title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-12 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identifying communities from multiplex biological networks link: https://peerj.com/articles/1525 last-modified: 2015-12-22 description: Various biological networks can be constructed, each featuring gene/protein relationships of different meanings (e.g., protein interactions or gene co-expression). However, this diversity is classically not considered and the different interaction categories are usually aggregated in a single network. The multiplex framework, where biological relationships are represented by different network layers reflecting the various nature of interactions, is expected to retain more information. Here we assessed aggregation, consensus and multiplex-modularity approaches to detect communities from multiple network sources. By simulating random networks, we demonstrated that the multiplex-modularity method outperforms the aggregation and consensus approaches when network layers are incomplete or heterogeneous in density. Application to a multiplex biological network containing 4 layers of physical or functional interactions allowed recovering communities more accurately annotated than their aggregated counterparts. Overall, taking into account the multiplexity of biological networks leads to better-defined functional modules. A user-friendly graphical software to detect communities from multiplex networks, and corresponding C source codes, are available at GitHub (https://github.com/gilles-didier/MolTi). creator: Gilles Didier creator: Christine Brun creator: Anaïs Baudot uri: https://doi.org/10.7717/peerj.1525 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Didier et al. title: The systematic relationships and biogeographic history of ornithischian dinosaurs link: https://peerj.com/articles/1523 last-modified: 2015-12-22 description: The systematic relationships of taxa traditionally referred to as ‘basal ornithopods’ or ‘hypsilophodontids’ remain poorly resolved since it was discovered that these taxa are not a monophyletic group, but rather a paraphyletic set of neornithischian taxa. Thus, even as the known diversity of these taxa has dramatically increased over the past two decades, our knowledge of their placement relative to each other and the major ornithischian subclades remained incomplete. This study employs the largest phylogenetic dataset yet compiled to assess basal ornithischian relationships (255 characters for 65 species level terminal taxa). The resulting strict consensus tree is the most well-resolved, stratigraphically consistent hypothesis of basal ornithischian relationships yet hypothesized. The only non-iguanodontian ornithopod (=basal ornithopod) recovered in this analysis is Hypsilophodon foxii. The majority of former ‘hypsilophodontid’ taxa are recovered within a single clade (Parksosauridae) that is situated as the sister-taxon to Cerapoda. The Parksosauridae is divided between two subclades, the Orodrominae and the Thescelosaurinae. This study does not recover a clade consisting of the Asian taxa Changchunsaurus, Haya, and Jeholosaurus (=Jeholosauridae). Rather, the former two taxa are recovered as basal members of Thescelosaurinae, while the latter taxon is recovered in a clade with Yueosaurus near the base of Neornithischia.The endemic South American clade Elasmaria is recovered within the Thescelosaurinae as the sister taxon to Thescelosaurus. This study supports the origination of Dinosauria and the early diversification of Ornithischia within Gondwana. Neornithischia first arose in Africa by the Early Jurassic before dispersing to Asia before the late Middle Jurassic, where much of the diversification among non-cerapodan neornithischians occurred. Under the simplest scenario the Parksosauridae originated in North America, with at least two later dispersals to Asia and one to South America. However, when ghost lineages are considered, an alternate dispersal hypothesis has thescelosaurines dispersing from Asia into South America (via North America) during the Early Cretaceous, then back into North America in the latest Cretaceous. The latter hypothesis may explain the dominance of orodromine taxa prior to the Maastrichtian in North America and the sudden appearance and wide distribution of thescelosaurines in North America beginning in the early Maastrichtian. While the diversity of parksosaurids has greatly increased over the last fifteen years, a ghost lineage of over 40 myr is present between the base of Parksosauridae and Cerapoda, indicating that much of the early history and diversity of this clade is yet to be discovered. This new phylogenetic hypothesis provides a comprehensive framework for testing further hypotheses regarding evolutionary patterns and processes within Ornithischia. creator: Clint A. Boyd uri: https://doi.org/10.7717/peerj.1523 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Boyd title: Development of a Taqman real-time PCR assay for rapid detection and quantification of Vibrio tapetis in extrapallial fluids of clams link: https://peerj.com/articles/1484 last-modified: 2015-12-22 description: The Gram-negative bacterium Vibrio tapetis is known as the causative agent of Brown Ring Disease (BRD) in the Manila clam Venerupis (=Ruditapes) philippinarum. This bivalve is the second most important species produced in aquaculture and has a high commercial value. In spite of the development of several molecular methods, no survey has been yet achieved to rapidly quantify the bacterium in the clam. In this study, we developed a Taqman real-time PCR assay targeting virB4 gene for accurate and quantitative identification of V. tapetis strains pathogenic to clams. Sensitivity and reproducibility of the method were assessed using either filtered sea water or extrapallial fluids of clam injected with the CECT4600TV. tapetis strain. Quantification curves of V. tapetis strain seeded in filtered seawater (FSW) or extrapallial fluids (EF) samples were equivalent showing reliable qPCR efficacies. With this protocol, we were able to specifically detect V. tapetis strains down to 1.125 101 bacteria per mL of EF or FSW, taking into account the dilution factor used for appropriate template DNA preparation. This qPCR assay allowed us to monitor V. tapetis load both experimentally or naturally infected Manila clams. This technique will be particularly useful for monitoring the kinetics of massive infections by V. tapetis and for designing appropriate control measures for aquaculture purposes. creator: Adeline Bidault creator: Gaëlle G. Richard creator: Cédric Le Bris creator: Christine Paillard uri: https://doi.org/10.7717/peerj.1484 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Bidault et al. title: The revised Temperament and Character Inventory: normative data by sex and age from a Spanish normal randomized sample link: https://peerj.com/articles/1481 last-modified: 2015-12-22 description: Objectives. The psychometric properties regarding sex and age for the revised version of the Temperament and Character Inventory (TCI-R) and its derived short version, the Temperament and Character Inventory (TCI-140), were evaluated with a randomized sample from the community.Methods. A randomized sample of 367 normal adult subjects from a Spanish municipality, who were representative of the general population based on sex and age, participated in the current study. Descriptive statistics and internal consistency according to α coefficient were obtained for all of the dimensions and facets. T-tests and univariate analyses of variance, followed by Bonferroni tests, were conducted to compare the distributions of the TCI-R dimension scores by age and sex.Results. On both the TCI-R and TCI-140, women had higher scores for Harm Avoidance, Reward Dependence and Cooperativeness than men, whereas men had higher scores for Persistence. Age correlated negatively with Novelty Seeking, Reward Dependence and Cooperativeness and positively with Harm Avoidance and Self-transcendence. Young subjects between 18 and 35 years had higher scores than older subjects in NS and RD. Subjects between 51 and 77 years scored higher in both HA and ST. The alphas for the dimensions were between 0.74 and 0.87 for the TCI-R and between 0.63 and 0.83 for the TCI-140.Conclusion. Results, which were obtained with a randomized sample, suggest that there are specific distributions of personality traits by sex and age. Overall, both the TCI-R and the abbreviated TCI-140 were reliable in the ‘good-to-excellent’ range. A strength of the current study is the representativeness of the sample. creator: Alfonso Gutierrez-Zotes creator: Javier Labad creator: Lourdes Martorell creator: Ana Gaviria creator: Carmen Bayón creator: Elisabet Vilella creator: C. Robert Cloninger uri: https://doi.org/10.7717/peerj.1481 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gutierrez-Zotes et al. title: Reliability and validity of neurobehavioral function on the Psychology Experimental Building Language test battery in young adults link: https://peerj.com/articles/1460 last-modified: 2015-12-22 description: Background. The Psychology Experiment Building Language (PEBL) software consists of over one-hundred computerized tests based on classic and novel cognitive neuropsychology and behavioral neurology measures. Although the PEBL tests are becoming more widely utilized, there is currently very limited information about the psychometric properties of these measures.Methods. Study I examined inter-relationships among nine PEBL tests including indices of motor-function (Pursuit Rotor and Dexterity), attention (Test of Attentional Vigilance and Time-Wall), working memory (Digit Span Forward), and executive-function (PEBL Trail Making Test, Berg/Wisconsin Card Sorting Test, Iowa Gambling Test, and Mental Rotation) in a normative sample (N = 189, ages 18–22). Study II evaluated test–retest reliability with a two-week interest interval between administrations in a separate sample (N = 79, ages 18–22).Results. Moderate intra-test, but low inter-test, correlations were observed and ceiling/floor effects were uncommon. Sex differences were identified on the Pursuit Rotor (Cohen’s d = 0.89) and Mental Rotation (d = 0.31) tests. The correlation between the test and retest was high for tests of motor learning (Pursuit Rotor time on target r = .86) and attention (Test of Attentional Vigilance response time r = .79), intermediate for memory (digit span r = .63) but lower for the executive function indices (Wisconsin/Berg Card Sorting Test perseverative errors = .45, Tower of London moves = .15). Significant practice effects were identified on several indices of executive function.Conclusions. These results are broadly supportive of the reliability and validity of individual PEBL tests in this sample. These findings indicate that the freely downloadable, open-source PEBL battery (http://pebl.sourceforge.net) is a versatile research tool to study individual differences in neurocognitive performance. creator: Brian J. Piper creator: Shane T. Mueller creator: Alexander R. Geerken creator: Kyle L. Dixon creator: Gregory Kroliczak creator: Reid H.J. Olsen creator: Jeremy K. Miller uri: https://doi.org/10.7717/peerj.1460 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Piper et al. title: Comparative analyses of olfactory systems in terrestrial crabs (Brachyura): evidence for aerial olfaction? link: https://peerj.com/articles/1433 last-modified: 2015-12-22 description: Adaptations to a terrestrial lifestyle occurred convergently multiple times during the evolution of the arthropods. This holds also true for the “true crabs” (Brachyura), a taxon that includes several lineages that invaded land independently. During an evolutionary transition from sea to land, animals have to develop a variety of physiological and anatomical adaptations to a terrestrial life style related to respiration, reproduction, development, circulation, ion and water balance. In addition, sensory systems that function in air instead of in water are essential for an animal’s life on land. Besides vision and mechanosensory systems, on land, the chemical senses have to be modified substantially in comparison to their function in water. Among arthropods, insects are the most successful ones to evolve aerial olfaction. Various aspects of terrestrial adaptation have also been analyzed in those crustacean lineages that evolved terrestrial representatives including the taxa Anomala, Brachyura, Amphipoda, and Isopoda. We are interested in how the chemical senses of terrestrial crustaceans are modified to function in air. Therefore, in this study, we analyzed the brains and more specifically the structure of the olfactory system of representatives of brachyuran crabs that display different degrees of terrestriality, from exclusively marine to mainly terrestrial. The methods we used included immunohistochemistry, detection of autofluorescence- and confocal microscopy, as well as three-dimensional reconstruction and morphometry. Our comparative approach shows that both the peripheral and central olfactory pathways are reduced in terrestrial members in comparison to their marine relatives, suggesting a limited function of their olfactory system on land. We conclude that for arthropod lineages that invaded land, evolving aerial olfaction is no trivial task. creator: Jakob Krieger creator: Philipp Braun creator: Nicole T. Rivera creator: Christoph D. Schubart creator: Carsten H.G. Müller creator: Steffen Harzsch uri: https://doi.org/10.7717/peerj.1433 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Krieger et al. title: Quantitative analysis of the interplay between hsc70 and its co-chaperone HspBP1 link: https://peerj.com/articles/1530 last-modified: 2015-12-21 description: Background. Chaperones and their co-factors are components of a cellular network; they collaborate to maintain proteostasis under normal and harmful conditions. In particular, hsp70 family members and their co-chaperones are essential to repair damaged proteins. Co-chaperones are present in different subcellular compartments, where they modulate chaperone activities.Methods and Results. Our studies assessed the relationship between hsc70 and its co-factor HspBP1 in human cancer cells. HspBP1 promotes nucleotide exchange on hsc70, but has also chaperone-independent functions. We characterized the interplay between hsc70 and HspBP1 by quantitative confocal microscopy combined with automated image analyses and statistical evaluation. Stress and the recovery from insult changed significantly the subcellular distribution of hsc70, but had little effect on HspBP1. Single-cell measurements and regression analysis revealed that the links between the chaperone and its co-factor relied on (i) the physiological state of the cell and (ii) the subcellular compartment. As such, we identified a linear relationship and strong correlation between hsc70 and HspBP1 distribution in control and heat-shocked cells; this correlation changed in a compartment-specific fashion during the recovery from stress. Furthermore, we uncovered significant stress-induced changes in the colocalization between hsc70 and HspBP1 in the nucleus and cytoplasm.Discussion. Our quantitative approach defined novel properties of the co-chaperone HspBP1 as they relate to its interplay with hsc70. We propose that changes in cell physiology promote chaperone redistribution and thereby stimulate chaperone-independent functions of HspBP1. creator: Hicham Mahboubi creator: Ursula Stochaj uri: https://doi.org/10.7717/peerj.1530 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Mahboubi and Stochaj title: Genome-wide identification of hypoxia-induced enhancer regions link: https://peerj.com/articles/1527 last-modified: 2015-12-21 description: Here we present a genome-wide method for de novo identification of enhancer regions. This approach enables massively parallel empirical investigation of DNA sequences that mediate transcriptional activation and provides a platform for discovery of regulatory modules capable of driving context-specific gene expression. The method links fragmented genomic DNA to the transcription of randomer molecule identifiers and measures the functional enhancer activity of the library by massively parallel sequencing. We transfected a Drosophila melanogaster library into S2 cells in normoxia and hypoxia, and assayed 4,599,881 genomic DNA fragments in parallel. The locations of the enhancer regions strongly correlate with genes up-regulated after hypoxia and previously described enhancers. Novel enhancer regions