland plantation forests link: https://peerj.com/articles/1568 last-modified: 2016-01-12 description: Most European forests have been converted into forest plantations that are managed for timber production. The main goal of this paper was to determine the difference between mature native sessile oak (Quercus petraea) stands and non-indigenous Norway spruce (Picea abies) plantations, with respect to communities of Athous click beetles in approximately 6,500 ha of lowland plantation forest area in the Czech Republic. Athous subfuscus was the most abundant and widespread species, followed by A. zebei and A.haemorrhoidalis, while A. vittatus was considered rare. Spatial analysis of environmental variables inside studied patches showed that the species composition of Athous beetles best responded to a 20 m radius surrounding traps. The species’ responses to the environment showed that A. vittatus and A. haemorrhoidalis preferred oak stands, while A. zebei and A. subfuscus were associated with spruce plantations. In addition, oak stands showed higher diversity of beetle communities. The studied species are important for their ecosystem services (e.g. predation on pests or bioturbation) and seem to tolerate certain degrees of human disturbances, which is especially beneficial for forest plantations managed for timber production. creator: Tereza Loskotová creator: Jakub Horák uri: https://doi.org/10.7717/peerj.1568 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Loskotová & Horák title: Validation of the “Quality of Life in School” instrument in Canadian elementary school students link: https://peerj.com/articles/1567 last-modified: 2016-01-12 description: Background. School is an integral component of the life of a child, and thus quality of school life is an important part of the overall quality of life experienced by a child. There are a few instruments available to measure the quality of school life but they are often not available in English, or they are not appropriate for use alongside other instruments in a survey of young children. The Quality of Life in School (QoLS) instrument is a short, self-report measure to assess elementary school students’ perception of their quality of school life in four domains. The instrument was developed in Israel and has been validated among Hebrew-speaking children. The aim of the current study was to evaluate the psychometric properties of the QoLS measure in Canadian elementary school children.Methods. A total of 629 children attending grades 4–6 were recruited in a population-based cross-sectional study. The QoLS measure was administered to participating children by trained research assistants. In addition, their socio-demographic details and academic data were also obtained. The psychometric testing included exploratory factor analysis and reliability estimation using internal consistency (Cronbach’s Alpha). Construct validity was investigated using the known groups comparisons for discriminative validity and via convergent validity.Results. A four-factor structure was generated explaining 39% of the total variance in the model. The results showed good internal consistency and acceptable floor and ceiling effects. Cronbach’s Alpha ranged from 0.75 to 0.93. Known groups comparisons showed that the QoLS measure discriminated well between subgroups on the basis of gender, grade, and academic achievement, thus providing evidence of construct validity. The convergent validity was also appropriate with all the four domains demonstrating moderate to strong correlations to each other and to the total QoLS score.Conclusions. QoLS appears to be a valid and reliable measure for quality of school life assessment in young Canadian children. creator: Satvinder Ghotra creator: Jessie-Lee D. McIsaac creator: Sara F.L. Kirk creator: Stefan Kuhle uri: https://doi.org/10.7717/peerj.1567 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ghotra et al. title: Characterization of the artisanal fishing communities in Nepal and potential implications for the conservation and management of Ganges River Dolphin (Platanista gangetica gangetica) link: https://peerj.com/articles/1563 last-modified: 2016-01-12 description: The Ganges River dolphin (Platanista gangetica gangetica) (GRD) is classified as one of the most endangered of all cetaceans in the world and the second scarcest freshwater cetacean. The population is estimated to be less than 2,000 individuals. In Nepal’s Narayani, Sapta Koshi, and Karnali river systems, survival of GRD continues to be threatened by various anthropogenic activities, such as dam construction and interactions with artisanal fisheries. A basic description of the geographic scope, economics, and types of gear used in these fisheries would help managers understand the fishery-dolphin interaction conflict and assist with developing potential solutions. The main goal was to provide new information on the artisanal fishing communities in Nepal. The specific objectives were to identify, compile, and investigate the demographics, economics, fishing characteristics, and perception of fishermen about GRD conservation in the Narayani, Sapta Koshi, and Karnali rivers so conservation managers can develop and implement a potential solution to the GRD-fishery interaction problem in Nepal. Based on 169 interviews, 79% of Nepalese fishermen indicated fishing was their primary form of income. Fishermen reported fishing effort was greater in summer than winter; greatest in the afternoon (14:30 hrs ± 0:27) and during low water level conditions; and gear was set 4.8 ± 0.2 days/week. Fishermen reported using eight different types of monofilament nets (gillnets and cast nets). Sixty percent used gillnets less than 10 m long, and nearly 30% preferred gillnets between 10 and 100 m long; a few used gillnets longer than 100 m. Most fishermen reported they believed education, awareness, and changing occupations were important for GRD conservation, but they indicated that alternative occupational options were currently limited in Nepal. Nepalese fishermen acknowledged that fisheries posed a risk to GRD, but they believed water pollution, and dam/irrigation developments were the greatest threats. creator: Shambhu Paudel creator: Juan C. Levesque creator: Camilo Saavedra creator: Cristina Pita creator: Prabhat Pal uri: https://doi.org/10.7717/peerj.1563 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Paudel et al. title: Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective link: https://peerj.com/articles/1556 last-modified: 2016-01-12 description: The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers. creator: Rosa Alicia Jiménez creator: Juan Francisco Ornelas uri: https://doi.org/10.7717/peerj.1556 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Jiménez & Ornelas title: Molecular phylogeny and taxonomy of the Epictia goudotii Species complex (Serpentes: Leptotyphlopidae: Epictinae) in Middle America and northern South America link: https://peerj.com/articles/1551 last-modified: 2016-01-12 description: Here we review the systematics of the threadsnakes of the Epictia goudotii Species complex in Middle and northern South America using external morphology and molecular data. Two species, Epictia goudotii and E. magnamaculata, are currently recognized from that region, but we provide evidence for recognizing, as species, three other nominal forms usually treated as subspecies of E. goudotii: E. ater, E. bakewelli, and E. phenops. Thus, together with E. columbi (Bahamas), we recognize six species in the Epictia goudotii Species complex. Because E. albifrons from northern South America has been confused with E. goudotii in the past, we also briefly discuss the taxonomic status of that species and its apparent close relative E. tenella, which are not members of the E. goudotii complex. creator: James R. McCranie creator: S. Blair Hedges uri: https://doi.org/10.7717/peerj.1551 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 McCranie and Hedges title: Unveiling the status of alien animals in the arid zone of Asia link: https://peerj.com/articles/1545 last-modified: 2016-01-12 description: Biological invasion is one of the most threatening factors for biodiversity conservation. Lacking information on alien species in certain regions of the world hampers a balanced understanding of invasion processes and efficient data exchange among stakeholders. Current knowledge gaps are in need of urgent concern. We therefore conducted a review on alien animals in Xinjiang, an unknown region of invasion ecology. Xinjiang lies