title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2016-07 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I? link: https://peerj.com/articles/2299 last-modified: 2016-07-28 description: 1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the less reactive C4-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere. creator: Pedro J. Silva uri: https://doi.org/10.7717/peerj.2299 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Silva title: Vocal correlates of individual sooty mangabey travel speed and direction link: https://peerj.com/articles/2298 last-modified: 2016-07-28 description: Many group-living animals coordinate movements with acoustic signals, but so far most studies have focused on how group movements are initiated. In this study, we investigated movement patterns of wild sooty mangabeys (Cercocebus atys), a mostly terrestrial, forest-dwelling primate. We provide quantitative results showing that vocalization rates of mangabey subgroups, but not of focal individuals, correlated with focal individuals’ current movement patterns. More interestingly, vocal behaviour predicted whether individuals changed future speed, and possibly future travel direction. The role of vocalizations as a potential mechanism for the regulation of group movement was further highlighted by interaction effects that include subgroup size and the quality of poly-specific associations. Collectively, our results suggest that primate vocal behaviour can function beyond travel initiation in coordination and regulation of group movements. creator: Christof Neumann creator: Klaus Zuberbühler uri: https://doi.org/10.7717/peerj.2298 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Neumann & Zuberbühler title: Larval settlement and metamorphosis in a marine gastropod in response to multiple conspecific cues link: https://peerj.com/articles/2295 last-modified: 2016-07-28 description: Larvae of the marine gastropod Crepidula fornicata must complete a transition from the plankton, where they are highly dispersed, to an aggregated group of benthic adults. Previous research has shown that selective settlement of larvae on conspecific adults is mediated by a water-borne chemical cue. However, variable experimental conditions have been used to study this cue, and standardization is needed in order to investigate factors that may have weak effects on settlement. In this study, we developed a time-course bioassay based on a full-factorial design with temporal blocking and statistical analysis of larval settlement rates in the lab. We tested this bioassay by examining settlement in the presence of an abiotic cue (KCl), and biotic cues (water conditioned with adult conspecifics and conspecific pedal mucus). Results confirmed settlement in the presence of both KCl and adult-conditioned water, and discovered the induction of settlement by pedal mucus. This optimized, standardized bioassay will be used in future experiments to characterize the complex process of larval settlement in C. fornicata, particularly to measure components of potentially small effect. creator: Abigail E. Cahill creator: Spencer A. Koury uri: https://doi.org/10.7717/peerj.2295 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cahill and Koury title: Engineering a light-controlled F1 ATPase using structure-based protein design link: https://peerj.com/articles/2286 last-modified: 2016-07-28 description: The F1 sub-complex of ATP synthase is a biological nanomotor that converts the free energy of ATP hydrolysis into mechanical work with an astonishing efficiency of up to 100% (Kinosita et al., 2000). To probe the principal mechanics of the machine, I re-engineered the active site of E.coli F1 ATPase with a structure-based protein design approach: by incorporation of a site-specific, photoswitchable crosslinker, whose end-to-end distance can be modulated by illumination with light of two different wavelengths, a dynamic constraint was imposed on the inter-atomic distances of the α and β subunits. Crosslinking reduced the ATP hydrolysis activity of four designs tested in vitro and in one case created a synthetic ATPase whose activity can be reversibly modulated by subsequent illumination with near UV and blue light. The work is a first step into the direction of the long-term goal to design nanoscaled machines based on biological parts that can be precisely controlled by light. creator: Daniel Hoersch uri: https://doi.org/10.7717/peerj.2286 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hoersch title: Site fidelity, size, and morphology may differ by tidal position for an intertidal fish, Bathygobius cocosensis (Perciformes-Gobiidae), in Eastern Australia link: https://peerj.com/articles/2263 last-modified: 2016-07-28 description: The intertidal zone is a transitional environment that undergoes daily environmental fluctuations as tides rise and fall. Relatively few fish species are adapted to endure the physiological pressures of this environment. This study focused on Bathygobius cocosensis (Gobiidae), a common intertidal fish in New South Wales, Australia. We investigated whether shore height impacted site fidelity, survival probability, fish size, and morphological traits with respect to tidal height. Mark-recapture