were identified and integrated with RNAseq data and transcription factor motifs to describe the hypoxic response on a genome-wide basis as a complex regulatory network involving multiple stress-response pathways. This work provides a novel method for high-throughput assay of enhancer activity and the genome-scale identification of 31 hypoxia-activated enhancers in Drosophila. creator: Nick Kamps-Hughes creator: Jessica L. Preston creator: Melissa A. Randel creator: Eric A. Johnson uri: https://doi.org/10.7717/peerj.1527 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Kamps-Hughes et al. title: Artificial neural network cascade identifies multi-P450 inhibitors in natural compounds link: https://peerj.com/articles/1524 last-modified: 2015-12-21 description: Substantial evidence has shown that most exogenous substances are metabolized by multiple cytochrome P450 (P450) enzymes instead of by merely one P450 isoform. Thus, multi-P450 inhibition leads to greater drug-drug interaction risk than specific P450 inhibition. Herein, we innovatively established an artificial neural network cascade (NNC) model composed of 23 cascaded networks in a ladder-like framework to identify potential multi-P450 inhibitors among natural compounds by integrating 12 molecular descriptors into a P450 inhibition score (PIS). Experimental data reporting in vitro inhibition of five P450 isoforms (CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4) were obtained for 8,148 compounds from the Cytochrome P450 Inhibitors Database (CPID). The results indicate significant positive correlation between the PIS values and the number of inhibited P450 isoforms (Spearman’s ρ = 0.684, p < 0.0001). Thus, a higher PIS indicates a greater possibility for a chemical to inhibit the enzyme activity of at least three P450 isoforms. Ten-fold cross-validation of the NNC model suggested an accuracy of 78.7% for identifying whether a compound is a multi-P450 inhibitor or not. Using our NNC model, 22.2% of the approximately 160,000 natural compounds in TCM Database@Taiwan were identified as potential multi-P450 inhibitors. Furthermore, chemical similarity calculations suggested that the prevailing parent structures of natural multi-P450 inhibitors were alkaloids. Our findings show that dissection of chemical structure contributes to confident identification of natural multi-P450 inhibitors and provides a feasible method for virtually evaluating multi-P450 inhibition risk for a known structure. creator: Zhangming Li creator: Yan Li creator: Lu Sun creator: Yun Tang creator: Lanru Liu creator: Wenliang Zhu uri: https://doi.org/10.7717/peerj.1524 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Li et al. title: Orphan nuclear receptor NR4A2 inhibits hepatic stellate cell proliferation through MAPK pathway in liver fibrosis link: https://peerj.com/articles/1518 last-modified: 2015-12-21 description: Hepatic stellate cells (HSCs) play a crucial role in liver fibrosis, which is a pathological process characterized by extracellular matrix accumulation. NR4A2 is a nuclear receptor belonging to the NR4A subfamily and vital in regulating cell growth, metabolism, inflammation and other biological functions. However, its role in HSCs is unclear. We analyzed NR4A2 expression in fibrotic liver and stimulated HSCs compared with control group and studied the influence on cell proliferation, cell cycle, cell apoptosis and MAPK pathway after NR4A2 knockdown. NR4A2 expression was examined by real-time polymerase chain reaction, Western blotting, immunohistochemistry and immunofluorescence analyses. NR4A2 expression was significantly lower in fibrotic liver tissues and PDGF BB or TGF-β stimulated HSCs compared with control group. After NR4A2 knockdown α-smooth muscle actin and Col1 expression increased. In addition, NR4A2 silencing led to the promotion of cell proliferation, increase of cell percentage in S phase and reduced phosphorylation of ERK1/2, P38 and JNK in HSCs. These results indicate that NR4A2 can inhibit HSC proliferation through MAPK pathway and decrease extracellular matrix in liver fibrogenesis. NR4A2 may be a promising therapeutic target for liver fibrosis. creator: Pengguo Chen creator: Jie Li creator: Yan Huo creator: Jin Lu creator: Lili Wan creator: Bin Li creator: Run Gan creator: Cheng Guo uri: https://doi.org/10.7717/peerj.1518 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Chen et al. title: Digital preparation and osteology of the skull of Lesothosaurus diagnosticus (Ornithischia: Dinosauria) link: https://peerj.com/articles/1494 last-modified: 2015-12-21 description: Several skulls of the ornithischian dinosaur Lesothosaurus diagnosticus (Lower Jurassic, southern Africa) are known, but all are either incomplete, deformed, or incompletely prepared. This has hampered attempts to provide a comprehensive description of skull osteology in this crucial early dinosaurian taxon. Using visualization software, computed tomographic scans of the Lesothosaurus syntypes were digitally segmented to remove matrix, and identify and separate individual cranial and mandibular bones, revealing new anatomical details such as sutural morphology and the presence of several previously undescribed elements. Together with visual inspection of exposed skull bones, these CT data enable a complete description of skull anatomy in this taxon. Comparisons with our new data suggest that two specimens previously identified as Lesothosaurus sp. (MNHN LES 17 and MNHN LES 18) probably represent additional individuals of Lesothosaurus diagnosticus. creator: Laura B. Porro creator: Lawrence M. Witmer creator: Paul M. Barrett uri: https://doi.org/10.7717/peerj.1494 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Porro et al. title: A novel method to determine perineal artery occlusion among male bicyclists link: https://peerj.com/articles/1477 last-modified: 2015-12-21 description: Background. Perineal pressure due to bicycle riding has been associated with erectile dysfunction. We developed a novel method to measure the occlusive force exerted over the perineal arteries and determined perineal artery occlusion by a variety of seat designs.Methods. Doppler ultrasonography facilitated perineal artery localization and determination of the force required for perineal artery occlusion in 20 healthy men. Flexiforce® sensors were affixed over the proximal and distal aspects of the perineal arteries bilaterally. Individuals completed bicycle rides in the road- and stationary-settings with six distinct seat designs, including those with and without an anterior “nose.”Results. The occlusion time proportion of the total ride time was calculated for each trial. The overall occlusion time proportion was 0.59 (95% CI [0.45–0.73]) across all seats and settings. The “no-nose” bicycle seat and the stationary-setting demonstrated significantly lower occlusion proportion times than the traditional nose bicycle seat and road-setting, respectively. However, all bicycle seats yielded an occlusion time proportion of 0.41 or greater.Discussion. Our method of real-time, non-invasive force measurement localized to the perineal arteries may be used to validate future bicycle seat design. It also underscores the significant risk of perineal artery insufficiency in men who are avid bicyclists. This risk may be minimized by using newer “no-nose” bicycle seats. creator: Sujeeth Parthiban creator: James M. Hotaling creator: Martin Kathrins creator: Amit P. Baftiri creator: Sally Freels creator: Craig S. Niederberger uri: https://doi.org/10.7717/peerj.1477 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Parthiban et al. title: A late-surviving apatemyid (Mammalia: Apatotheria) from the latest Oligocene of Florida, USA link: https://peerj.com/articles/1509 last-modified: 2015-12-17 description: A new species of Apatemyidae, Sinclairella simplicidens, is based on four isolated teeth that were screenwashed from fissure fillings at the late Oligocene Buda locality, Alachua County, Florida. Compared to its only congener Sinclairella dakotensis, the new species is characterized by upper molars with more simplified crowns, with the near absence of labial shelves and stylar cusps except for a strong parastyle on M1, loss of paracrista and paraconule on M2 (paraconule retained but weak on M1), lack of anterior cingulum on M1–M3, straighter centrocristae, smaller hypocone on M1 and M2, larger hypocone on M3, distal edge of M2 continuous from hypocone to postmetacrista supporting a large posterior basin, and with different tooth proportions in which M2 is the smallest rather than the largest molar in the toothrow. The relatively rare and poorly-known family Apatemyidae has a long temporal range in North America from the late Paleocene (early Tiffanian) to early Oligocene (early Arikareean). The new species from Florida significantly extends this temporal range by roughly 5 Ma to the end of the Paleogene near the Oligocene-Miocene boundary (from early Arikareean, Ar1, to late Arikareean, Ar3), and greatly extends the geographic range of the family into eastern North America some 10° of latitude farther south and 20° of longitude farther east (about 2,200 km farther southeast) than previously known. This late occurrence probably represents a retreat of this subtropically adapted family into the Gulf Coastal Plain subtropical province at the end of the Paleogene and perhaps the end of the apatemyid lineage in North America. creator: Nicholas J. Czaplewski creator: Gary S. Morgan uri: https://doi.org/10.7717/peerj.1509 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Czaplewski and Morgan title: Feasibility of progressive sit-to-stand training among older hospitalized patients link: https://peerj.com/articles/1500 last-modified: 2015-12-17 description: Background. In older patients, hospitalization is associated with a decline in functional performance and loss of muscle strength. Loss of muscle strength and functional performance can be prevented by systematic strength training, but details are lacking regarding the optimal exercise program and dose for older patients. Therefore, our aim was to test the feasibility of a progression model for loaded sit-to-stand training among older hospitalized patients.Methods. This is a prospective cohort study conducted as a feasibility study prior to a full-scale trial. We included twenty-four older patients (≥65 yrs) acutely admitted from their own home to the medical services of the hospital. We developed an 8-level progression model for loaded sit-to-stands, which we named STAND. We used STAND as a model to describe how to perform the sit-to-stand exercise as a strength training exercise aimed at reaching a relative load of 8–12 repetitions maximum (RM) for 8–12 repetitions. Weight could be added by the use of a weight vest when needed. The ability of the patients to reach the intended relative load (8–12 RM), while performing sit-to-stands following the STAND model, was tested once during hospitalization and once following discharge in their own homes. A structured interview including assessment of possible modifiers (cognitive status by the Short Orientation Memory test and mobility by the De Morton Mobility Index) was administered both on admission to the hospital and in the home setting. The STAND model was considered feasible if: (1) 75% of the assessed patients could perform the exercise at a given level of the model reaching 8–12 repetitions at a relative load of 8–12 RM for one set of exercise in the hospital and two sets of exercise at home; (2) no ceiling or floor effect was seen; (3) no indication of adverse events were observed. The outcomes assessed were: level of STAND attained, the number of sets performed, perceived exertion (the Borg scale), and pain (the Verbal Ranking Scale).Results. Twenty-four patients consented to participate. Twenty-three of the patients were tested in the hospital and 19 patients were also tested in their home. All three criteria for feasibility were met: (1) in the hospital, 83% could perform the exercise at a given level of STAND, reaching 8–12 repetitions at 8–12 RM for one set, and 79% could do so for two sets in the home setting; (2) for all assessed patients, a possibility of progression or regression was possible—no ceiling or floor effect was observed; (3) no indication of adverse events (pain) was observed. Also, those that scored higher on the De Morton Mobility Index performed the exercise at higher levels of STAND, whereas performance was independent of cognitive status.Conclusions. We found a simple progression model for loaded sit-to-stands (STAND) feasible in acutely admitted older medical patients (≥65 yrs), based on our pre-specified criteria for feasibility. creator: Mette Merete Pedersen creator: Janne Petersen creator: Jonathan F. Bean creator: Lars Damkjaer creator: Helle Gybel Juul-Larsen creator: Ove Andersen creator: Nina Beyer creator: Thomas Bandholm uri: https://doi.org/10.7717/peerj.1500 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pedersen et al. title: Differential scanning calorimetry of whole Escherichia coli treated with the antimicrobial peptide MSI-78 indicate a multi-hit mechanism with ribosomes as a novel target link: https://peerj.com/articles/1516 last-modified: 2015-12-17 description: Differential Scanning Calorimetry (DSC) of intact Escherichia coli (E. coli) was used to identify non-lipidic targets of the antimicrobial peptide (AMP) MSI-78. The DSC thermograms revealed that, in addition to its known lytic properties, MSI-78 also has a striking effect on ribosomes. MSI-78’s effect on DSC scans of bacteria was similar to that of kanamycin, an antibiotic drug known to target the 30S small ribosomal subunit. An in vitro transcription/translation assay helped confirm MSI-78’s targeting of ribosomes. The scrambled version of MSI-78 also affected the ribosome peak of the DSC scans, but required greater amounts of peptide to cause a similar effect to the unscrambled peptide. Furthermore, the effect of the scrambled peptide was not specific to the ribosomes; other regions of the DSC thermogram were also affected. These results suggest that MSI-78’s effects on E. coli are at least somewhat dependent on its particular structural features, rather than a sole function of its overall charge and hydrophobicity. When considered along with earlier work detailing MSI-78’s membrane lytic properties, it appears that MSI-78 operates via a multi-hit mechanism with multiple targets. creator: Alexander M. Brannan creator: William A. Whelan creator: Emma Cole creator: Valerie Booth uri: https://doi.org/10.7717/peerj.1516 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Brannan et al. title: Establishing the role of honest broker: bridging the gap between protecting personal health data and clinical research efficiency link: https://peerj.com/articles/1506 last-modified: 2015-12-17 description: Background. The objective of this study is to propose the four conditions for the roles of honest brokers through a review of literature published by ten institutions that are successfully utilizing honest brokers. Furthermore, the study aims to examine whether the Asan Medical Center’s (AMC) honest brokers satisfy the four conditions, and examine the need to enhance their roles.Methods. We analyzed the roles, tasks, and types of honest brokers at 10 organizations by reviewing the literature. We also established a Task Force (TF) in our institution for setting the roles and processes of the honest broker system and the honest brokers. The findings of the literature search were compared with the existing systems at AMC—which introduced the honest broker system for the first time in Korea.Results. Only one organization employed an honest broker for validating anonymized clinical data and monitoring the anonymity verifications of the honest broker system. Six organizations complied with HIPAA privacy regulations, while four organizations did not disclose compliance. By comparing functions with those of the AMC, the following four main characteristics of honest brokers were determined: (1) de-identification of clinical data; (2) independence; (3) checking that the data are used only for purposes approved by the IRB; and (4) provision of de-identified data to researchers. These roles were then compared with those of honest brokers at the AMC.Discussion. First, guidelines that regulate the definitions, purposes, roles, and requirements for honest brokers are needed, since there are no currently existing regulations. Second, Korean clinical research institutions and national regulatory departments need to reach a consensus