in the heartland of the Asian continent, covering an area of 1,664,900 km2. In the past 64 years, 128 alien animal species were recorded in this region, 39% of which became invasive and led to loss of native biodiversity. Most of these species were introduced through diversification of local agriculture and aquaculture. This process was aggravated by improving transportation and flourishing trade. Multiple linear regression models and correlation analysis were run for explaining influence of environmental and anthropogenic factors on status of alien animals: economically developed areas with abundant water resource, oases in particular, were prone to be hotspots of alien animal species in this arid and semi-arid region. This study also revealed that taxonomically biased and lagged research were critical problems that impeded studies on biological invasions in Xinjiang, and proposed feasible solutions. creator: Lyubing Zhang creator: Zhigang Jiang uri: https://doi.org/10.7717/peerj.1545 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang and Jiang title: Fibroblast growth factors as tissue repair and regeneration therapeutics link: https://peerj.com/articles/1535 last-modified: 2016-01-12 description: Cell communication is central to the integration of cell function required for the development and homeostasis of multicellular animals. Proteins are an important currency of cell communication, acting locally (auto-, juxta-, or paracrine) or systemically (endocrine). The fibroblast growth factor (FGF) family contributes to the regulation of virtually all aspects of development and organogenesis, and after birth to tissue maintenance, as well as particular aspects of organism physiology. In the West, oncology has been the focus of translation of FGF research, whereas in China and to an extent Japan a major focus has been to use FGFs in repair and regeneration settings. These differences have their roots in research history and aims. The Chinese drive into biotechnology and the delivery of engineered clinical grade FGFs by a major Chinese research group were important enablers in this respect. The Chinese language clinical literature is not widely accessible. To put this into context, we provide the essential molecular and functional background to the FGF communication system covering FGF ligands, the heparan sulfate and Klotho co-receptors and FGF receptor (FGFR) tyrosine kinases. We then summarise a selection of clinical reports that demonstrate the efficacy of engineered recombinant FGF ligands in treating a wide range of conditions that require tissue repair/regeneration. Alongside, the functional reasons why application of exogenous FGF ligands does not lead to cancers are described. Together, this highlights that the FGF ligands represent a major opportunity for clinical translation that has been largely overlooked in the West. creator: Quentin M. Nunes creator: Yong Li creator: Changye Sun creator: Tarja K. Kinnunen creator: David G. Fernig uri: https://doi.org/10.7717/peerj.1535 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Nunes et al. title: Solid phase extraction and metabolic profiling of exudates from living copepods link: https://peerj.com/articles/1529 last-modified: 2016-01-12 description: Copepods are ubiquitous in aquatic habitats. They exude bioactive compounds that mediate mate finding or induce defensive traits in prey organisms. However, little is known about the chemical nature of the copepod exometabolome that contributes to the chemical landscape in pelagic habitats. Here we describe the development of a closed loop solid phase extraction setup that allows for extraction of exuded metabolites from live copepods. We captured exudates from male and female Temora longicornis and analyzed the content with high resolution LC-MS. Chemometric methods revealed 87 compounds that constitute a specific chemical pattern either qualitatively or quantitatively indicating copepod presence. The majority of the compounds were present in both female and male exudates, but nine compounds were mainly or exclusively present in female exudates and hence potential pheromone candidates. Copepodamide G, known to induce defensive responses in phytoplankton, was among the ten compounds of highest relative abundance in both male and female extracts. The presence of copepodamide G shows that the method can be used to capture and analyze chemical signals from living source organisms. We conclude that solid phase extraction in combination with metabolic profiling of exudates is a useful tool to develop our understanding of the chemical interplay between pelagic organisms. creator: Erik Selander creator: Jan Heuschele creator: Göran M. Nylund creator: Georg Pohnert creator: Henrik Pavia creator: Oda Bjærke creator: Larisa A. Pender-Healy creator: Peter Tiselius creator: Thomas Kiørboe uri: https://doi.org/10.7717/peerj.1529 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Selander et al. title: One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples link: https://peerj.com/articles/1560 last-modified: 2016-01-11 description: Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8–100% sensitivity, 100% specificity, 86–89% efficiency and a limit of detection of 12–400 copies per singleplex reactions. The VP4 qRT-PCRs exhibited 82–90% efficiency and limit of detection of 120–4000 copies in multiplex reaction. Discussion. The one-step multiplex qRT-PCR assay will facilitate high-throughput rotavirus genotype characterization for monitoring circulating rotavirus wild-type strains causing rotavirus infections, determining the frequency of Rotarix® and RotaTeq® vaccine strains and vaccine-derived reassortants associated with AGE, and help to identify novel rotavirus strains derived by reassortment between vaccine and wild-type strains. creator: Rashi Gautam creator: Slavica Mijatovic-Rustempasic creator: Mathew D. Esona creator: Ka Ian Tam creator: Osbourne Quaye creator: Michael D. Bowen uri: https://doi.org/10.7717/peerj.1560 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Non-native species in the vascular flora of highlands and mountains of Iceland link: https://peerj.com/articles/1559 last-modified: 2016-01-11 description: The highlands and mountains of Iceland are one of the largest remaining wilderness areas in Europe. This study aimed to provide comprehensive and up-to-date data on non-native plant species in these areas and to answer the following questions: (1) How many non-native vascular plant species inhabit highland and mountainous environments in Iceland? (2) Do temporal trends in the immigration of alien species to Iceland differ between highland and lowland areas? (3) Does the incidence of alien species in the disturbed and undisturbed areas within Icelandic highlands differ? (4) Does the spread of non-native species in Iceland proceed from lowlands to highlands? and (5) Can we detect hot-spots in the distribution of non-native taxa within the highlands? Overall, 16 non-native vascular plant species were detected, including 11 casuals and 5 naturalized taxa (1 invasive). Results showed that temporal trends in alien species immigration to highland and lowland areas are similar, but it is clear that the process of colonization of highland areas is still in its initial phase. Non-native plants tended to occur close to man-made infrastructure and buildings including huts, shelters, roads etc. Analysis of spatio-temporal patterns showed that the spread within highland areas is a second step in non-native plant colonization in Iceland. Several statically significant hot spots of alien plant occurrences were identified using the Getis-Ord Gi* statistic and these were linked to human disturbance. This research suggests that human-mediated dispersal is the main driving force increasing the risk of invasion in Iceland’s highlands and mountain areas. creator: Pawel Wasowicz uri: https://doi.org/10.7717/peerj.1559 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Wasowicz title: Rates and modes of body size evolution in early carnivores and herbivores: a case study from Captorhinidae link: https://peerj.com/articles/1555 last-modified: 2016-01-11 description: Body size is an extremely important characteristic, impacting on a variety of ecological and life-history traits. It is therefore important to understand the factors which may affect its evolution, and diet has attracted much interest in this context. A recent study which examined the evolution of the earliest terrestrial herbivores in the Late Carboniferous and Early Permian