on a Korean version of Limited Data Sets (LDS), since there are no lists that describe the use of personal identification information. Lastly, satisfaction surveys on honest brokers by researchers are necessary to improve the quality of honest brokers. creator: Hyo Joung Choi creator: Min Joung Lee creator: Chang-Min Choi creator: JaeHo Lee creator: Soo-Yong Shin creator: Yungman Lyu creator: Yu Rang Park creator: Soyoung Yoo uri: https://doi.org/10.7717/peerj.1506 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Choi et al. title: 2015 Middle East Respiratory Syndrome Coronavirus (MERS-CoV) nosocomial outbreak in South Korea: insights from modeling link: https://peerj.com/articles/1505 last-modified: 2015-12-17 description: Background. Since the emergence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012, more than 1,300 laboratory confirmed cases of MERS-CoV infections have been reported in Asia, North Africa, and Europe by July 2015. The recent MERS-CoV nosocomial outbreak in South Korea quickly became the second largest such outbreak with 186 total cases and 36 deaths in a little more than one month, second only to Saudi Arabia in country-specific number of reported cases.Methods. We use a simple mathematical model, the Richards model, to trace the temporal course of the South Korea MERS-CoV outbreak. We pinpoint its outbreak turning point and its transmissibility via basic reproduction number R0 in order to ascertain the occurrence of this nosocomial outbreak and how it was quickly brought under control.Results. The estimated outbreak turning point of ti = 23.3 days (95% CI [22.6–24.0]), or 23–24 days after the onset date of the index case on May 11, pinpoints June 3–4 as the time of the turning point or the peak incidence for this outbreak by onset date. R0 is estimated to range between 7.0 and 19.3.Discussion and Conclusion. The turning point of the South Korea MERS-CoV outbreak occurred around May 27–29, when control measures were quickly implemented after laboratory confirmation of the first cluster of nosocomial infections by the index patient. Furthermore, transmissibility of MERS-CoV in the South Korea outbreak was significantly higher than those reported from past MERS-CoV outbreaks in the Middle East, which is attributable to the nosocomial nature of this outbreak. Our estimate of R0 for the South Korea MERS-CoV nosocomial outbreak further highlights the importance and the risk involved in cluster infections and superspreading events in crowded settings such as hospitals. Similar to the 2003 SARS epidemic, outbreaks of infectious diseases with low community transmissibility like MERS-CoV could still occur initially with large clusters of nosocomial infections, but can be quickly and effectively controlled with timely intervention measures. creator: Ying-Hen Hsieh uri: https://doi.org/10.7717/peerj.1505 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Hsieh title: Are attractive male crickets better able to pay the costs of an immune challenge? link: https://peerj.com/articles/1501 last-modified: 2015-12-17 description: Reproduction and immunity are fitness-related traits that trade-off with each other. Parasite-mediated theories of sexual selection suggest, however, that higher-quality males should suffer smaller costs to reproduction-related traits and behaviours (e.g., sexual display) from an immune challenge because these males possess more resources with which to deal with the challenge. We used Gryllus texensis field crickets to test the prediction that attractive males should better maintain the performance of fitness-related traits (e.g., calling effort) in the face of an immune challenge compared with unattractive males. We found no support for our original predictions. However, that immune activation causes attractive males to significantly increase their calling effort compared with unattractive males suggests that these males might terminally invest in order to compensate for decreased future reproduction. creator: Clint D. Kelly creator: Melissa S.C. Telemeco creator: Lyric C. Bartholomay uri: https://doi.org/10.7717/peerj.1501 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Kelly et al. title: Evidence of macrophagous teleosaurid crocodylomorphs in the Corallian Group (Oxfordian, Late Jurassic) of the UK link: https://peerj.com/articles/1497 last-modified: 2015-12-17 description: Teleosaurids were a group of semi-aquatic crocodylomorphs with a fossil record that spanned the Jurassic Period. In the UK, abundant specimens are known from the Oxford Clay Formation (OCF, Callovian to lower Oxfordian), but are very rare in the Kimmeridge Clay Formation (KCF, Kimmeridgian to lower Tithonian), despite their abundance in some contemporaneous deposits in continental Europe. Unfortunately, due to the paucity of material from the intermediate ‘Corallian Gap’ (middle to upper Oxfordian), we lack an understanding of how and why teleosaurid taxic abundance and diversity declined from the OCF to the KCF. The recognition of an incomplete teleosaurid lower jaw from the Corallian of Weymouth (Dorset, UK) begins to rectify this. The vertically oriented dentition, blunt tooth apices, intense enamel ornamentation that shifts to an anastomosed pattern apically, and deep reception pits on the dentary unambiguously demonstrates the affinity of this specimen with an unnamed sub-clade of macrophagous/durophagous teleosaurids (‘Steneosaurus’ obtusidens + Machimosaurus). The high symphyseal tooth count allows us to exclude the specimen from M. hugii and M. mosae, but in absence of more diagnostic material we cannot unambiguously assign DORCM G.3939 to a more specific level. Nevertheless, this specimen represents the first mandibular material referable to Teleosauridae from the poorly sampled middle-upper Oxfordian time-span in the UK. creator: Davide Foffa creator: Mark T. Young creator: Stephen L. Brusatte uri: https://doi.org/10.7717/peerj.1497 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Foffa et al. title: Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens link: https://peerj.com/articles/1435 last-modified: 2015-12-17 description: Sponges are well known for hosting dense and diverse microbial communities, but how these associations vary with biogeography and environment is less clear. Here we compared the microbiome of an ecologically important sponge species, Carteriospongia foliascens, over a large geographic area and identified environmental factors likely responsible for driving microbial community differences between inshore and offshore locations using co-occurrence networks (NWs). The microbiome of C. foliascens exhibited exceptionally high microbial richness, with more than 9,000 OTUs identified at 97% sequence similarity. A large biogeographic signal was evident at the OTU level despite similar phyla level diversity being observed across all geographic locations. The C. foliascens bacterial community was primarily comprised of Gammaproteobacteria (34.2% ± 3.4%) and Cyanobacteria (32.2% ± 3.5%), with lower abundances of Alphaproteobacteria, Bacteroidetes, unidentified Proteobacteria, Actinobacteria, Acidobacteria and Deltaproteobacteria. Co-occurrence NWs revealed a consistent increase in the proportion of Cyanobacteria over Bacteroidetes between turbid inshore and oligotrophic offshore locations, suggesting that the specialist microbiome of C. foliascens is driven by environmental factors. creator: Heidi M. Luter creator: Stefanie Widder creator: Emmanuelle S. Botté creator: Muhammad Abdul Wahab creator: Stephen Whalan creator: Lucas Moitinho-Silva creator: Torsten Thomas creator: Nicole S. Webster uri: https://doi.org/10.7717/peerj.1435 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Luter et al. title: Why did the UV-A-induced photoluminescent blue–green glow in trilobite eyes and exoskeletons not cause problems for trilobites? link: https://peerj.com/articles/1492 last-modified: 2015-12-15 description: The calcitic lenses in the eyes of Palaeozoic trilobites are unique in the animal kingdom, although the use of calcite would have conveyed great advantages for vision in aquatic systems. Calcite lenses are transparent, and due to their high refractive index they would facilitate the focusing of light. In some respects, however, calcite lenses bear evident disadvantages. Birefringence would cause double images at different depths, but this is not a problem for trilobites since the difference in the paths of the ordinary and extraordinary rays is less than the diameter of the receptor cells. Another point, not discussed hitherto, is that calcite fluoresces when illuminated with UV-A. Here we show experimentally that calcite lenses fluoresce, and we discuss why fluorescence does not diminish the optical quality of these lenses and the image formed by them. In the environments in which the trilobites lived, UV-A would not have been a relevant factor, and thus fluorescence would not have disturbed or confused their visual system. We also argue that whatever the reason that calcite was never again used successfully in the visual systems of aquatic arthropods, it was not fluorescence. creator: Brigitte Schoenemann creator: Euan N.K. Clarkson creator: Gábor Horváth uri: https://doi.org/10.7717/peerj.1492 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Schoenemann et al. title: The dentary of Australovenator wintonensis (Theropoda, Megaraptoridae); implications for megaraptorid dentition link: https://peerj.com/articles/1512 last-modified: 2015-12-15 description: Megaraptorid theropods were an enigmatic group of medium-sized predatory dinosaurs, infamous for the hypertrophied claw on the first manual digit. Megaraptorid dentition is largely restricted to isolated teeth found in association with skeletal parts; however, the in situ maxillary dentition of Megaraptor was recently described. A newly discovered right dentary pertaining to the Australovenator holotype preserves in situ dentition, permitting unambiguous characterisation of the dentary tooth morphology. The new jaw is virtually complete, with an overall elongate, shallow profile, and fifteen visible in situ teeth at varying stages of eruption. In situ teeth confirm Australovenator exhibited modest pseudoheterodonty, recurved lateral teeth with a serrate distal carina and reduced mesial carina, similar to other megaraptorids. Australovenator also combines of figure-of-eight basal cross-section with a lanceolate shape due to the presence of labial and lingual depressions and the lingual twist of the distal carina. Computed tomography and three-dimensional imagery provided superior characterisation of the dentary morphology and enabled an accurate reconstruction to a pre-fossilised state. The newly established dental morphology also afforded re-evaluation of isolated theropod teeth discovered at the Australovenator holotype locality and from several additional Winton Formation localities. The isolated Winton teeth are qualitatively and quantitatively similar to the in situ dentary teeth of Australovenator, but are also morphometrically similar to Abelisauridae, Allosauridae, Coelophysoidea, Megalosauridae and basal Tyrannosauroidea. Qualitative characters, however, clearly distinguish the teeth of Australovenator and the isolated Winton teeth from all other theropods. Evidence from teeth suggests megaraptorids were the dominant predators in the Winton Formation, which contrasts with other penecontemporaneous Gondwanan ecosystems. creator: Matt A. White creator: Phil R. Bell creator: Alex G. Cook creator: Stephen F. Poropat creator: David A. Elliott uri: https://doi.org/10.7717/peerj.1512 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 White et al. title: Creating a Chinese suicide dictionary for identifying suicide risk on social media link: https://peerj.com/articles/1455 last-modified: 2015-12-15 description: Introduction. Suicide has become a serious worldwide epidemic. Early detection of individual suicide risk in population is important for reducing suicide rates. Traditional methods are ineffective in identifying suicide risk in time, suggesting a need for novel techniques. This paper proposes to detect suicide risk on social media using a Chinese suicide dictionary.Methods. To build the Chinese suicide dictionary, eight researchers were recruited to select initial words from 4,653 posts published on Sina Weibo (the largest social media service provider in China) and two Chinese sentiment dictionaries (HowNet and NTUSD). Then, another three researchers were recruited to filter out irrelevant words. Finally, remaining words were further expanded using a corpus-based method. After building the Chinese suicide dictionary, we tested its performance in identifying suicide risk on Weibo. First, we made a comparison of the performance in both detecting suicidal expression in Weibo posts and evaluating individual levels of suicide risk between the dictionary-based identifications and the expert ratings. Second, to differentiate between individuals with high and non-high scores on self-rating measure of suicide risk (Suicidal Possibility Scale, SPS), we built Support Vector Machines (SVM) models on the Chinese suicide dictionary and the Simplified Chinese Linguistic Inquiry and Word Count (SCLIWC) program, respectively. After that, we made a comparison of the classification performance between two types of SVM models.Results and Discussion. Dictionary-based identifications were significantly correlated with expert ratings in terms of both detecting suicidal expression (r = 0.507) and evaluating individual suicide risk (r = 0.455). For the differentiation between individuals with high and non-high scores on SPS, the Chinese suicide dictionary (t1: F1 = 0.48; t2: F1 = 0.56) produced a more accurate identification than SCLIWC (t1: F1 = 0.41; t2: F1 = 0.48) on different observation windows.Conclusions. This paper confirms that, using social media, it is possible to implement real-time monitoring individual suicide risk in population. Results of this study may be useful to improve Chinese suicide prevention programs and may be insightful for other countries. creator: Meizhen Lv creator: Ang Li creator: Tianli Liu creator: Tingshao Zhu uri: https://doi.org/10.7717/peerj.1455 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lv et al. title: The first South American sandownid turtle from the Lower Cretaceous of Colombia link: https://peerj.com/articles/1431 last-modified: 2015-12-15 description: Sandownids are a group of Early Cretaceous-Paleocene turtles that for several decades have been only known by cranial and very fragmentary postcranial elements. Here I report and describe the most complete sandownid turtle known so far, including articulated skull, lower jaw and postcranial elements, from the Early Cretaceous (upper Barremian-lower Aptian, >120 Ma), Paja Formation, Villa de Leyva town, Colombia. The new Colombian sandownid is defined here as Leyvachelys cipadi new genus, new species and because of its almost identical skull morphology with a previously reported turtle from the Glen Rose Formation, Texas, USA, both are grouped in a single and officially (ICNZ rules) defined taxon. Phylogenetic analysis including L. cipadi supports once again the monophyly of Sandownidae, as belonging to the large and recently redefined Pan-Chelonioidea clade. The morphology of L. cipadi indicates that sandownids were not open marine turtles, but instead littoral to shallow marine durophagous dwellers. Leyvachelys cipadi not only constitutes the first record of sandowinds in South America, but also the earliest global record for the group. creator: Edwin Cadena uri: https://doi.org/10.7717/peerj.1431 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Cadena title: Analysis of synonymous codon usage patterns in sixty-four different bivalve species link: https://peerj.com/articles/1520 last-modified: 2015-12-14 description: Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across different genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 different species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable differences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational efficiency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon in this large, commercially and environmentally important, class of marine invertebrates. creator: Marco Gerdol creator: Gianluca De Moro creator: Paola Venier creator: Alberto Pallavicini uri: https://doi.org/10.7717/peerj.1520 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gerdol et al. title: Evaluating pharmacological models of high and low anxiety in sheep link: https://peerj.com/articles/1510 last-modified: 2015-12-14 description: New tests of animal affect and welfare require validation in subjects experiencing putatively different states. Pharmacological manipulations of affective state are advantageous because they can be administered in a standardised fashion, and the duration of their action can be established and tailored to suit the length of a particular test. To this end, the current study aimed to evaluate a pharmacological model of high and low anxiety in an important agricultural and laboratory species, the sheep. Thirty-five 8-month-old female sheep received either an intramuscular injection of the putatively anxiogenic drug 1-(m-chlorophenyl)piperazine (mCPP; 1 mg/kg; n = 12), an intravenous injection of the putatively anxiolytic drug diazepam (0.1 mg/kg; n = 12), or acted as a control (saline intramuscular injection n = 11). Thirty minutes after the treatments, sheep were individually exposed to a variety of tests assessing their general movement, performance in a ‘runway task’ (moving down a raceway for a food reward), response to startle, and behaviour in isolation. A test to assess feeding motivation was performed 2 days later following administration of the drugs to the same animals in the same manner. The mCPP sheep had poorer performance in the two runway tasks (6.8 and 7.7 × slower respectively than control group; p < 0.001), a greater startle response (1.4 vs. 0.6; p = 0.02), a higher level of movement during isolation (9.1 steps vs. 5.4; p < 0.001), and a lower feeding motivation (1.8 × slower; p < 0.001) than the control group, all of which act as indicators of anxiety. These results show that mCPP is an effective pharmacological model of high anxiety in sheep. Comparatively, the sheep treated with diazepam did not display any differences compared to the control sheep. Thus we suggest that mCPP is an effective treatment to validate future tests aimed at assessing anxiety in sheep, and that future studies should include other subtle indicators of positive affective states, as well as dosage studies, so conclusions on the efficacy of diazepam as a model of low anxiety can be drawn. creator: Rebecca E. Doyle creator: Caroline Lee creator: David M. McGill creator: Michael Mendl uri: https://doi.org/10.7717/peerj.1510 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Doyle et al. title: Modeling the ecologic niche of plague in sylvan and domestic animal hosts to delineate sources of human exposure in the western United States link: https://peerj.com/articles/1493 last-modified: 2015-12-14 description: Plague has been established in the western United States (US) since 1900 following the West Coast introduction of commensal rodents infected with Yersinia pestis via early industrial shipping. Over the last century, plague ecology has transitioned through cycles of widespread human transmission, urban domestic transmission among commensal rodents, and ultimately settled into the predominantly sylvan foci that remain today where it is maintained alternatively by enzootic and epizootic transmission. While zoonotic transmission to humans is much less common in modern times, significant plague risk remains in parts of the western US. Moreover, risk to some threatened species that are part of the epizootic cycle can be quite substantive. This investigation attempted to predict the risk of plague across the western US by modeling the ecologic niche of plague in sylvan and domestic animals identified between 2000 and 2015. A Maxent machine learning algorithm was used to predict this niche based on climate, altitude, land cover, and the presence of an important enzootic species, Peromyscus maniculatus. This model demonstrated good predictive ability (AUC = 86%) and identified areas of high risk in central Colorado, north-central New Mexico, and southwestern and northeastern California. The presence of P. maniculatus, altitude, precipitation during the driest and wettest quarters, and distance to artificial surfaces, all contributed substantively to maximizing the gain function. These findings add to the known landscape epidemiology and infection ecology of plague in the western US and may suggest locations of particular risk to be targeted for wild and domestic animal intervention. creator: Michael Walsh creator: MA Haseeb uri: https://doi.org/10.7717/peerj.1493 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Walsh and Haseeb title: Emerging semantics to link phenotype and environment link: https://peerj.com/articles/1470 last-modified: 2015-12-14 description: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments. creator: Anne E. Thessen creator: Daniel E. Bunker creator: Pier Luigi Buttigieg creator: Laurel D. Cooper creator: Wasila M. Dahdul creator: Sami Domisch creator: Nico M. Franz creator: Pankaj Jaiswal creator: Carolyn J. Lawrence-Dill creator: Peter E. Midford creator: Christopher J. Mungall creator: Martín J. Ramírez creator: Chelsea D. Specht creator: Lars Vogt creator: Rutger Aldo Vos creator: Ramona L. Walls creator: Jeffrey W. White creator: Guanyang Zhang creator: Andrew R. Deans creator: Eva Huala creator: Suzanna E. Lewis creator: Paula M. Mabee uri: https://doi.org/10.7717/peerj.1470 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Thessen et al. title: Best practices for assessing ocean health in multiple contexts using tailorable frameworks link: https://peerj.com/articles/1503 last-modified: 2015-12-10 description: Marine policy is increasingly calling for maintaining or restoring healthy oceans while human activities continue to intensify. Thus, successful prioritization and management of competing objectives requires a comprehensive assessment of the current state of the ocean. Unfortunately, assessment frameworks to define and quantify current ocean state are often site-specific, limited to a few ocean components, and difficult to reproduce in different geographies or even through time, limiting spatial or temporal comparisons as well as the potential for shared learning. Ideally, frameworks should be tailorable to accommodate use in disparate locations and contexts, removing the need to develop frameworks de novo and allowing efforts to focus on the assessments themselves to advise action. Here, we present some of our experiences using the Ocean Health Index (OHI) framework, a tailorable and repeatable approach that measures health of coupled human-ocean ecosystems in different contexts by accommodating differences in local environmental characteristics, cultural priorities, and information availability and quality. Since its development in 2012, eleven assessments using the OHI framework have been completed at global, national, and regional scales, four of which have been led by independent academic or government groups. We have found the following to be best practices for conducting assessments: Incorporate key characteristics and priorities into the assessment framework design before gathering information; Strategically define spatial boundaries to balance information availability and decision-making scales; Maintain the key characteristics and priorities of the assessment framework regardless of information limitations; and Document and share the assessment process, methods, and tools. These best practices are relevant to most ecosystem assessment processes, but also provide tangible guidance for assessments using the OHI framework. These recommendations also promote transparency around which decisions were made and why, reproducibility through access to detailed methods and computational code, repeatability via the ability to modify methods and computational code, and ease of communication to wide audiences, all of which are critical for any robust assessment process. creator: Julia S. Stewart Lowndes creator: Erich J. Pacheco creator: Benjamin D. Best creator: Courtney Scarborough creator: Catherine Longo creator: Steven K. Katona creator: Benjamin S. Halpern uri: https://doi.org/10.7717/peerj.1503 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lowndes et al. title: On the embryonic cell division beyond the contractile ring mechanism: experimental and computational investigation of effects of vitelline confinement, temperature and egg size link: https://peerj.com/articles/1490 last-modified: 2015-12-10 description: Embryonic cell division is a mechanical process which is predominantly driven by contraction of the cleavage furrow and response of the remaining cellular matter. While most previous studies focused on contractile ring mechanisms of cytokinesis, effects of environmental factors such as pericellular vitelline membrane and temperature on the mechanics of dividing cells were rarely studied. Here, we apply a model-based analysis to the time-lapse imaging data of two species (Saccoglossus kowalevskii and Xenopus laevis) with relatively large eggs, with the goal of revealing the effects of temperature and vitelline envelope on the mechanics of the first embryonic cell division. We constructed a numerical model of cytokinesis to estimate the effects of vitelline confinement on cellular deformation and to predict deformation of cellular contours. We used the deviations of our computational predictions from experimentally observed cell elongation to adjust variable parameters of the contractile ring model and to quantify the contribution of other factors (constitutive cell properties, spindle polarization) that may influence the mechanics and shape of dividing cells. We find that temperature affects the size and rate of dilatation of the vitelline membrane surrounding fertilized eggs and show that in native (not artificially devitellinized) egg cells the effects of temperature and vitelline envelope on mechanics of cell division are tightly interlinked. In particular, our results support the view that vitelline membrane fulfills an important role of micromechanical environment around the early embryo the absence or improper function of which under moderately elevated temperature impairs normal development. Furthermore, our findings suggest the existence of scale-dependent mechanisms that contribute to cytokinesis in species with different egg size, and challenge the view of mechanics of embryonic cell division as a scale-independent phenomenon. creator: Evgeny Gladilin creator: Roland Eils creator: Leonid Peshkin uri: https://doi.org/10.7717/peerj.1490 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gladilin et al. title: Efficiently detecting outlying behavior in video-game players link: https://peerj.com/articles/1502 last-modified: 2015-12-10 description: In this paper, we propose a method for automatically detecting the times during which game players exhibit specific behavior, such as when players commonly show excitement, concentration, immersion, and surprise. The proposed method detects such outlying behavior based on the game players’ characteristics. These characteristics are captured non-invasively in a general game environment. In this paper, cameras were used to analyze observed data such as facial expressions and player movements. Moreover, multimodal data from the game players (i.e., data regarding adjustments to the volume and the use of the keyboard and mouse) was used to analyze high-dimensional game-player data. A support vector machine was used to efficiently detect outlying behaviors. We verified the effectiveness of the proposed method using games from several genres. The recall rate of the outlying behavior pre-identified by industry experts was approximately 70%. The proposed method can also be used for feedback analysis of various interactive content provided in PC environments. creator: Young Bin Kim creator: Shin Jin Kang creator: Sang Hyeok Lee creator: Jang Young Jung creator: Hyeong Ryeol Kam creator: Jung Lee creator: Young Sun Kim creator: Joonsoo Lee creator: Chang Hun Kim uri: https://doi.org/10.7717/peerj.1502 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kim et al. title: Volatile anesthetics suppress glucose-stimulated insulin secretion in MIN6 cells by inhibiting glucose-induced activation of hypoxia-inducible factor 1 link: https://peerj.com/articles/1498 last-modified: 2015-12-10 description: Proper glycemic control is one of the most important goals in perioperative patient management. Insulin secretion from pancreatic β-cells in response to an increased blood glucose concentration plays the most critical role in glycemic control. Several animal and human studies have indicated that volatile anesthetics impair glucose-stimulated insulin secretion (GSIS). A convincing GSIS model has been established, in which the activity of ATP-dependent potassium channels (KATP) under the control of intracellular ATP plays a critical role. We previously reported that pimonidazole adduct formation and stabilization of hypoxia-inducible factor-1α (HIF-1α) were detected in response to glucose stimulation and that MIN6 cells overexpressing HIF-1α were resistant to glucose-induced hypoxia. Genetic ablation of HIF-1α or HIF-1β significantly inhibited GSIS in mice. Moreover, we previously reported that volatile anesthetics suppressed hypoxia-induced HIF activation in vitro and in vivo.To examine the direct effect of volatile anesthetics on GSIS, we used the MIN6 cell line, derived from mouse pancreatic β-cells. We performed a series of experiments to examine the effects of volatile anesthetics (sevoflurane and isoflurane) on GSIS and demonstrated that these compounds inhibited the glucose-induced ATP increase, which is dependent on intracellular hypoxia-induced HIF-1 activity, and suppressed GSIS at a clinically relevant dose in these cells. creator: Kengo Suzuki creator: Yoshifumi Sato creator: Shinichi Kai creator: Kenichiro Nishi creator: Takehiko Adachi creator: Yoshiyuki Matsuo creator: Kiichi Hirota uri: https://doi.org/10.7717/peerj.1498 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Suzuki et al. title: Metagenomic and satellite analyses of red snow in the Russian Arctic link: https://peerj.com/articles/1491 last-modified: 2015-12-10 description: Cryophilic algae thrive in liquid water within snow and ice in alpine and polar regions worldwide. Blooms of these algae lower albedo (reflection of sunlight), thereby altering melting patterns (Kohshima, Seko & Yoshimura, 1993; Lutz et al., 2014; Thomas & Duval, 1995). Here metagenomic DNA analysis and satellite imaging were used to investigate red snow in Franz Josef Land in the Russian Arctic. Franz Josef Land red snow metagenomes confirmed that the communities are composed of the autotroph Chlamydomonas nivalis that is supporting a complex viral and heterotrophic bacterial community. Comparisons with white snow communities from other sites suggest that white snow and ice are initially colonized by fungal-dominated communities and then succeeded by the more complex C. nivalis-heterotroph red snow. Satellite image analysis showed that red snow covers up to 80% of the surface of snow and ice fields in Franz Josef Land and globally. Together these results show that C. nivalis supports a local food web that is on the rise as temperatures warm, with potential widespread impacts on alpine and polar environments worldwide. creator: Nao Hisakawa creator: Steven D. Quistad creator: Eric R. Hester creator: Daria Martynova creator: Heather Maughan creator: Enric Sala creator: Maria V. Gavrilo creator: Forest Rohwer uri: https://doi.org/10.7717/peerj.1491 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hisakawa et al. title: Drug delivery systems for ovarian cancer treatment: a systematic review and meta-analysis of animal studies link: https://peerj.com/articles/1489 last-modified: 2015-12-10 description: Current ovarian cancer treatment involves chemotherapy that has serious limitations, such as rapid clearance, unfavorable biodistribution and severe side effects. To overcome these limitations, drug delivery systems (DDS) have been developed to encapsulate chemotherapeutics for delivery to tumor cells. However, no systematic assessment of the efficacy of chemotherapy by DDS compared to free chemotherapy (not in a DDS) has been performed for animal studies. Here, we assess the efficacy of chemotherapy in DDS on survival and tumor growth inhibition in animal studies. We searched PubMed and EMBASE (via OvidSP) to systematically identify studies evaluating chemotherapeutics encapsulated in DDS for ovarian cancer treatment in animal studies. Studies were assessed for quality and risk of bias. Study characteristics were collected and outcome data (survival/hazard ratio or tumor growth inhibition) were extracted and used