concluded that in the four herbivorous clades examined there was a trend towards increased body size, and that this increase was more substantial than that observed in closely related carnivorous clades. However, this hypothesis was not based on quantitative examination, and phylogenetic comparative methods provide a more robust means of testing such hypotheses. Here, the evolution of body size within different dietary regimes is examined in Captorhinidae, the most diverse and longest lived of these earliest high fibre herbivores. Evolutionary models were fit to their phylogeny to test for variation in rate and mode of evolution between the carnivorous and herbivorous members of this clade, and an analysis of rate variation throughout the tree was carried out. Estimates of ancestral body sizes were calculated in order to compare the rates and direction of evolution of lineages with different dietary regimes. Support for the idea that the high fibre herbivores within captorhinids are being drawn to a higher adaptive peak in body size than the carnivorous members of this clade is weak. A shift in rates of body size evolution is identified, but this does not coincide with the evolution of high-fibre herbivory, instead occurring earlier in time and at a more basal node. Herbivorous lineages which show an increase in size are not found to evolve at a faster rate than those which show a decrease; in fact, it is those which experience a size decrease which evolve at higher rates. It is possible the shift in rates of evolution is related to the improved food processing ability of the more derived captorhinids rather than a shift in diet, but the evidence for this is circumstantial. creator: Neil Brocklehurst uri: https://doi.org/10.7717/peerj.1555 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Brocklehurst title: The identity of the South African toad Sclerophrys capensis Tschudi, 1838 (Amphibia, Anura) link: https://peerj.com/articles/1553 last-modified: 2016-01-11 description: The toad species Sclerophrys capensis Tschudi, 1838 was erected for a single specimen from South Africa which has never been properly studied and allocated to a known species. A morphometrical and morphological analysis of this specimen and its comparison with 75 toad specimens referred to five South African toad species allowed to allocate this specimen to the species currently known as Amietophrynus rangeri. In consequence, the nomen Sclerophrys must replace Amietophrynus as the valid nomen of the genus, and capensis as the valid nomen of the species. This work stresses the usefulness of natural history collections for solving taxonomic and nomenclatural problems. creator: Annemarie Ohler creator: Alain Dubois uri: https://doi.org/10.7717/peerj.1553 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ohler and Dubois title: Occurrence of ferredoxin:NAD+ oxidoreductase activity and its ion specificity in several Gram-positive and Gram-negative bacteria link: https://peerj.com/articles/1515 last-modified: 2016-01-11 description: A ferredoxin:NAD+ oxidoreductase was recently discovered as a redox-driven ion pump in the anaerobic, acetogenic bacterium Acetobacterium woodii. The enzyme is assumed to be encoded by the rnf genes. Since these genes are present in the genomes of many bacteria, we tested for ferredoxin:NAD+ oxidoreductase activity in cytoplasmic membranes from several different Gram-positive and Gram-negative bacteria that have annotated rnf genes. We found this activity in Clostridium tetanomorphum, Clostridium ljungdahlii, Bacteroides fragilis, and Vibrio cholerae but not in Escherichia coli and Rhodobacter capsulatus. As in A. woodii, the activity was Na+-dependent in C. tetanomorphum and B. fragilis but Na+-independent in C. ljungdahlii and V. cholerae. We deleted the rnf genes from B. fragilis and demonstrated that the mutant has greatly reduced ferredoxin:NAD+ oxidoreductase activity. This is the first genetic proof that the rnf genes indeed encode the reduced ferredoxin:NAD+ oxidoreductase activity. creator: Verena Hess creator: Rene Gallegos creator: J Andrew Jones creator: Blanca Barquera creator: Michael H Malamy creator: Volker Müller uri: https://doi.org/10.7717/peerj.1515 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hess et al. title: Convex-hull mass estimates of the dodo (Raphus cucullatus): application of a CT-based mass estimation technique link: https://peerj.com/articles/1432 last-modified: 2016-01-11 description: The external appearance of the dodo (Raphus cucullatus, Linnaeus, 1758) has been a source of considerable intrigue, as contemporaneous accounts or depictions are rare. The body mass of the dodo has been particularly contentious, with the flightless pigeon alternatively reconstructed as slim or fat depending upon the skeletal metric used as the basis for mass prediction. Resolving this dichotomy and obtaining a reliable estimate for mass is essential before future analyses regarding dodo life history, physiology or biomechanics can be conducted. Previous mass estimates of the dodo have relied upon predictive equations based upon hind limb dimensions of extant pigeons. Yet the hind limb proportions of dodo have been found to differ considerably from those of their modern relatives, particularly with regards to midshaft diameter. Therefore, application of predictive equations to unusually robust fossil skeletal elements may bias mass estimates. We present a whole-body computed tomography (CT) -based mass estimation technique for application to the dodo. We generate 3D volumetric renders of the articulated skeletons of 20 species of extant pigeons, and wrap minimum-fit ‘convex hulls’ around their bony extremities. Convex hull volume is subsequently regressed against mass to generate predictive models based upon whole skeletons. Our best-performing predictive model is characterized by high correlation coefficients and low mean squared error (a = − 2.31, b = 0.90, r2 = 0.97, MSE = 0.0046). When applied to articulated composite skeletons of the dodo (National Museums Scotland, NMS.Z.1993.13; Natural History Museum, NHMUK A.9040 and S/1988.50.1), we estimate eviscerated body masses of 8–10.8 kg. When accounting for missing soft tissues, this may equate to live masses of 10.6–14.3 kg. Mass predictions presented here overlap at the lower end of those previously published, and support recent suggestions of a relatively slim dodo. CT-based reconstructions provide a means of objectively estimating mass and body segment properties of extinct species using whole articulated skeletons. creator: Charlotte A. Brassey creator: Thomas G. O’Mahoney creator: Andrew C. Kitchener creator: Phillip L. Manning creator: William I. Sellers uri: https://doi.org/10.7717/peerj.1432 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Brassey et al. title: Trends and topics in eye disease research in PubMed from 2010 to 2014 link: https://peerj.com/articles/1557 last-modified: 2016-01-07 description: Background: The purpose of this study is to provide a report on scientific production during the period 2010–2014 in order to identify the major topics as well as the predominant actors (journals, countries, continents) involved in the field of eye disease. Methods: A PubMed search was carried out to extract articles related to eye diseases during the period 2010–2014. Data were downloaded and processed through developed PHP scripts for further analysis. Results: A total of 62,123 articles were retrieved. A total of 3,368 different journals were found, and 19 journals were identified as “core journals” according to Braford’s law. English was by far the predominant language. A total of 853,182 MeSH terms were found, representing an average of 13.73 (SD = 4.98) MeSH terms per article. Among these 853,182 MeSH terms, 14,689 different MeSH terms were identified. Vision Disorders, Glaucoma, Diabetic Retinopathy, Macular Degeneration, and Cataract were the most frequent five MeSH terms related to eye diseases. The analysis of the total number of publications showed that Europe and Asia were the most productive continents, and the USA and China the most productive countries. Interestingly, using the mean Five-Year Impact Factor, the two most productive continents were North America and Oceania. After adjustment for population, the overall ranking positions changed in favor of smaller countries (i.e. Iceland, Switzerland, Denmark, and New Zealand), while after adjustment for Gross Domestic Product (GDP), the overall ranking positions changed in favor of some developing countries (Malawi, Guatemala, Singapore). Conclusions: Due to the large number of articles included and the numerous parameters analyzed, this study provides a wide view of scientific productivity related to eye diseases during the period 2010–2014 and allows us to better understand this field. creator: Christophe Boudry creator: Eric Denion creator: Bruno Mortemousque creator: Fréderic Mouriaux uri: https://doi.org/10.7717/peerj.1557 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Boudry et al. title: Anatomical barriers in the right atrium to the coronary sinus cannulation link: https://peerj.com/articles/1548 last-modified: 2016-01-07 description: Background. The coronary venous system is an increasingly frequent target of minimally invasive cardiac procedures. The purpose of this paper is to assess the anatomical barriers in the right atrium to coronary sinus cannulation.Methods. We examined the anatomy of the right atrium, coronary sinus ostium, inferior and superior vena cava ostia in 110 randomly selected autopsied human hearts of both sexes (27% females; mean age 49.2 ± 17.5 years).Results. The Eustachian valve was present in 79 cases (71.8%) with mean height =4.9 ± 2.6 mm. The valve was perforated in 11 cases (13.9%). It is typically too small to hinder the coronary sinus catheterization, but in some cases (about 2%) a significantly protruding valve may be an obstacle. Chiari’s network (4.6%) is not a barrier to catheter entry into the right atrium but may significantly impede further catheter manipulations inside the heart venous system. A typical Thebesian valve leaves enough space for the passage of the standard catheter to the coronary sinus.Discussion. Detailed anatomy of various anatomical structures within the right atrium that could play a potential role in coronary sinus cannulation is discussed. creator: Wiesława Klimek-Piotrowska creator: Mateusz K. Hołda creator: Mateusz Koziej creator: Marcin Strona uri: https://doi.org/10.7717/peerj.1548 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Klimek-Piotrowska et al. title: The complete mitochondrial genome of Lerema accius and its phylogenetic implications link: https://peerj.com/articles/1546 last-modified: 2016-01-07 description: Butterflies and moths (Lepidoptera) are becoming model organisms for genetics and evolutionary biology. Decoding the Lepidoptera genomes, both nuclear and mitochondrial, is an essential step in these studies. Here we describe a protocol to assemble mitogenomes from Next Generation Sequencing reads obtained through whole-genome sequencing and report the 15,338 bp mitogenome of Lerema accius. The mitogenome is AT-rich and encodes 13 proteins, 22 transfer-RNAs, and two ribosomal-RNAs, with a gene order typical for Lepidoptera mitogenomes. A phylogenetic study based on the protein sequences using both Bayesian Inference and Maximum Likelihood methods consistently place Lerema accius with other grass skippers (Hesperiinae). creator: Qian Cong creator: Nick V. Grishin uri: https://doi.org/10.7717/peerj.1546 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cong and Grishin title: L-Canavanine potentiates the cytotoxicity of doxorubicin and cisplatin in arginine deprived human cancer cells link: https://peerj.com/articles/1542 last-modified: 2016-01-07 description: The non-protein amino acid L-canavanine (L-CAV), an antimetabolite of L-arginine (L-ARG), can alter the 3D conformation of proteins when incorporated into a protein instead of L-ARG. L-CAV inhibits the proliferation of some tumour cells. The deprivation of L-ARG in the culture medium enhances the response of cells to L-CAV. This study aimed to investigate the interaction of L-CAV in combination with the chemotherapeutic drugs, doxorubicin (DOX) or cisplatin (CIS), in cancer cells, especially in the absence of L-ARG. A combination method based on the median-effect principle and mass-action law was used. The following cancer cells were employed: HeLa and Caco-2 cells, overexpressing argininosuccinate synthase (ASS), pancreatic cells (MIA PaCa-2 and BxPC-3) and hepatocellular carcinoma cells (Hep G2 and SK-HEP-1), with down-regulated ASS. When constant and non-constant ratios of L-CAV were combined with DOX and CIS, a synergistic potentiation of cytotoxicity was recorded. Cells expressing high levels of ASS were more sensitive to the treatment as compared to the cells with reduced ASS levels. Overall, this study may provide a new approach to targeting some cancer cells with L-CAV in combination with DNA-targeting drugs such as DOX and CIS, especially those cells which overexpress ASS, such as human cervical and colorectal carcinoma cells. creator: Agustina DR Nurcahyanti creator: Michael Wink uri: https://doi.org/10.7717/peerj.1542 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Nurcahyanti and Wink title: Impact of demographics on human gut microbial diversity in a US Midwest population link: https://peerj.com/articles/1514 last-modified: 2016-01-07 description: The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior-related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2 values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies. creator: Jun Chen creator: Euijung Ryu creator: Matthew Hathcock creator: Karla Ballman creator: Nicholas Chia creator: Janet E Olson creator: Heidi Nelson uri: https://doi.org/10.7717/peerj.1514 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chen et al. title: Deciphering the microRNA transcriptome of skeletal muscle during porcine development link: https://peerj.com/articles/1504 last-modified: 2016-01-07 description: MicroRNAs (miRNAs) play critical roles in many important biological processes, such as growth and development in mammals. Various studies of porcine muscle development have mainly focused on identifying miRNAs that are important for fetal and adult muscle development; however, little is known about the role of miRNAs in middle-aged muscle development. Here, we present a comprehensive investigation of miRNA transcriptomes across five porcine muscle development stages, including one prenatal and four postnatal stages. We identified 404 known porcine miRNAs, 118 novel miRNAs, and 101 miRNAs that are conserved in other mammals. A set of universally abundant miRNAs was found across the distinct muscle development stages. This set of miRNAs may play important housekeeping roles that are involved in myogenesis. A short time-series expression miner analysis indicated significant variations in miRNA expression across distinct muscle development stages. We also found enhanced differentiation- and morphogenesis-related miRNA levels in the embryonic stage; conversely, apoptosis-related miRNA levels increased relatively later in muscle development. These results provide integral insight into miRNA function throughout pig muscle development stages. Our findings will promote further development of the pig as a model organism for human age-related muscle disease research. creator: Miaomiao Mai creator: Long Jin creator: Shilin Tian creator: Rui Liu creator: Wenyao Huang creator: Qianzi Tang creator: Jideng Ma creator: An’an Jiang creator: Xun Wang creator: Yaodong Hu creator: Dawei Wang creator: Zhi Jiang creator: Mingzhou Li creator: Chaowei Zhou creator: Xuewei Li uri: https://doi.org/10.7717/peerj.1504 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Mai et al. title: The role of 2,4-dihydroxyquinoline (DHQ) in Pseudomonas aeruginosa pathogenicity link: https://peerj.com/articles/1495 last-modified: 2016-01-07 description: Bacteria synchronize group behaviors using quorum sensing, which is advantageous during an infection to thwart immune cell attack and resist deleterious changes in the environment. In Pseudomonas aeruginosa, the Pseudomonas quinolone signal (Pqs) quorum-sensing system is an important component of an interconnected intercellular communication network. Two alkylquinolones, 2-heptyl-4-quinolone (HHQ) and 2-heptyl-3-hydroxy-4-quinolone (PQS), activate transcriptional regulator PqsR to promote the production of quinolone signals and virulence factors. Our work focused on the most abundant quinolone produced from the Pqs system, 2,4-dihydroxyquinoline (DHQ), which was shown previously to sustain pyocyanin production and antifungal activity of P. aeruginosa. However, little is known about how DHQ affects P. aeruginosa pathogenicity. Using C. elegans as a model for P. aeruginosa infection, we found pqs mutants only able to produce DHQ maintained virulence towards the nematodes similar to wild-type. In addition, DHQ-only producing mutants displayed increased colonization of C. elegans and virulence factor production compared to a quinolone-null strain. DHQ also bound to PqsR and activated the transcription of pqs operon. More importantly, high extracellular concentration of DHQ was maintained in both aerobic and anaerobic growth. High levels of DHQ were also detected in the sputum samples of cystic fibrosis patients. Taken together, our findings suggest DHQ may play an important role in sustaining P. aeruginosa pathogenicity under oxygen-limiting conditions. creator: Jordon D. Gruber creator: Wei Chen creator: Stuart Parnham creator: Kevin Beauchesne creator: Peter Moeller creator: Patrick A. Flume creator: Yong-Mei Zhang uri: https://doi.org/10.7717/peerj.1495 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gruber et al. title: Extra-pair paternity in the long-tailed finch Poephila acuticauda link: https://peerj.com/articles/1550 last-modified: 2016-01-05 description: Although the majority of passerine birds are socially monogamous, true genetic monogamy is rare, with extra-pair paternity (EPP) occurring in almost 90% of surveyed socially monogamous species. We present the first molecular data on the genetic breeding system of the long-tailed finch, Poephila acuticauda, a grass finch endemic to the tropical northern savannah of Australia. Although the species forms socially monogamous pair bonds during the breeding season, we found that extra-pair males sired 12.8% of 391 offspring, in 25.7% of 101 broods. Our findings provide only the second estimate of extra-pair paternity in the estrildid finch family. creator: Erica P. van Rooij creator: Lee A. Rollins creator: Clare E. Holleley creator: Simon C. Griffith uri: https://doi.org/10.7717/peerj.1550 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 van Rooij et al. title: In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum link: https://peerj.com/articles/1549 last-modified: 2016-01-05 description: Background. Ralstonia solanacearum is an economically important plant pathogen with an unusually large host range. The Moko (banana) and NPB (not pathogenic to banana) strain groups are closely related but are adapted to distinct hosts. Previous comparative genomics studies uncovered very few differences that could account for the host range difference between these pathotypes. To better understand the basis of this host specificity, we used RNAseq to profile the transcriptomes of an R. solanacearum Moko strain and an NPB strain under in vitro and in planta conditions.Results. RNAs were sequenced from bacteria grown in rich and minimal media, and from bacteria extracted from mid-stage infected tomato, banana and melon plants. We computed differential expression between each pair of conditions to identify constitutive and host-specific gene expression differences between Moko and NPB. We found that type III secreted effectors were globally up-regulated upon plant cell contact in the NPB strain compared with the Moko strain. Genes encoding siderophore biosynthesis and nitrogen assimilation genes were highly up-regulated in the NPB strain during melon pathogenesis, while denitrification genes were up-regulated in the Moko strain during banana pathogenesis. The relatively lower expression of oxidases and the denitrification pathway during banana pathogenesis suggests that R. solanacearum experiences higher oxygen levels in banana pseudostems than in tomato or melon xylem.Conclusions. This study provides the first report of differential gene expression associated with host range variation. Despite minimal genomic divergence, the pathogenesis of Moko and NPB strains is characterized by striking differences in expression of virulence- and metabolism-related genes. creator: Florent Ailloud creator: Tiffany M. Lowe creator: Isabelle Robène creator: Stéphane Cruveiller creator: Caitilyn Allen creator: Philippe Prior uri: https://doi.org/10.7717/peerj.1549 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ailloud et al. title: Age-related changes in the distributions of depressive symptom items in the general population: a cross-sectional study using the exponential distribution model link: https://peerj.com/articles/1547 last-modified: 2016-01-05 description: Background. Previous research has reported inconsistent evidence of the trajectory of depressive symptoms across the adult lifespan. We investigated how the distributions of each item score change with age and determined whether the trajectory of depressive symptoms varied with the scoring methods of the questionnaire.Methods. We analyzed data collected from 21,040 subjects who participated in the national survey in Japan. Depressive symptoms were assessed using the Center for Epidemiologic Studies Depression Scale (CES-D). The CES-D has 20 items, each of which is scored in four grades of “rarely,” “some,” “much,” and “most of the time.” We used the exponential distribution model which fits the distributions of 16 negative symptom items of CES-D, with the probabilities of “some,” “much,” “most,” and “rarely” expressed as P, Pr, Pr2, and 1 − P × (r2 + r + 1).Results. The distributions of the responses to 16 negative symptom items followed the common exponential model across all age groups. The mean of the estimated parameter r of 16 negative items showed a U-shape pattern, being high during 12–29 years, remaining low during 30–50 years, and then increasing again over 60 years. The trajectory of depressive symptom scores simulating the binary method was different from that of the empirical scores using the Likert method.Conclusions. Our findings show that the increase in the depressive symptoms score during older age is based on the increase of the parameter r. The differences in the scoring method may contribute to the different age-related patterns across the adult lifespan. creator: Shinichiro Tomitaka creator: Yohei Kawasaki creator: Kazuki Ide creator: Hiroshi Yamada creator: Toshiaki A. Furukawa creator: Yutaka Ono uri: https://doi.org/10.7717/peerj.1547 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tomitaka et al. title: Assessing conservation status of resident and migrant birds on Hispaniola with mist-netting link: https://peerj.com/articles/1541 last-modified: 2016-01-05 description: We analyzed temporal trends in mist-net capture rates of resident (n = 8) and overwintering Nearctic-Neotropical migrant (n = 3) bird species at two sites in montane broadleaf forest of the Sierra de Bahoruco, Dominican Republic, with the goal of providing quantitative information on population trends that could inform conservation assessments. We conducted sampling at least once annually during the winter months of January–March from 1997 to 2010. We found evidence of declines in capture rates for three resident species, including one species endemic to Hispaniola. Capture rate of Rufous-throated Solitaire (Myadestes genibarbis) declined by 3.9% per year (95% CL = 0%, 7.3%), Green-tailed Ground-Tanager (Microligea palustris) by 6.8% (95% CL = 3.9%, 8.8%), and Greater Antillean Bullfinch (Loxigilla violacea) by 4.9% (95% CL = 0.9%, 9.2%). Two rare and threatened endemics, Hispaniolan Highland-Tanager (Xenoligea montana) and Western Chat-Tanager (Calyptophilus tertius), showed statistically significant declines, but we have low confidence in these findings because trends were driven by exceptionally high capture rates in 1997 and varied between sites. Analyses that excluded data from 1997 revealed no trend in capture rate over the course of the study. We found no evidence of temporal trends in capture rates for any other residents or Nearctic-Neotropical migrants. We do not know the causes of the observed declines, nor can we conclude that these declines are not a purely local phenomenon. However, our findings, along with other recent reports of declines in these same species, suggest that a closer examination of their conservation status is warranted. Given the difficulty in obtaining spatially extensive, long-term estimates of population change for Hispaniolan birds, we suggest focusing on other metrics of vulnerability that are more easily quantified yet remain poorly described, such as extent of occurrence. creator: John D. Lloyd creator: Christopher C. Rimmer creator: Kent P. McFarland uri: https://doi.org/10.7717/peerj.1541 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lloyd et al. title: The role of coral colony health state in the recovery of lesions link: https://peerj.com/articles/1531 last-modified: 2016-01-05 description: Coral disease literature has focused, for