for meta-analyses. Meta-analysis was performed to identify and explore which characteristics of DDS influenced treatment efficacy. A total of 44 studies were included after thorough literature screening (2,735 studies found after initial search). The risk of bias was difficult to assess, mainly because of incomplete reporting. A total of 17 studies (377 animals) and 16 studies (259 animals) could be included in the meta-analysis for survival and tumor growth inhibition, respectively. In the majority of the included studies chemotherapeutics entrapped in a DDS significantly improved efficacy over free chemotherapeutics regarding both survival and tumor growth inhibition. Subgroup analyses, however, revealed that cisplatin entrapped in a DDS did not result in additional tumor growth inhibition compared to free cisplatin, although it did result in improved survival. Micelles did not show a significant tumor growth inhibition compared to free chemotherapeutics, which indicates that micelles may not be a suitable DDS for ovarian cancer treatment. Other subgroup analyses, such as targeted versus non-targeted DDS or IV versus IP administration route, did not identify specific characteristics of DDS that affected treatment efficacy. This systematic review shows the potential, but also the limitations of chemotherapy by drug delivery systems for ovarian cancer treatment. For future animal research, we emphasize that data need to be reported with ample attention to detailed reporting. creator: René Raavé creator: Rob B.M. de Vries creator: Leon F. Massuger creator: Toin H. van Kuppevelt creator: Willeke F. Daamen uri: https://doi.org/10.7717/peerj.1489 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Raavé et al. title: Low oxygen alters mitochondrial function and response to oxidative stress in human neural progenitor cells link: https://peerj.com/articles/1486 last-modified: 2015-12-10 description: Oxygen concentration should be carefully regulated in all living tissues, beginning at the early embryonic stages. Unbalances in oxygen regulation can lead to cell death and disease. However, to date, few studies have investigated the consequences of variations in oxygen levels for fetal-like cells. Therefore, in the present work, human neural progenitor cells (NPCs) derived from pluripotent stem cells grown in 3% oxygen (v/v) were compared with NPCs cultured in 21% (v/v) oxygen. Low oxygen concentrations altered the mitochondrial content and oxidative functions of the cells, which led to improved ATP production, while reducing generation of reactive oxygen species (ROS). NPCs cultured in both conditions showed no differences in proliferation and glucose metabolism. Furthermore, antioxidant enzymatic activity was not altered in NPCs cultured in 3% oxygen under normal conditions, however, when exposed to external agents known to induce oxidative stress, greater susceptibility to DNA damage was observed. Our findings indicate that the management of oxygen levels should be considered for in vitro models of neuronal development and drug screening. creator: Yury M. Lages creator: Juliana M. Nascimento creator: Gabriela A. Lemos creator: Antonio Galina creator: Leda R. Castilho creator: Stevens K. Rehen uri: https://doi.org/10.7717/peerj.1486 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lages et al. title: Flood induced phenotypic plasticity in amphibious genus Elatine (Elatinaceae) link: https://peerj.com/articles/1473 last-modified: 2015-12-10 description: Vegetative characters are widely used in the taxonomy of the amphibious genus Elatine L. However, these usually show great variation not just between species but between their aquatic and terrestrial forms. In the present study we examine the variation of seed and vegetative characters in nine Elatine species (E. brachysperma, E. californica, E. gussonei, E. hexandra, E. hungarica, E. hydropiper, E. macropoda, E. orthosperma and E. triandra) to reveal the extension of plasticity induced by the amphibious environment, and to test character reliability for species identification. Cultivated plant clones were kept under controlled conditions exposed to either aquatic or terrestrial environmental conditions. Six vegetative characters (length of stem, length of internodium, length of lamina, width of lamina, length of petioles, length of pedicel) and four seed characters (curvature, number of pits / lateral row, 1st and 2nd dimension) were measured on 50 fruiting stems of the aquatic and on 50 stems of the terrestrial form of the same clone. MDA, NPMANOVA Random Forest classification and cluster analysis were used to unravel the morphological differences between aquatic and terrestrial forms. The results of MDA cross-validated and Random Forest classification clearly indicated that only seed traits are stable within species (i.e., different forms of the same species keep similar morphology). Consequently, only seed morphology is valuable for taxonomic purposes since vegetative traits are highly influenced by environmental factors. creator: Attila Molnár V. creator: János Pál Tóth creator: Gábor Sramkó creator: Orsolya Horváth creator: Agnieszka Popiela creator: Attila Mesterházy creator: Balázs András Lukács uri: https://doi.org/10.7717/peerj.1473 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Molnár et al. title: An evaluation of community pharmacy-based services for type 2 diabetes in an Indonesian setting: patient survey link: https://peerj.com/articles/1449 last-modified: 2015-12-10 description: Background. Diabetes is an emerging chronic disease in developing countries. Its management in developing countries is mainly hospital/clinic based. The increasing diabetes burden in developing countries provides opportunities for community pharmacists to deliver a range of services. Since the management of diabetes requires the patient’s own involvement, it is important to gain their views in order to develop pharmacy-based diabetes services. Studies on diabetes patients’ views have been limited to developed countries.Objectives. To investigate, within a developing country setting (Indonesia), current use of pharmacy services by type 2 diabetes patients, and to evaluate their views regarding community pharmacists’ roles, and the characteristics that influence their views.Methods. A questionnaire survey was conducted within 10 purposefully selected community pharmacies in Surabaya, Indonesia. Each pharmacy recruited approximately 20 patients seeking antidiabetic medications. Usage of pharmacy services was identified using binary responses (‘yes’/‘no’) and views on pharmacists’ roles were rated using Likert scales; an open-ended question was used to identify patient perceived priority roles. Logistic regression models were used to determine characteristics associated with patients’ views.Results. A total of 196 pharmacy patients with type 2 diabetes responded (58.3% response rate). Most patients used community pharmacies for dispensing (100%) and education on how to use medications (79.6%). There were mixed views towards pharmacists providing services beyond dispensing. The highest priorities identified were from the ‘patient education’ domain: education on medications (i.e., directions for use (64.5%), storage (26.6%), common/important adverse effects (25.5%)); and the ‘monitoring’ domain: monitoring medication compliance (37.3%). Patients with higher incomes or who were working were less supportive of these expanded services, whereas patients who previously used a service, those with risk factors for complications or having poor/unknown glycaemic control were more supportive.Conclusions. Community pharmacies in Surabaya, Indonesia in this study were mainly utilised for dispensing. However, many type 2 diabetes patients using these pharmacies report limited monitoring of blood glucose levels and poor glycaemic control, which indicates an opportunity for greater pharmacist involvement. Yet for this to occur, patients’ limited expectations of pharmacists roles will need to be broadened. Characteristics influencing these views should inform the development of pharmacy-based diabetes services in the environment of the burgeoning burden of diabetes. creator: Yosi Wibowo creator: Richard Parsons creator: Bruce Sunderland creator: Jeffery Hughes uri: https://doi.org/10.7717/peerj.1449 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wibowo et al. title: Baseline seabed habitat and biotope mapping for a proposed marine reserve link: https://peerj.com/articles/1446 last-modified: 2015-12-10 description: Seabed mapping can quantify the extent of benthic habitats that comprise marine ecosystems, and assess the impact of fisheries on an ecosystem. In this study, the distribution of seabed habitats in a proposed no-take Marine Reserve along the northeast coast of Great Barrier Island, New Zealand, was mapped using underwater video combined with bathymetry and substratum data. As a result of the boundary extending to the 12 nautical mile Territorial Limit, it would have been the largest coastal Marine Reserve in the country. Recreational and commercial fisheries occur in the region and would be expected to affect species’ abundance. The seabed of the study area and adjacent coastal waters has been trawled up to five times per year. Benthic communities were grouped by multivariate cluster analysis into four biotope classes; namely (1) shallow water macroalgae Ecklonia sp. and Ulva sp. on rocky substrata (Eck.Ulv); and deeper (2) diverse epifauna of sponges and bryozoans on rocky substrata (Por.Bry), (3) brittle star Amphiura sp. and sea anemone Edwardsia sp. on muddy sand (Amph.Edw), and (4) hydroids on mud (Hyd). In biotopes Por.Bry, Amph.Edw and Hyd, there where boulders and rocks were present, and diverse sponge, bryozoan and coral communities. Fifty species were recorded in the deep water survey including significant numbers of the shallow-water hexactinellid glass sponges Symplectella rowiDendy, 1924 and Rossella ijimaiDendy, 1924, the giant pipe demosponge Isodictya cavicornutaDendy, 1924, black corals, and locally endemic gorgonians. The habitats identified in the waters to the northeast of Great Barrier Island are likely to be representative of similar depth ranges in northeast New Zealand. This study provides a baseline of the benthic habitats so that should the area become a Marine Reserve, any habitat change might be related to protection from fishing activities and impacts, such as recovery of epifauna following cessation of trawling. The habitat map may also be used to stratify future sampling that would aim to collect and identify epifauna and infauna for identification, and thus better describe the biodiversity of the area. creator: Sonny T.M. Lee creator: Michelle Kelly creator: Tim J. Langlois creator: Mark J. Costello uri: https://doi.org/10.7717/peerj.1446 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lee et al. title: Swarm v2: highly-scalable and high-resolution amplicon clustering link: https://peerj.com/articles/1420 last-modified: 2015-12-10 description: Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks. creator: Frédéric Mahé creator: Torbjørn Rognes creator: Christopher Quince creator: Colomban de Vargas creator: Micah Dunthorn uri: https://doi.org/10.7717/peerj.1420 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Mahé et al. title: Determinants of antiretroviral therapy coverage in Sub-Saharan Africa link: https://peerj.com/articles/1496 last-modified: 2015-12-08 description: Among 35 million people living with the human immunodeficiency virus (HIV) in 2013, only 37% had access to antiretroviral therapy (ART). Despite global concerted efforts to provide the universal access to the ART treatment, the ART coverage varies among countries and regions. At present, there is a lack of systematic empirical analyses on factors that determine the ART coverage. Therefore, the current study aimed to identify the determinants of the ART coverage in 41 countries in Sub-Saharan Africa. It employed statistical analyses for this purpose. Four elements, namely, the HIV prevalence, the level of national income, the level of medical expenditure and the number of nurses, were hypothesised to determine the ART coverage. The findings revealed that among the four proposed determinants only the HIV prevalence had a statistically significant impact on the ART coverage. In other words, the HIV prevalence was the sole determinant of the ART coverage in Sub-Saharan Africa. creator: Fumitaka Furuoka creator: Mohammad Zahirul Hoque uri: https://doi.org/10.7717/peerj.1496 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Furuoka and Hoque title: De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units link: https://peerj.com/articles/1487 last-modified: 2015-12-08 description: Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important.Methods. Our analysis implemented six de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew’s Correlation Coefficient (MCC) to assess the stability and quality of OTU assignments.Results. The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and VSEARCH have a high level of sensitivity to detect reference sequences, the specificity of those matches was poor relative to the true best match.Discussion. Our analysis calls into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME. This study demonstrates that de novo methods are the optimal method of assigning sequences into OTUs and that the quality of these assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset. creator: Sarah L. Westcott creator: Patrick D. Schloss uri: https://doi.org/10.7717/peerj.1487 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Westcott and Schloss title: Intramale variation in sperm size: functional significance in a polygynous mammal link: https://peerj.com/articles/1478 last-modified: 2015-12-08 description: Studies concerning the relationships between sperm size and velocity at the intraspecific level are quite limited and often yielded contradictory results across the animal kingdom. Intramale variation in sperm size may represent a meaningful factor to predict sperm velocity, due to its relationship with the level of sperm competition among related taxa. Because sperm phenotype is under post-copulatory sexual selection, we hypothesized that a reduced intramale variation in sperm size is associated with sperm competitiveness in red deer. Our results show that low variation in sperm size is strongly related to high sperm velocity and normal sperm morphology, which in turn are good predictors of male fertility in this species. Furthermore, it is well known that the red deer show high variability in testicular mass but there is limited knowledge concerning the significance of this phenomenon at intraspecific level, even though it may reveal interesting processes of sexual selection. Thereby, as a preliminary result, we found that absolute testes mass is negatively associated with intramale variation in sperm size. Our findings suggest that sperm size variation in red deer is under a strong selective force leading to increase sperm function efficiency, and reveal new insights into sexual selection mechanisms. creator: José Luis Ros-Santaella creator: Eliana Pintus creator: José Julián Garde uri: https://doi.org/10.7717/peerj.1478 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ros-Santaella et al. title: Cranial osteology of the ankylosaurian dinosaur formerly known as Minmi sp. (Ornithischia: Thyreophora) from the Lower Cretaceous Allaru Mudstone of Richmond, Queensland, Australia link: https://peerj.com/articles/1475 last-modified: 2015-12-08 description: Minmi is the only known genus of ankylosaurian dinosaur from Australia. Seven specimens are known, all from the Lower Cretaceous of Queensland. Only two of these have been described in any detail: the holotype specimen Minmi paravertebra from the Bungil Formation near Roma, and a near complete skeleton from the Allaru Mudstone on Marathon Station near Richmond, preliminarily referred to a possible new species of Minmi. The Marathon specimen represents one of the world’s most complete ankylosaurian skeletons and the best-preserved dinosaurian fossil from eastern Gondwana. Moreover, among ankylosaurians, its skull is one of only a few in which the majority of sutures have not been obliterated by dermal ossifications or surface remodelling. Recent preparation of the Marathon specimen has revealed new details of the palate and narial regions, permitting a comprehensive description and thus providing new insights cranial osteology of a basal ankylosaurian. The skull has also undergone