the most part, on the etiology of the more than 35 coral afflictions currently described. Much less understood are the factors that underpin the capacity of corals to regenerate lesions, including the role of colony health. This lack of knowledge with respect to the factors that influence tissue regeneration significantly limits our understanding of the impact of diseases at the colony, population, and community level. In this study, we experimentally compared tissue regeneration capacity of diseased versus healthy fragments of Gorgonia ventalina colonies at 5 m and 12 m of depth. We found that the initial health state of colonies (i.e., diseased or healthy) had a significant effect on tissue regeneration (healing). All healthy fragments exhibited full recovery regardless of depth treatment, while diseased fragments did not. Our results suggest that being diseased or healthy has a significant effect on the capacity of a sea fan colony to repair tissue, but that environmental factors associated with changes in depth, such as temperature and light, do not. We conclude that disease doesn’t just compromise vital functions such as growth and reproduction in corals but also compromises their capacity to regenerate tissue and heal lesions. creator: Claudia P. Ruiz-Diaz creator: Carlos Toledo-Hernandez creator: Alex E. Mercado-Molina creator: María-Eglée Pérez creator: Alberto M. Sabat uri: https://doi.org/10.7717/peerj.1531 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ruiz-Diaz et al. title: Activity and biophysical inhibition resistance of a novel synthetic lung surfactant containing Super-Mini-B DATK peptide link: https://peerj.com/articles/1528 last-modified: 2016-01-05 description: Background/objectives. This study examines the surface activity, resistance to biophysical inhibition, and pulmonary efficacy of a synthetic lung surfactant containing glycerophospholipids combined with Super Mini-B (S-MB) DATK, a novel and stable molecular mimic of lung surfactant protein (SP)-B. The objective of the work is to test whether S-MB DATK synthetic surfactant has favorable biophysical and physiological activity for future use in treating surfactant deficiency or dysfunction in lung disease or injury.Methods. The structure of S-MB DATK peptide was analyzed by homology modeling and by FTIR spectroscopy. The in vitro surface activity and inhibition resistance of synthetic S-MB DATK surfactant was assessed in the presence and absence of albumin, lysophosphatidylcholine (lyso-PC), and free fatty acids (palmitoleic and oleic acid). Adsorption and dynamic surface tension lowering were measured with a stirred subphase dish apparatus and a pulsating bubble surfactometer (20 cycles/min, 50% area compression, 37 °C). In vivo pulmonary activity of S-MB DATK surfactant was measured in ventilated rabbits with surfactant deficiency/dysfunction induced by repeated lung lavages that resulted in arterial PO2 values <100 mmHg.Results. S-MB DATK surfactant had very high surface activity in all assessments. The preparation adsorbed rapidly to surface pressures of 46–48 mN/m at 37 °C (low equilibrium surface tensions of 22–24 mN/m), and reduced surface tension to <1 mN/m under dynamic compression on the pulsating bubble surfactometer. S-MB DATK surfactant showed a significant ability to resist inhibition by serum albumin, C16:0 lyso-PC, and free fatty acids, but surfactant inhibition was mitigated by increasing surfactant concentration. S-MB DATK synthetic surfactant quickly improved arterial oxygenation and lung compliance after intratracheal instillation to ventilated rabbits with severe surfactant deficiency.Conclusions. S-MB DATK is an active mimic of native SP-B. Synthetic surfactants containing S-MB DATK (or related peptides) combined with lipids appear to have significant future potential for treating clinical states of surfactant deficiency or dysfunction, such as neonatal and acute respiratory distress syndromes. creator: Robert H. Notter creator: Zhengdong Wang creator: Frans J. Walther uri: https://doi.org/10.7717/peerj.1528 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Notter et al. title: Comparison of growth characteristics between skeletal muscle satellite cell lines from diploid and triploid olive flounder Paralichthys olivaceus link: https://peerj.com/articles/1519 last-modified: 2016-01-05 description: Objectives. According to myosatellite cell lines (MSCs) established in vitro from diploid and triploid flounder, we compared the characters of growth and differentiation of their MSCs. The results would be useful for learning the muscle development mechanism in teleosts.Materials and Methods. The skeletal muscle cells from the diploid and triploid olive flounder Paralichthys olivaceus were isolated and cultured in vitro, respectively, and the cells were characterized at the morphology and molecular level; meanwhile, the performance of these cells’ proliferation and differentiation were analyzed.Results. Two new skeletal muscle cell lines (POMSCS(2n) and POMSCS(3n)) from diploid and triploid flounder have been respectively subcultured for 67 times and 66 times. The cultured cells were mostly spindle-like mononuclear cells. They have normal flounder diploid karyotype (2n=48t) and triploid karyotype (3n=72t), respectively. Muscle satellite cell gene marker (pax7b) and myogenic cell protein marker (Desmin) were all expressed in cells of two cell lines. Both of the cells could differentiate into the large polynucleated muscle fibre cells, and immunofluorescence reactions of myosin heavy chain (MyHC) were positive. There were more cells of POMSCS(3n) to differentiate into the muscle fibre cells than that of POMSCS(2n). However, POMSCS(2n) cells proliferated more rapidly than those of POMSCS(3n) (P < 0.05). The significant fluorescent signals were observed in both POMSCS(2n) and POMSCS(3n) cells after transfected with pEGFP-N3 reporter plasmid.Conclusions. The two cell lines have been established and characterized as MSCs. We suppose that it might be the differentiation capacity, rather than the proliferation activity of MSCs to play a key role in the better growth of triploid ones than diploid. Both cell lines will become the ideal tools to learn the mechanism of fish MSCs proliferation, differentiation and regeneration during muscle development in the future. creator: Li-min Peng creator: Yuan Zheng creator: Feng You creator: Zhi-hao Wu creator: Xungang Tan creator: Shuang Jiao creator: Pei-jun Zhang uri: https://doi.org/10.7717/peerj.1519 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Peng et al. title: A simple and rapid method for measuring α-D-phosphohexomutases activity by using anion-exchange chromatography coupled with an electrochemical detector link: https://peerj.com/articles/1517 last-modified: 2016-01-05 description: The interconversion of hexose-6-phosphate and hexose-1-phosphate can be directly analyzed by high-performance anion-exchange chromatography coupled with an electrochemical detector (HPAEC-PAD). Thus, this method can be used to measure the activities of N-acetylglucosamine-phosphate mutase (AGM), glucosamine-phosphate mutase (GlmM) and phosphoglucomutase (PGM), which are the members of α-D-phosphohexomutases superfamily. The detection limits were extremely low as 2.747 pmol, 1.365 pmol, 0.512 pmol, 0.415 pmol, 1.486 pmol and 0.868 pmol for N-acetylglucosamine-1-phosphate (GlcNAc-1-P), N-acetylglucosamine-6-phosphate (GlcNAc-6-P), glucosamine-1-phosphate (GlcN-1-P), glucosamine-6-phosphate (GlcN-6-P), glucose-1-phosphate (Glc-1-P) and glucose-6-phosphate (Glc-6-P), respectively. By employing HPAEC-PAD, activities of AtAGM (AGM from Arabidopsis thaliana) on these six phosphohexoses can be detected. The Km of AtAGM on Glc-1-P determined by HPAEC-PAD was 679.18 ± 156.40 µM, which is comparable with the Km of 707.09 ± 170.36 µM detected by traditional coupled assay. Moreover, the activity of MtGlmM (GlmM from Mycobacterium tuberculosis) on GlcN-6-P tested by HPAEC-PAD was 7493.40 ± 309.12 nmol∕min ⋅ mg, which is much higher than 288.97 ± 35.28 nmol∕min ⋅ mg obtained by the traditional coupled assay. Accordingly, HPAEC-PAD is a more rapid and simple method than the traditional coupled assays given its high specificity and sensitivity, and will certainly bring convenience to further research of α-D-phosphohexomutases. creator: Xiaochen Jia creator: Jian Kang creator: Heng Yin uri: https://doi.org/10.7717/peerj.1517 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jia et al. title: Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events link: https://peerj.com/articles/1511 last-modified: 2016-01-05 description: The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics. creator: Florent E. Angly creator: Candice Heath creator: Thomas C. Morgan creator: Hemerson Tonin creator: Virginia Rich creator: Britta Schaffelke creator: David G. Bourne creator: Gene W. Tyson uri: https://doi.org/10.7717/peerj.1511 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Angly et al. title: Intermediate-term emotional bookkeeping is necessary for long-term reciprocal grooming partner preferences in an agent-based model of macaque groups link: https://peerj.com/articles/1488 last-modified: 2016-01-05 description: Whether and how primates are able to maintain long-term affiliative relationships is still under debate. Emotional bookkeeping (EB), the partner-specific accumulation of emotional responses to earlier interactions, is a candidate mechanism that does not require high cognitive abilities. EB is difficult to study in real animals, due to the complexity of primate social life. Therefore, we developed an agent-based model based on macaque behavior, the EMO-model, that implements arousal and two emotional dimensions, anxiety-FEAR and satisfaction-LIKE, which regulate social behavior. To implement EB, model individuals assign dynamic LIKE attitudes towards their group members, integrating partner-specific emotional responses to earlier received grooming episodes. Two key parameters in the model were varied to explore their effects on long-term affiliative relationships: (1) the timeframe over which earlier affiliation is accumulated into the LIKE attitudes; and (2) the degree of partner selectivity. EB over short and long timeframes gave rise to low variation in LIKE attitudes, and grooming partner preferences were only maintained over one to two months. Only EB over intermediate-term timeframes resulted in enough variation in LIKE attitudes, which, in combination with high partner selectivity, enables individuals to differentiate between regular and incidental grooming partners. These specific settings resulted in a strong feedback between differentiated LIKE attitudes and the distribution of grooming, giving rise to strongly reciprocated partner preferences that could be maintained for longer periods, occasionally up to one or two years. Moreover, at these settings the individual’s internal, socio-emotional memory of earlier affiliative episodes (LIKE attitudes) corresponded best to observable behavior (grooming partner preferences). In sum, our model suggests that intermediate-term LIKE dynamics and high partner selectivity seem most plausible for primates relying on emotional bookkeeping to maintain their social bonds. creator: Ellen Evers creator: Han de Vries creator: Berry M. Spruijt creator: Elisabeth H.M. Sterck uri: https://doi.org/10.7717/peerj.1488 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Evers et al. title: Disruption of de novo purine biosynthesis in Pseudomonas fluorescens Pf0-1 leads to reduced biofilm formation and a reduction in cell size of surface-attached but not planktonic cells link: https://peerj.com/articles/1543 last-modified: 2016-01-04 description: Pseudomonas fluorescens Pf0-1 is one of the model organisms for biofilm research. Our previous transposon mutagenesis study suggested a requirement for the de novo purine nucleotide biosynthesis pathway for biofilm formation by this organism. This study was performed to verify that observation and investigate the basis for the defects in biofilm formation shown by purine biosynthesis mutants. Constructing deletion mutations in 8 genes in this pathway, we found that they all showed reductions in biofilm formation that could be partly or completely restored by nucleotide supplementation or genetic complementation. We demonstrated that, despite a reduction in biofilm formation, more viable mutant cells were recovered from the surface-attached population than from the planktonic phase under conditions of purine deprivation. Analyses using scanning electron microscopy revealed that the surface-attached mutant cells were 25 ∼ 30% shorter in length than WT, which partly explains the reduced biomass in the mutant biofilms. The laser diffraction particle analyses confirmed this finding, and further indicated that the WT biofilm cells were smaller than their planktonic counterparts. The defects in biofilm formation and reductions in cell size shown by the mutants were fully recovered upon adenine or hypoxanthine supplementation, indicating that the purine shortages caused reductions in cell size. Our results are consistent with surface attachment serving as a survival strategy during nutrient deprivation, and indicate that changes in the cell size may be a natural response of P. fluorescens to growth on a surface. Finally, cell sizes in WT biofilms became slightly smaller in the presence of exogenous adenine than in its absence. Our findings suggest that purine nucleotides or related metabolites may influence the regulation of cell size in this bacterium. creator: Shiro Yoshioka creator: Peter D. Newell uri: https://doi.org/10.7717/peerj.1543 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yoshioka and Newell title: Does suicidal desire moderate the association between frontal delta power and psychological pain? link: https://peerj.com/articles/1538 last-modified: 2016-01-04 description: Psychological pain frequently underlies thoughts of suicide. We investigated if recent suicidal desire moderated the association between potential neurophysiological markers and psychological pain assessed on the Psychache Scale (PS) and the Orbach & Mikulincer Mental Pain Questionnaire (OMMP). The OMMP specifically assesses current psychological pain that may more readily capture emotions present during recent suicidal desire. In contrast, the PS leaves the timeframe undefined. A secondary analysis was conducted of resting-state EEG data and heart rate obtained in adults with a history of depression. In simultaneous multiple regression models, while controlling for depressive symptoms, recent suicidal desire moderated associations with right-frontal EEG delta power (ΔR2 = .07, p < .01) and low-frequency heart rate variability (nonsignificantly) for pain assessed on the PS. No indication for moderation was found for pain on the OMMP. The relationship between the two measures of psychological pain was stronger for individuals with recent suicidal desire (r = .75, p < .01 vs. r = .50, p < .05). The findings suggest that, unless a respondent’s psychological pain is recent and substantial, the PS may not capture the intensity of current psychological pain as effectively as the OMMP. creator: Esther L. Meerwijk creator: Sandra J. Weiss uri: https://doi.org/10.7717/peerj.1538 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Meerwijk and Weiss title: The yeast telomerase RNA, TLC1, participates in two distinct modes of TLC1-TLC1 association processes in vivo link: https://peerj.com/articles/1534 last-modified: 2016-01-04 description: Telomerase core enzyme minimally consists of the telomerase reverse transcriptase domain-containing protein (Est2 in budding yeast S. cerevisiae) and telomerase RNA, which contains the template specifying the telomeric repeat sequence synthesized. Here we report that in vivo, a fraction of S. cerevisiae telomerase RNA (TLC1) molecules form complexes containing at least two molecules of TLC1, via two separable modes: one requiring a sequence in the 3′ region of the immature TLC1 precursor and the other requiring Ku and Sir4. Such physical TLC1-TLC1 association peaked in G1 phase and did not require telomere silencing, telomere tethering to the nuclear periphery, telomerase holoenzyme assembly, or detectable Est2-Est2 protein association. These data indicate that TLC1-TLC1 associations reflect processes occurring during telomerase biogenesis; we propose that TLC1-TLC1 associations and subsequent reorganization may be regulatory steps in telomerase enzymatic activation. creator: Tet Matsuguchi creator: Elizabeth Blackburn uri: https://doi.org/10.7717/peerj.1534 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Matsuguchi and Blackburn title: Goodness of fit to a mathematical model for Drosophila sleep behavior is reduced in hyposomnolent mutants link: https://peerj.com/articles/1533 last-modified: 2016-01-04 description: The conserved nature of sleep in Drosophila has allowed the fruit fly to emerge in the last decade as a powerful model organism in which to study sleep. Recent sleep studies in