computed tomography, digital segmentation and 3D computer visualisation enabling the reconstruction of its nasal cavity and endocranium. The airways of the Marathon specimen are more complicated than non-ankylosaurian dinosaurs but less so than derived ankylosaurians. The cranial (brain) endocast is superficially similar to those of other ankylosaurians but is strongly divergent in many important respects. The inner ear is extremely large and unlike that of any dinosaur yet known. Based on a high number of diagnostic differences between the skull of the Marathon specimen and other ankylosaurians, we consider it prudent to assign this specimen to a new genus and species of ankylosaurian. Kunbarrasaurus ieversi gen. et sp. nov. represents the second genus of ankylosaurian from Australia and is characterised by an unusual melange of both primitive and derived characters, shedding new light on the evolution of the ankylosaurian skull. creator: Lucy G. Leahey creator: Ralph E. Molnar creator: Kenneth Carpenter creator: Lawrence M. Witmer creator: Steven W. Salisbury uri: https://doi.org/10.7717/peerj.1475 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Leahey et al. title: Cyclic mechanical stretch down-regulates cathelicidin antimicrobial peptide expression and activates a pro-inflammatory response in human bronchial epithelial cells link: https://peerj.com/articles/1483 last-modified: 2015-12-07 description: Mechanical ventilation (MV) of patients can cause damage to bronchoalveolar epithelium, leading to a sterile inflammatory response, infection and in severe cases sepsis. Limited knowledge is available on the effects of MV on the innate immune defense system in the human lung. In this study, we demonstrate that cyclic stretch of the human bronchial epithelial cell lines VA10 and BCi NS 1.1 leads to down-regulation of cathelicidin antimicrobial peptide (CAMP) gene expression. We show that treatment of VA10 cells with vitamin D3 and/or 4-phenyl butyric acid counteracted cyclic stretch mediated down-regulation of CAMP mRNA and protein expression (LL-37). Further, we observed an increase in pro-inflammatory responses in the VA10 cell line subjected to cyclic stretch. The mRNA expression of the genes encoding pro-inflammatory cytokines IL-8 and IL-1β was increased after cyclic stretching, where as a decrease in gene expression of chemokines IP-10 and RANTES was observed. Cyclic stretch enhanced oxidative stress in the VA10 cells. The mRNA expression of toll-like receptor (TLR) 3, TLR5 and TLR8 was reduced, while the gene expression of TLR2 was increased in VA10 cells after cyclic stretch. In conclusion, our in vitro results indicate that cyclic stretch may differentially modulate innate immunity by down-regulation of antimicrobial peptide expression and increase in pro-inflammatory responses. creator: Harpa Karadottir creator: Nikhil Nitin Kulkarni creator: Thorarinn Gudjonsson creator: Sigurbergur Karason creator: Gudmundur Hrafn Gudmundsson uri: https://doi.org/10.7717/peerj.1483 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Karadottir et al. title: The first dromaeosaurid (Dinosauria: Theropoda) from the Lower Cretaceous Bayan Gobi Formation of Nei Mongol, China link: https://peerj.com/articles/1480 last-modified: 2015-12-07 description: The first dromaeosaurid theropod from the Lower Cretaceous Bayan Gobi Formation is identified based on an incompletely preserved partially-articulated left leg, increasing the known diversity of its understudied ecosystem. The leg belongs to specimen IVPP V22530 and includes a typical deinonychosaurian pedal phalanx II-2 with a distinct constriction between the enlarged proximal end and the distal condyle as well as a typical deinonychosaurian enlarged pedal phalanx II-3. It possesses a symmetric metatarsus and a slender and long MT V that together suggest it is a dromaeosaurid. Two anatomical traits suggest the leg is microraptorine-like, but a more precise taxonomic referral was not possible: metatarsals II, III and IV are closely appressed distally and the ventral margin of the medial ligament pit of phalanx II-2 is close to the centre of the rounded distal condyle. This taxonomic status invites future efforts to discover additional specimens at the study locality because—whether it is a microraptorine or a close relative—this animal is expected to make important contributions to our understanding of dromaeosaurid evolution and biology. IVPP V22530 also comprises of an isolated dromaeosaurid manual ungual, a proximal portion of a right theropod anterior dorsal rib and an indeterminate bone mass that includes a collection of ribs. Neither the rib fragment nor the bone mass can be confidently referred to Dromaeosauridae, although they may very well belong to the same individual to whom the left leg belongs. creator: Michael Pittman creator: Rui Pei creator: Qingwei Tan creator: Xing Xu uri: https://doi.org/10.7717/peerj.1480 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pittman et al. title: Wolbachia co-infection in a hybrid zone: discovery of horizontal gene transfers from two Wolbachia supergroups into an animal genome link: https://peerj.com/articles/1479 last-modified: 2015-12-07 description: Hybrid zones and the consequences of hybridization have contributed greatly to our understanding of evolutionary processes. Hybrid zones also provide valuable insight into the dynamics of symbiosis since each subspecies or species brings its unique microbial symbionts, including germline bacteria such as Wolbachia, to the hybrid zone. Here, we investigate a natural hybrid zone of two subspecies of the meadow grasshopper Chorthippus parallelus in the Pyrenees Mountains. We set out to test whether co-infections of B and F Wolbachia in hybrid grasshoppers enabled horizontal transfer of phage WO, similar to the numerous examples of phage WO transfer between A and B Wolbachia co-infections. While we found no evidence for transfer between the divergent co-infections, we discovered horizontal transfer of at least three phage WO haplotypes to the grasshopper genome. Subsequent genome sequencing of uninfected grasshoppers uncovered the first evidence for two discrete Wolbachia supergroups (B and F) contributing at least 448 kb and 144 kb of DNA, respectively, into the host nuclear genome. Fluorescent in situ hybridization verified the presence of Wolbachia DNA in C. parallelus chromosomes and revealed that some inserts are subspecies-specific while others are present in both subspecies. We discuss our findings in light of symbiont dynamics in an animal hybrid zone. creator: Lisa J. Funkhouser-Jones creator: Stephanie R. Sehnert creator: Paloma Martínez-Rodríguez creator: Raquel Toribio-Fernández creator: Miguel Pita creator: José L. Bella creator: Seth R. Bordenstein uri: https://doi.org/10.7717/peerj.1479 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Funkhouser-Jones et al. title: Mismatched anti-predator behavioral responses in predator-naïve larval anurans link: https://peerj.com/articles/1472 last-modified: 2015-12-07 description: Organisms are adept at altering behaviors to balance the tradeoff between foraging and predation risk in spatially and temporally shifting predator environments. In order to optimize this tradeoff, prey need to be able to display an appropriate response based on degree of predation risk. To be most beneficial in the earliest life stages in which many prey are vulnerable to predation, innate anti-predator responses should scale to match the risk imposed by predators until learned anti-predator responses can occur. We conducted an experiment that examined whether tadpoles with no previous exposure to predators (i.e., predator-naive) exhibit innate antipredator behavioral responses (e.g., via refuge use and spatial avoidance) that match the actual risk posed by each predator. Using 7 treatments (6 free-roaming, lethal predators plus no-predator control), we determined the predation rates of each predator on Lithobates sphenocephalus tadpoles. We recorded behavioral observations on an additional 7 nonlethal treatments (6 caged predators plus no-predator control). Tadpoles exhibited innate responses to fish predators, but not non-fish predators, even though two non-fish predators (newt and crayfish) consumed the most tadpoles. Due to a mismatch between innate response and predator consumption, tadpoles may be vulnerable to greater rates of predation at the earliest life stages before learning can occur. Thus, naïve tadpoles in nature may be at a high risk to predation in the presence of a novel predator until learned anti-predator responses provide additional defenses to the surviving tadpoles. creator: Molly Albecker creator: Heather D. Vance-Chalcraft uri: https://doi.org/10.7717/peerj.1472 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Albecker and Vance-Chalcraft title: Production of fatty acids in Ralstonia eutropha H16 by engineering β-oxidation and carbon storage link: https://peerj.com/articles/1468 last-modified: 2015-12-07 description: Ralstonia eutropha H16 is a facultatively autotrophic hydrogen-oxidizing bacterium capable of producing polyhydroxybutyrate (PHB)-based bioplastics. As PHB’s physical properties may be improved by incorporation of medium-chain-length fatty acids (MCFAs), and MCFAs are valuable on their own as fuel and chemical intermediates, we engineered R. eutropha for MCFA production. Expression of UcFatB2, a medium-chain-length-specific acyl-ACP thioesterase, resulted in production of 14 mg/L laurate in wild-type R. eutropha. Total fatty acid production (22 mg/L) could be increased up to 2.5-fold by knocking out PHB synthesis, a major sink for acetyl-CoA, or by knocking out the acyl-CoA ligase fadD3, an entry point for fatty acids into β-oxidation. As ΔfadD3 mutants still consumed laurate, and because the R. eutropha genome is predicted to encode over 50 acyl-CoA ligases, we employed RNA-Seq to identify acyl-CoA ligases upregulated during growth on laurate. Knockouts of the three most highly upregulated acyl-CoA ligases increased fatty acid yield significantly, with one strain (ΔA2794) producing up to 62 mg/L free fatty acid. This study demonstrates that homologous β-oxidation systems can be rationally engineered to enhance fatty acid production, a strategy that may be employed to increase yield for a range of fuels, chemicals, and PHB derivatives in R. eutropha. creator: Janice S. Chen creator: Brendan Colón creator: Brendon Dusel creator: Marika Ziesack creator: Jeffrey C. Way creator: Joseph P. Torella uri: https://doi.org/10.7717/peerj.1468 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Chen et al. title: Triple therapy in type 2 diabetes; a systematic review and network meta-analysis link: https://peerj.com/articles/1461 last-modified: 2015-12-07 description: Aims. The purpose was to evaluate the evidence for triple therapy regimen using medicines available in Australia for type 2 diabetes.Methods. A systematic literature review was performed to update the relevant evidence from 2002 to 2014 on triple therapy for type 2 diabetes. A multiple-treatments network meta-analysis was undertaken to summarise the comparative efficacy and harms of different triple therapies.Results. Twenty seven trials were identified, most were six months of duration. The following combinations were included in the network meta-analysis: metformin (MET) + sulfonylureas (SU) (used as reference combination); MET + SU+ dipeptidyl peptidase 4 inhibitors (DPP-4-i); MET + SU+ thiazolidinediones (TZD); MET + SU+ glucagon-like peptide-1 receptor agonists (GLP-1-RA); MET + SU+ insulins; MET + TZD + DPP-4-i; and MET + SU+ sodium/glucose cotransporter 2 inhibitors (SGLT2-i). For HbA1c reduction, all triple therapies were statistically superior to MET+SU dual therapy, except for MET + TZD + DPP-4-i. None of the triple therapy combinations demonstrated differences in HbA1c compared with other triple therapies. MET + SU + SGLT2-i and MET + SU + GLP-1-RA resulted in significantly lower body weight than MET + SU + DPP-4-i, MET+SU+insulin and MET + SU + TZDs; MET + SU + DPP-4-i resulted in significantly lower body weight than MET + SU + insulin and MET + SU + TZD. MET + SU + insulin, MET + SU + TZD and MET + SU + DPP-4-i increased the odds of hypoglycaemia when compared to MET + SU. MET + SU + GLP-1-RA reduced the odds of hypoglycaemia compared to MET + SU + insulin.Conclusion. Care when choosing a triple therapy combination is needed as there is often a risk of increased hypoglycaemia events associated with this regimen and there are very limited data surrounding the long-term effectiveness and safety of combined therapies. creator: Martin J. Downes creator: Emilie K. Bettington creator: Jenny E. Gunton creator: Erika Turkstra uri: https://doi.org/10.7717/peerj.1461 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Downes et al. title: Large-scale structure of brown rat (Rattus norvegicus) populations in England: effects on rodenticide resistance link: https://peerj.com/articles/1458 last-modified: 2015-12-07 description: The brown rat (Rattus norvegicus) is a relatively recent (<300 years) addition to the British fauna, but by association with negative impacts on public health, animal health and agriculture, it is regarded as one of the most important vertebrate pest species. Anticoagulant rodenticides were introduced for brown rat control in the 1950s and are widely used for rat control in the UK, but long-standing resistance has been linked to control failures in some regions. One thus far ignored aspect of resistance biology is the population structure of the brown rat. This paper investigates the role population structure has on the development of anticoagulant resistance. Using mitochondrial and microsatellite DNA, we examined 186 individuals (from 15 counties in England and one location in Wales near the Wales–England border) to investigate the population structure of rural brown rat populations. We also examined individual rats for variations of the VKORC1 gene previously associated with resistance to anticoagulant rodenticides. We show that the populations were structured to some degree, but that this was only apparent in the microsatellite data and not the mtDNA data. We discuss various reasons why this is the case. We show that the population as a whole appears not to be at equilibrium. The relative lack of diversity in the mtDNA sequences examined can be explained by founder effects and a subsequent spatial expansion of a species introduced to the UK relatively recently. We found there was a geographical distribution of resistance mutations, and relatively low rate of gene flow between populations, which has implications for the development and management of anticoagulant resistance. creator: Mohd Z.H. Haniza creator: Sally Adams creator: Eleanor P. Jones creator: Alan MacNicoll creator: Eamonn B. Mallon creator: Robert H. Smith creator: Mark S. Lambert uri: https://doi.org/10.7717/peerj.1458 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: Low effect of young afforestations on bird communities inhabiting heterogeneous Mediterranean cropland link: https://peerj.com/articles/1453 last-modified: 2015-12-07 description: Afforestation programs such as the one promoted by the EU Common Agricultural Policy have spread tree plantations on former cropland. These afforestations attract generalist forest and ubiquitous species but may cause severe damage to open habitat species, especially birds of high conservation value. We investigated the effects of young (<20 yr) tree plantations dominated by pine P. halepensis on bird communities inhabiting the adjacent open farmland habitat in central Spain. We hypothesize that pine plantations located at shorter distances from open fields and with larger surface would affect species richness and conservation value of bird communities. Regression models controlling for the influence of land use types around plantations revealed positive effects of higher distance to pine plantation edge on community species richness in winter, and negative effects on an index of conservation concern (SPEC) during the breeding season. However, plantation area did not have any effect on species richness or community conservation value. Our results indicate that the effects of pine afforestation on bird communities inhabiting Mediterranean cropland are diluted by heterogeneous agricultural landscapes. creator: Juan S. Sánchez-Oliver creator: José M. Rey Benayas creator: Luis M. Carrascal uri: https://doi.org/10.7717/peerj.1453 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sánchez-Oliver et al. title: Palaeogeographic implications of a new iocrinid crinoid (Disparida) from the Ordovician (Darriwillian) of Morocco link: https://peerj.com/articles/1450 last-modified: 2015-12-07 description: Complete, articulated crinoids from the Ordovician peri-Gondwanan margin are rare. Here, we describe a new species, Iocrinus africanus sp. nov., from the Darriwilian-age Taddrist Formation of Morocco. The anatomy of this species was studied using a combination of traditional palaeontological methods and non-destructive X-ray micro-tomography (micro-CT). This revealed critical features of the column, distal arms, and aboral cup, which were hidden in the surrounding rock and would have been inaccessible without the application of micro-CT. Iocrinus africanus sp. nov. is characterized by the presence of seven to thirteen tertibrachials, three in-line bifurcations per ray, and an anal sac that is predominantly unplated or very lightly plated. Iocrinus is a common genus in North America (Laurentia) and has also been reported from the United Kingdom (Avalonia) and Oman (middle east Gondwana). Together with Merocrinus, it represents one of the few geographically widespread crinoids during the Ordovician and serves to demonstrate that faunal exchanges between Laurentia and Gondwana occurred at this time. This study highlights the advantages of using both conventional and cutting-edge techniques (such as micro-CT) to describe the morphology of new fossil specimens. creator: Samuel Zamora creator: Imran A. Rahman creator: William I. Ausich uri: https://doi.org/10.7717/peerj.1450 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Zamora et al. title: Biofouling of inlet pipes affects water quality in running seawater aquaria and compromises sponge cell proliferation link: https://peerj.com/articles/1430 last-modified: 2015-12-07 description: Marine organism are often kept, cultured, and experimented on in running seawater aquaria. However, surprisingly little attention is given to the nutrient composition of the water flowing through these systems, which is generally assumed to equal in situ conditions, but may change due to the presence of biofouling organisms. Significantly lower bacterial abundances and higher inorganic nitrogen species (nitrate, nitrite, and ammonium) were measured in aquarium water when biofouling organisms were present within a 7-year old inlet pipe feeding a tropical reef running seawater aquaria system, compared with aquarium water fed by a new, biofouling-free inlet pipe. These water quality changes are indicative of the feeding activity and waste production of the suspension- and filter-feeding communities found in the old pipe, which included sponges, bivalves, barnacles, and ascidians. To illustrate the physiological consequences of these water quality changes on a model organism kept in the aquaria system, we investigated the influence of the presence and absence of the biofouling community on the functioning of the filter-feeding sponge Halisarca caerulea, by determining its choanocyte (filter cell) proliferation rates. We found a 34% increase in choanocyte proliferation rates following the replacement of the inlet pipe (i.e., removal of the biofouling community). This indicates that the physiological functioning of the sponge was compromised due to suboptimal food conditions within the aquarium resulting from the presence of the biofouling organisms in the inlet pipe. This study has implications for the husbandry and performance of experiments with marine organisms in running seawater aquaria systems. Inlet pipes should be checked regularly, and replaced if necessary, in order to avoid excessive biofouling and to approach in situ water quality. creator: Brittany E. Alexander creator: Benjamin Mueller creator: Mark J.A. Vermeij creator: Harm H.G. van der Geest creator: Jasper M. de Goeij uri: https://doi.org/10.7717/peerj.1430 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Alexander et al. title: Trail Making Test performance contributes to subjective judgment of visual efficiency in older adults link: https://peerj.com/articles/1407 last-modified: 2015-12-07 description: Introduction. The determinant factors that influence self-reported quality of vision have yet to be fully elucidated. This study evaluated a range of contextual information, established psychophysical tests, and in particular, a series of cognitive tests as potentially novel determinant factors.Materials & Methods. Community dwelling adults (aged 50+) recruited to Wave 1 of The Irish Longitudinal Study on Ageing, excluding those registered blind, participated in this study (N = 5,021). Self-reports of vision were analysed in relation to visual acuity and contrast sensitivity, ocular pathology, visual (Choice Response Time task; Trail Making Test) and global cognition. Contextual factors such as having visited an optometrist and wearing glasses were also considered. Ordinal logistic regression was used to determine univariate and multivariate associations.Results and Discussion. Poor Trail Making Test performance (Odds ratio, OR = 1.36), visual acuity (OR = 1.72) and ocular pathology (OR = 2.25) were determinant factors for poor versus excellent vision in self-reports. Education, wealth, age, depressive symptoms and general cognitive fitness also contributed to determining self-reported vision.Conclusions. Trail Making Test contribution to self-reports may capture higher level visual processing and should be considered when using self-reports to assess vision and its role in cognitive and functional health. creator: Annalisa Setti creator: James Loughman creator: George M. Savva creator: RoseAnne Kenny uri: https://doi.org/10.7717/peerj.1407 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Setti et al. title: How word-beginnings constrain the pronunciations of word-ends in the reading aloud of English: the phenomena of head- and onset-conditioning link: https://peerj.com/articles/1482 last-modified: 2015-12-03 description: Background. A word whose body is pronounced in different ways in different words is body-inconsistent. When we take the unit that precedes the vowel into account for the calculation of body-consistency, the proportion of English words that are body-inconsistent is considerably reduced at the level of corpus analysis, prompting the question of whether humans actually use such head/onset-conditioning when they read.Methods. Four metrics for head/onset-constrained body-consistency were calculated: by the last grapheme of the head, by the last phoneme of the onset, by place and manner of articulation of the last phoneme of the onset, and by manner of articulation of the last phoneme of the onset. Since these were highly correlated, principal component analysis was performed on them.Results. Two out of four resulting principal components explained significant variance in the reading-aloud reaction times, beyond regularity and body-consistency.Discussion. Humans read head/onset-conditioned words faster than would be predicted based on their body-consistency and regularity only. We conclude that humans are sensitive to the dependency between word-beginnings and word-ends when they read aloud, and that this dependency is phonological in nature, rather than orthographic. creator: Anastasia Ulicheva creator: Max Coltheart uri: https://doi.org/10.7717/peerj.1482 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ulicheva and Coltheart title: Bioactivities by a crude extract from the Greenlandic Pseudomonas sp. In5 involves the nonribosomal peptides, nunamycin and nunapeptin link: https://peerj.com/articles/1476 last-modified: 2015-12-03 description: Background. Bioactive microbial metabolites provide a successful source of novel compounds with pharmaceutical potentials. The bacterium Pseudomonas sp. In5 is a biocontrol strain isolated from a plant disease suppressive soil in Greenland, which produces two antimicrobial nonribosomal peptides (NRPs), nunapeptin and nunamycin.Methods. In this study, we used in vitro antimicrobial and anticancer bioassays to evaluate the potential bioactivities of both a crude extract derived from Pseudomonas sp. In5 and NRPs purified from the crude extract.Results. We verified that the crude extract derived from Pseudomonas sp. In5 showed suppressive activity against the basidiomycete Rhizoctonia solani by inducing a mitochondrial stress-response. Furthermore, we confirmed suppressive activity against the oomycete Pythium aphanidermatum by the Pseudomonas sp. In5 crude extract, and that the purified nunamycin and nunapeptin displayed distinct antimicrobial activities. In addition to the antimicrobial activity, we found that treatment of the cancer cell lines, Jurkat T-cells, Granta cells, and melanoma cells, with the Pseudomonas sp. In5 crude extract increased staining with the apoptotic marker Annexin V while no staining of healthy normal cells, i.e., naïve or activated CD4 T-cells, was observed. Treatment with either of the NRPs alone did not increase Annexin V staining of the Jurkat T-cells, despite individually showing robust antimicrobial activity, whereas an anticancer activity was detected when nunamycin and nunapeptin were used in combination.Discussion. Our results suggest that the bioactivity of a crude extract derived from Pseudomonas sp. In5 involves the presence of both nunamycin and nunapeptin and highlight the possibility of synergy between multiple microbial metabolites. creator: Charlotte F. Michelsen creator: Helle Jensen creator: Vincent J. Venditto creator: Rosanna C. Hennessy creator: Peter Stougaard uri: https://doi.org/10.7717/peerj.1476 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Michelsen et al. title: Sound signatures and production mechanisms of three species of pipefishes (Family: Syngnathidae) link: https://peerj.com/articles/1471 last-modified: 2015-12-03 description: Background. Syngnathid fishes produce three kinds of sounds, named click, growl and purr. These sounds are generated by different mechanisms to give a consistent signal pattern or signature which is believed to play a role in intraspecific and interspecific communication. Commonly known sounds are produced when the fish feeds (click, purr) or is under duress (growl). While there are more acoustic studies on seahorses, pipefishes have not received much attention. Here we document the differences in feeding click signals between three species of pipefishes and relate them to cranial morphology and kinesis, or the sound-producing mechanism.Methods. The feeding clicks of two species of freshwater pipefishes, Doryichthys martensii and Doryichthys deokhathoides and one species of estuarine pipefish, Syngnathoides biaculeatus, were recorded by a hydrophone in acoustic dampened tanks. The acoustic signals were analysed using time-scale distribution (or scalogram) based on wavelet transform. A detailed time-varying analysis of the spectral contents of the localized acoustic signal was obtained by jointly interpreting the oscillogram, scalogram and power spectrum. The heads of both Doryichthys species were prepared for microtomographical scans which were analysed using a 3D imaging software. Additionally, the cranial bones of all three species were examined using a clearing and double-staining method for histological studies.Results. The sound characteristics of the feeding click of the pipefish is species-specific, appearing to be dependent on three bones: the supraoccipital, 1st postcranial plate and 2nd postcranial plate. The sounds are generated when the head of the Dorichthyes pipefishes flexes backward during the feeding strike, as the supraoccipital slides backwards, striking and pushing the 1st postcranial plate against (and striking) the 2nd postcranial plate. In the Syngnathoides pipefish, in the absence of the 1st postcranial plate, the supraoccipital rubs against the 2nd postcranial plate twice as it is pulled backward and released on the return. Cranial morphology and kinesis produce acoustic signals consistent with the bone strikes that produce sharp energy spikes (discrete or merged), or stridulations between bones that produce repeated or multimodal sinusoidal waveforms.Discussion. The variable structure of the sound-producing mechanism explains the unique acoustic signatures of the three species of pipefish. The differences in cranial bone morphology, cranial kinesis and acoustic signatures among pipefishes (and seahorses) could be attributed to independent evolution within the Syngnathidae, which warrants further investigation. creator: Adam Chee Ooi Lim creator: Ving Ching Chong creator: Chiow San Wong creator: Sithi Vinayakam Muniandy uri: https://doi.org/10.7717/peerj.1471 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lim et al. title: Academic inequality through the lens of community ecology: a meta-analysis link: https://peerj.com/articles/1457 last-modified: 2015-12-03 description: Ecological assemblages are generally characterized by a few dominant species and numerous others. Such unequal distributions of dominance also emerge in human society, including in scientific communities. Here, based on formal community ecological analyses, we show the temporal trends in the number of scientific publication in the discipline of “ecology.” Based on this, we infer possible factors causing the imbalance of reputation and dominance among countries. We relied on 454 ecological meta-analysis papers published from 1998 to 2014, which sourced over 29,000 original publications. Formal meta-analyses are essential for synthesizing findings from individual studies and are critical for assessing issues and informing policy. We found that, despite the rapid expansion of outlets for ecology papers (analogous to an increase in carrying capacity, in ecological systems), country diversity as determined from first author affiliations (analogous to species diversity) did not increase. Furthermore, a country identity was more powerful than the popularity of the scientific topic and affected the chance of publication in high-profile journals, independent of the potential novelty of findings and arguments of the papers, suggesting possible academic injustice. Consequently, a rank order and hierarchy has been gradually formed among countries. Notably, this country-dominance rank is not only specific to this scientific domain but also universal across different societal situations including sports and economics, further emphasizing that inequality and hierarchical structure exist even in modern human society. Our study demonstrates a need for having robust frameworks to facilitate equality and diversity in the scientific domain in order to better inform society and policy. creator: Akira S. Mori creator: Shenhua Qian creator: Shinichi Tatsumi uri: https://doi.org/10.7717/peerj.1457 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Mori et al. title: Evaluation of Leymus chinensis quality using near-infrared reflectance spectroscopy with three different statistical analyses link: https://peerj.com/articles/1416 last-modified: 2015-12-03 description: Due to a boom in the dairy industry in Northeast China, the hay industry has been developing rapidly. Thus, it is very important to evaluate the hay quality with a rapid and accurate method. In this research, a novel technique that combines near infrared spectroscopy (NIRs) with three different statistical analyses (MLR, PCR and PLS) was used to predict the chemical quality of sheepgrass (Leymus chinensis) in Heilongjiang Province, China including the concentrations of crude protein (CP), acid detergent fiber (ADF), and neutral detergent fiber (NDF). Firstly, the linear partial least squares regression (PLS) was performed on the spectra and the predictions were compared to those with laboratory-based recorded spectra. Then, the MLR evaluation method for CP has a potential to be used for industry requirements, as it needs less sophisticated and cheaper instrumentation using only a few wavelengths. Results show that in terms of CP, ADF and NDF, (i) the prediction accuracy in terms of CP, ADF and NDF using PLS was obviously improved compared to the PCR algorithm, and comparable or even better than results generated using the MLR algorithm; (ii) the predictions were worse compared to laboratory-based spectra with the MLR algorithmin, and poor predictions were obtained (R2, 0.62, RPD, 0.9) using MLR in terms of NDF; (iii) a satisfactory accuracy with R2 and RPD by PLS method of 0.91, 3.2 for CP, 0.89, 3.1 for ADF and 0.88, 3.0 for NDF, respectively, was obtained. Our results highlight the use of the combined NIRs-PLS method could be applied as a valuable