Drosophila have focused on the discovery and characterization of hyposomnolent mutants. One common feature of these animals is a change in sleep architecture: sleep bout count tends to be greater, and sleep bout length lower, in hyposomnolent mutants. I propose a mathematical model, produced by least-squares nonlinear regression to fit the form Y = aX∧b, which can explain sleep behavior in the healthy animal as well as previously-reported changes in total sleep and sleep architecture in hyposomnolent mutants. This model, fit to sleep data, yields coefficient of determination R squared, which describes goodness of fit. R squared is lower, as compared to control, in hyposomnolent mutants insomniac and fumin. My findings raise the possibility that low R squared is a feature of all hyposomnolent mutants, not just insomniac and fumin. If this were the case, R squared could emerge as a novel means by which sleep researchers might assess sleep dysfunction. creator: Joshua M. Diamond uri: https://doi.org/10.7717/peerj.1533 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Diamond title: Odd versus even: a scientific study of the ‘rules’ of plating link: https://peerj.com/articles/1526 last-modified: 2016-01-04 description: We report on the results of a series of large-scale computer-based preference tests (conducted at The Science Museum in London and online) that evaluated the widely-held belief that food should be plated in odd rather than even numbers of elements in order to maximize the visual appeal of a dish. Participants were presented with pairs of plates of food showing odd versus even number of seared scallops (3 vs. 4; 1–6 in Experiment 7), arranged in a line, as a polygon or randomly, on either a round or square white plate. No consistent evidence for a preference for odd or even numbers of food items was found, thus questioning the oft-made assertion that odd number of items on a plate looks better than an even number. The implications of these results are discussed. creator: Andy T. Woods creator: Charles Michel creator: Charles Spence uri: https://doi.org/10.7717/peerj.1526 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Woods et al. title: First steps of bipedality in hominids: evidence from the atelid and proconsulid pelvis link: https://peerj.com/articles/1521 last-modified: 2016-01-04 description: Upright walking absent a bent-hip-bent-knee gait requires lumbar lordosis, a ubiquitous feature in all hominids for which it can be observed. Its first appearance is therefore a central problem in human evolution. Atelids, which use the tail during suspension, exhibit demonstrable lordosis and can achieve full extension of their hind limbs during terrestrial upright stance. Although obviously homoplastic with hominids, the pelvic mechanisms facilitating lordosis appear largely similar in both taxa with respect to abbreviation of upper iliac height coupled with broad sacral alae. Both provide spatial separation of the most caudal lumbar(s) from the iliac blades. A broad sacrum is therefore a likely facet of earliest hominid bipedality. All tailed monkeys have broad alae. By contrast all extant apes have very narrow sacra, which promote “trapping” of their most caudal lumbars to achieve lower trunk rigidity during suspension. The alae in the tailless proconsul Ekembo nyanzae appear to have been quite broad, a character state that may have been primitive in Miocene hominoids not yet adapted to suspension and, by extension, exaptive for earliest bipedality in the hominid/panid last common ancestor. This hypothesis receives strong support from other anatomical systems preserved in Ardipithecus ramidus. creator: Allison L. Machnicki creator: Linda B. Spurlock creator: Karen B. Strier creator: Philip L. Reno creator: C. Owen Lovejoy uri: https://doi.org/10.7717/peerj.1521 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Machnicki et al. title: Reproducibility of SNV-calling in multiple sequencing runs from single tumors link: https://peerj.com/articles/1508 last-modified: 2016-01-04 description: We examined 55 technical sequencing replicates of Glioblastoma multiforme (GBM) tumors from The Cancer Genome Atlas (TCGA) to ascertain the degree of repeatability in calling single-nucleotide variants (SNVs). We used the same mutation-calling pipeline on all pairs of samples, and we measured the extent of the overlap between two replicates; that is, how many specific point mutations were found in both replicates. We further tested whether additional filtering increased or decreased the size of the overlap. We found that about half of the putative mutations identified in one sequencing run of a given sample were also identified in the second, and that this percentage remained steady throughout orders of magnitude of variation in the total number of mutations identified (from 23 to 10,966). We further found that using filtering after SNV-calling removed the overlap completely. We concluded that there is variation in the frequency of mutations in GBMs, and that while some filtering approaches preferentially removed putative mutations found in only one replicate, others removed a large fraction of putative mutations found in both. creator: Dakota Z. Derryberry creator: Matthew C. Cowperthwaite creator: Claus O. Wilke uri: https://doi.org/10.7717/peerj.1508 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Derryberry et al. title: Lemmas induce dormancy but help the seed of Leymus chinensis to resist drought and salinity conditions in Northeast China link: https://peerj.com/articles/1485 last-modified: 2016-01-04 description: Leymus chinensis is a dominant grass in the Songnen grassland of Northern China. The lower germination caused by the presence of lemmas has proved to be an obstacle for the use of the seeds of this plant by humans. However, it is still unknown if the lemmas have other ecological roles such as resisting drought and saline conditions. Three experiments were designed to investigate the ecological roles of the lemmas in Leymus chinensis seeds. The results showed that lemmas significantly improved the amount of water uptake and slowed down the dehydration rate of the seeds under dry conditions. Likewise, the lemmas induced seed dormancy, and removal of the lemmas improved the germination at all temperatures. Although germination percentage of the seeds without lemmas were higher than that of seeds with lemmas under salinity stress, the recovery and total percentage were significantly lower than the seeds with lemmas, especially at 400 mM stress. These results suggest that the lemmas play a vital function in water uptake, dehydration and salt tolerance during the germination stage of the seeds as a response to adverse environmental conditions. Although lemmas showed a dormancy effect, if we want to plant this species in salinity soil in Northeast China, the approach of removing the lemmas by artificial means and improving the seed germination percentage is not feasible. creator: Jixiang Lin creator: Shuai Shao creator: Na Zhang creator: Yang Wang creator: Chunsheng Mu uri: https://doi.org/10.7717/peerj.1485 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lin et al. title: Real-life experience with personally familiar faces enhances discrimination based on global information link: https://peerj.com/articles/1465 last-modified: 2016-01-04 description: Despite the agreement that experience with faces leads to more efficient processing, the underlying mechanisms remain largely unknown. Building on empirical evidence from unfamiliar face processing in healthy populations and neuropsychological patients, the present experiment tested the hypothesis that personal familiarity is associated with superior discrimination when identity information is derived based on global, as opposed to local facial information. Diagnosticity and availability of local and global information was manipulated through varied physical similarity and spatial resolution of morph faces created from personally familiar or unfamiliar faces. We found that discrimination of subtle changes between highly similar morph faces was unaffected by familiarity. Contrariwise, relatively more pronounced physical (i.e., identity) differences were more efficiently discriminated for personally familiar faces, indicating more efficient processing of global, as opposed to local facial information through real-life experience. creator: Meike Ramon creator: Goedele Van Belle uri: https://doi.org/10.7717/peerj.1465 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ramon and Van Belle