technique to rapidly and accurately evaluate the quality of sheepgrass hay. creator: Jishan Chen creator: Ruifen Zhu creator: Ruixuan Xu creator: Wenjun Zhang creator: Yue Shen creator: Yingjun Zhang uri: https://doi.org/10.7717/peerj.1416 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Chen et al. title: Factors associated with extubation time in coronary artery bypass grafting patients link: https://peerj.com/articles/1414 last-modified: 2015-12-03 description: Background and Objectives. Cardiovascular diseases are the leading cause of death worldwide, with coronary artery disease being the most common. With increasing numbers of patients, Coronary Artery Bypass Grafting (CABG) has become the most common operation in the world. Respiratory disorder is one of the most prevalent complications of CABG. Thus, weaning off the mechanical ventilation and extubation are of great clinical importance for these patients. Some post-operative problems also relate to the tracheal tube and mechanical ventilation. Therefore, an increase in this leads to an increase in the number of complications, length of hospital stay, and treatment costs. Since a large number of factors affect the post-operative period, the present study aims to identify the predictors of extubation time in CABG patients using casualty network analysis.Method. This longitudinal study was conducted on 800 over 18 year old patients who had undergone CABG surgery in three treatment centers affiliated to Shiraz University of Medical Sciences. The patients’ information, including pre-operative, peri-operative, and post-operative variables, was retrospectively extracted from their medical records. Then, the data was comprehensively analyzed through path analysis using MPLUS-7.1 software.Results. The mean of extubation time was 10.27 + 4.39 h. Moreover, extubation time was significantly affected by packed cells during the Cardiopulmonary Bypass (CPB), packed cells after CPB, inotrope use on arrival at ICU, mean arterial pressure 1st ICU, packed cells 1st ICU, platelets 1st ICU, Blood Urea Nitrogen 1st ICU, and hematocrit 1st ICU.Conclusion. Considering all of the factors under investigation, some peri-operative and post-operative factors had significant effects. Therefore, considering the post-operative factors is important for designing a treatment plan and evaluating patients’ prognosis. creator: Abbas Rezaianzadeh creator: Behzad Maghsoudi creator: Hamidreza Tabatabaee creator: Sareh Keshavarzi creator: Zahra Bagheri creator: Javad Sajedianfard creator: Hamid Gerami creator: Javad Rasouli uri: https://doi.org/10.7717/peerj.1414 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Rezaianzadeh et al. title: ‘Degraded’ RNA profiles in Arthropoda and beyond link: https://peerj.com/articles/1436 last-modified: 2015-12-01 description: The requirement for high quality/non-degraded RNA is essential for an array of molecular biology analyses. When analysing the integrity of rRNA from the barnacle Lepas anatifera (Phylum Arthropoda, Subphylum Crustacea), atypical or sub-optimal rRNA profiles that were apparently degraded were observed on a bioanalyser electropherogram. It was subsequently discovered that the rRNA was not degraded, but arose due to a ‘gap deletion’ (also referred to as ‘hidden break’) in the 28S rRNA. An apparent excision at this site caused the 28S rRNA to fragment under heat-denaturing conditions and migrate along with the 18S rRNA, superficially presenting a ‘degraded’ appearance. Examination of the literature showed similar observations in a small number of older studies in insects; however, reading across multiple disciplines suggests that this is a wider issue that occurs across the Animalia and beyond. The current study shows that the 28S rRNA anomaly goes far beyond insects within the Arthropoda and is widespread within this phylum. We confirm that the anomaly is associated with thermal conversion because gap-deletion patterns were observed in heat-denatured samples but not in gels with formaldehyde-denaturing. creator: Sean D. McCarthy creator: Michel M. Dugon creator: Anne Marie Power uri: https://doi.org/10.7717/peerj.1436 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McCarthy et al. title: Non-inferiority of retrospective data collection for assessing perioperative morbidity link: https://peerj.com/articles/1466 last-modified: 2015-12-01 description: Background. Postoperative morbidity has immediate and delayed consequences for surgical patients, including excess risk of premature death. Capturing these data objectively and routinely in large electronic databases using tools such as the Postoperative Morbidity Survey (POMS) would offer tremendous clinical and translational potential. However, POMS has thus far only utilised prospective data collection by research staff. We hypothesised that retrospective data collection from routinely collated hospital data from paper and electronic charts, medical and nursing notes was non-inferior to prospective data collection requiring research staff capturing POMS-defined morbidity in real-time.Methods. Morbidity was recorded by a trained investigator as defined by POMS prospectively on postoperative days 3 and 7. Separately, an independent investigator blinded to prospectively acquired data retrospectively assessed the same patients’ morbidity as defined by POMS criteria, using medical charts, nursing summaries and electronic data. Equivalence was accepted when the confidence limits for both modes of data collection fell completely inside the equivalence bounds, with the maximum equivalence difference (i.e., the largest value of the difference in sensitivities deemed to reach a conclusion of equivalence) set a priori at 0.2. Differences for confidence limits between retrospective and prospective data collection were based on Nam’s RMLE method. The relationship between morbidity on postoperative day 3 as recorded by each data collection method on time to become morbidity free and length of hospital stay was compared using the log-rank test.Results. POMS data from 85 patients undergoing elective or emergency surgery were analyzed. At postoperative day 3, POMS-defined morbidity was similar regardless of whether data were collected prospectively or retrospectively (95% CI [−0.13–0.013]; p < 0.001). Non-inferiority for sensitivity was observed for all other POMS domains and timepoints. Time to become morbidity free Kaplan–Meier plots were indistinguishable between POMS obtained prospectively or retrospectively (hazard ratio: 1.09 (95% CI [0.76–1.57]); p = 0.33, log rank test). Similarly, the mode of data collection did not alter the association between early postoperative morbidity on postoperative day 3 and delayed hospital discharge.Conclusions. Postoperative morbidity as defined by the Post Operative Morbidity Survey can be assessed retrospectively. These data may therefore be easily captured using electronic patient record systems, thereby expanding the potential for bioinformatics approaches to generate new clinical and translational insights into recovery from surgery. creator: Amour B.U. Patel creator: Anna Reyes creator: Gareth L. Ackland uri: https://doi.org/10.7717/peerj.1466 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: The association of parental temperament and character on their children’s behavior problems link: https://peerj.com/articles/1464 last-modified: 2015-12-01 description: Purpose. Parents have important roles in child rearing, but the influence of their personality on rearing practices and their impact on the behavior of children has received surprisingly little attention. The aim of the current study was to investigate the relationship between parents’ personality and children’s problem behaviors.Materials and Methods. Participants consisted of 190 preschool outpatients (104 boys, 86 girls) and their parents who visited traditional Korean pediatric clinics with minor physical symptoms as chief complaints. The personality profiles of the both parents were measured by the Temperament and Character Inventory and children’s behavior problems by the Child Behavior Checklist 1.5–5. Correlation and stepwise regression analysis were employed for the statistical analyses.Results. The temperament trait of Harm Avoidance and the character traits of Self-Directedness and Self-Transcendence of the parents were significantly correlated with children’s problem behaviors. Character as well as temperament, played an important role in explaining children’s problem behaviors after age and gender of children were taken into account.Conclusion. The maturity of parents’ character appears to have a key role in reducing the risk of behavior problems in their children. Suggestions are made for parental education and future research. creator: Soo Jin Lee creator: C. Robert Cloninger creator: Soo Hyun Park creator: Han Chae uri: https://doi.org/10.7717/peerj.1464 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lee et al. title: Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches link: https://peerj.com/articles/1459 last-modified: 2015-12-01 description: Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. creator: Elena L.E.S. Wagner creator: Dominique G. Roche creator: Sandra A. Binning creator: Sharon Wismer creator: Redouan Bshary uri: https://doi.org/10.7717/peerj.1459 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wagner et al. title: Upright or inverted, entire or exploded: right-hemispheric superiority in face recognition withstands multiple spatial manipulations link: https://peerj.com/articles/1456 last-modified: 2015-12-01 description: Background. The ability to identify faces has been interpreted as a cerebral specialization based on the evolutionary importance of these social stimuli, and a number of studies have shown that this function is mainly lateralized in the right hemisphere. The aim of this study was to assess the right-hemispheric specialization in face recognition in unfamiliar circumstances.Methods. Using a divided visual field paradigm, we investigated hemispheric asymmetries in the matching of two subsequent faces, using two types of transformation hindering identity recognition, namely upside-down rotation and spatial “explosion” (female and male faces were fractured into parts so that their mutual spatial relations were left intact), as well as their combination.Results. We confirmed the right-hemispheric superiority in face processing. Moreover, we found a decrease of the identity recognition for more extreme “levels of explosion” and for faces presented upside-down (either as sample or target stimuli) than for faces presented upright, as well as an advantage in the matching of female compared to male faces.Discussion. We conclude that the right-hemispheric superiority for face processing is not an epiphenomenon of our expertise, because we are not often exposed to inverted and “exploded” faces, but rather a robust hemispheric lateralization. We speculate that these results could be attributable to the prevalence of right-handedness in humans and/or to early biases in social interactions. creator: Giulia Prete creator: Daniele Marzoli creator: Luca Tommasi uri: https://doi.org/10.7717/peerj.1456 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Prete et al. title: Cranial arterial pattern of the Sri Lankan spotted chevrotain, Moschiola memmina, and comparative basicranial osteology of the Tragulidae link: https://peerj.com/articles/1451 last-modified: 2015-12-01 description: The cranial arterial pattern of artiodactyls deviates significantly from the typical mammalian pattern. One of the most striking atypical features is the rete mirabile epidurale: a subdural arterial meshwork that functionally and anatomically replaces the arteria carotis interna. This meshwork facilitates an exceptional ability to cool the brain, and was thought to be present in all artiodactyls. Recent research, however, has found that species of mouse deer (Artiodactyla: Tragulidae) endemic to the Malay Archipelago possess a complete a. carotis interna instead of a rete mirabile epidurale. As tragulids are the sister group to pecoran ruminants, the lack of a rete mirabile epidurale in these species raises intriguing evolutionary questions about the origin and nature of artiodactyl thermoregulatory cranial vasculature. In this study, cranial arterial patterns are documented for the remaining species within the Tragulidae. Radiopaque latex vascular injection, computed tomography (CT-scanning), and digital 3-dimensional anatomical reconstruction are used to image the cranial arteries of a Sri Lankan spotted chevrotain, Moschiola meminna. Sites of hard and soft tissue interaction were identified, and these osteological correlates were then sought in nine skulls representative of the remaining tragulid species. Both hard and soft tissue surveys confirm that the presence of an a. carotis interna is the common condition for tragulids. Moreover, the use of a 3-D, radiographic anatomical imaging technique enabled identification of a carotico-maxillary anastomosis that may have implications for the evolution of the artiodactyl rete mirabile epidurale. creator: Haley D. O’Brien uri: https://doi.org/10.7717/peerj.1451 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 O’Brien title: A quick and robust method for quantification of the hypersensitive response in plants link: https://peerj.com/articles/1469 last-modified: 2015-12-01 description: One of the most studied defense reactions of plants against microbial pathogens is the hypersensitive response (HR). The HR is a complex multicellular process that involves programmed cell death at the site of infection. A standard method to quantify plant defense and the HR is to measure the release of cellular electrolytes into water after infiltration with pathogenic bacteria. In this type of experiment, the bacteria are typically delivered into the plant tissue through syringe infiltration. Here we report the development of a vacuum infiltration protocol that allows multiple plant lines to be infiltrated simultaneously and assayed for defense responses. Vacuum infiltration did not induce more wounding response in Arabidopsis leaf tissue than syringe inoculation, whereas throughput and reproducibility were improved. The method was used to study HR-induced electrolyte loss after treatment with the bacterium Pseudomonas syringae pv. tomato DC3000 harboring the effector AvrRpm1, AvrRpt2 or AvrRps4. Specifically, the influence of bacterial titer on AvrRpm1-induced HR was investigated. Not only the amplitude, but also the timing of the maximum rate of the HR reaction was found to be dose-dependent. Finally, using vacuum infiltration, we were able quantify induction of phospholipase D activity after AvrRpm1 recognition in leaves labeled with 33PO4. creator: Oskar N. Johansson creator: Anders K. Nilsson creator: Mikael B. Gustavsson creator: Thomas Backhaus creator: Mats X. Andersson creator: Mats Ellerström uri: https://doi.org/10.7717/peerj.1469 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Johansson et al. title: Watching eyes on potential litter can reduce littering: evidence from two field experiments link: https://peerj.com/articles/1443 last-modified: 2015-12-01 description: Littering constitutes a major societal problem, and any simple intervention that reduces its prevalence would be widely beneficial. In previous research, we have found that displaying images of watching eyes in the environment makes people less likely to litter. Here, we investigate whether the watching eyes images can be transferred onto the potential items of litter themselves. In two field experiments on a university campus, we created an opportunity to litter by attaching leaflets that either did or did not feature an image of watching eyes to parked bicycles. In both experiments, the watching eyes leaflets were substantially less likely to be littered than control leaflets (odds ratios 0.22–0.32). We also found that people were less likely to litter when there other people in the immediate vicinity than when there were not (odds ratios 0.04–0.25) and, in one experiment but not the other, that eye leaflets only reduced littering when there no other people in the immediate vicinity. We suggest that designing cues of observation into packaging could be a simple but fruitful strategy for reducing littering. creator: Melissa Bateson creator: Rebecca Robinson creator: Tim Abayomi-Cole creator: Josh Greenlees creator: Abby O’Connor creator: Daniel Nettle uri: https://doi.org/10.7717/peerj.1443 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Bateson et al.