methods were used over a five month period to determine if individuals in high shore pools had greater site fidelity; fish in high tide pools were more than twice as likely to be recaptured in their original pool than fish from low tide pools. High pool individuals were, on average, smaller with larger eyes and longer snouts relative to their size as compared to low pool individuals. We discuss several mechanisms that could cause the observed pattern in morphological variation. Ultimately, this study suggests that within species behaviour and morphology differ by tidal position for an intertidal fish. creator: Lucie A. Malard creator: Katrina McGuigan creator: Cynthia Riginos uri: https://doi.org/10.7717/peerj.2263 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Malard et al. title: Three-dimensional geometrical changes of the human tibialis anterior muscle and its central aponeurosis measured with three-dimensional ultrasound during isometric contractions link: https://peerj.com/articles/2260 last-modified: 2016-07-28 description: Background. Muscles not only shorten during contraction to perform mechanical work, but they also bulge radially because of the isovolumetric constraint on muscle fibres. Muscle bulging may have important implications for muscle performance, however quantifying three-dimensional (3D) muscle shape changes in human muscle is problematic because of difficulties with sustaining contractions for the duration of an in vivo scan. Although two-dimensional ultrasound imaging is useful for measuring local muscle deformations, assumptions must be made about global muscle shape changes, which could lead to errors in fully understanding the mechanical behaviour of muscle and its surrounding connective tissues, such as aponeurosis. Therefore, the aims of this investigation were (a) to determine the intra-session reliability of a novel 3D ultrasound (3DUS) imaging method for measuring in vivo human muscle and aponeurosis deformations and (b) to examine how contraction intensity influences in vivo human muscle and aponeurosis strains during isometric contractions.Methods. Participants (n = 12) were seated in a reclined position with their left knee extended and ankle at 90° and performed isometric dorsiflexion contractions up to 50% of maximal voluntary contraction. 3DUS scans of the tibialis anterior (TA) muscle belly were performed during the contractions and at rest to assess muscle volume, muscle length, muscle cross-sectional area, muscle thickness and width, fascicle length and pennation angle, and central aponeurosis width and length. The 3DUS scan involved synchronous B-mode ultrasound imaging and 3D motion capture of the position and orientation of the ultrasound transducer, while successive cross-sectional slices were captured by sweeping the transducer along the muscle.Results. 3DUS was shown to be highly reliable across measures of muscle volume, muscle length, fascicle length and central aponeurosis length (ICC ≥ 0.98, CV < 1%). The TA remained isovolumetric across contraction conditions and progressively shortened along its line of action as contraction intensity increased. This caused the muscle to bulge centrally, predominantly in thickness, while muscle fascicles shortened and pennation angle increased as a function of contraction intensity. This resulted in central aponeurosis strains in both the transverse and longitudinal directions increasing with contraction intensity.Discussion. 3DUS is a reliable and viable method for quantifying multidirectional muscle and aponeurosis strains during isometric contractions within the same session. Contracting muscle fibres do work in directions along and orthogonal to the muscle’s line of action and central aponeurosis length and width appear to be a function of muscle fascicle shortening and transverse expansion of the muscle fibres, which is dependent on contraction intensity. How factors other than muscle force change the elastic mechanical behaviour of the aponeurosis requires further investigation. creator: Brent J. Raiteri creator: Andrew G. Cresswell creator: Glen A. Lichtwark uri: https://doi.org/10.7717/peerj.2260 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Raiteri et al. title: Perception of the risk of adverse reactions to analgesics: differences between medical students and residents link: https://peerj.com/articles/2255 last-modified: 2016-07-28 description: Background. Medications are not exempt from adverse drug reactions (ADR) and how the physician perceives the risk of prescription drugs could influence their availability to report ADR and their prescription behavior.Methods. We assess the perception of risk and the perception of ADR associated with COX2-Inbitors, paracetamol, NSAIDs, and morphine in medical students and residents of northeast of Mexico.Results. The analgesic with the highest risk perception in both group of students was morphine, while the drug with the least risk perceived was paracetamol. Addiction and gastrointestinal bleeding were the ADR with the highest score for morphine and NSAIDs respectively.Discussion. Our findings show that medical students give higher risk scores than residents toward risk due to analgesics. Continuing training and informing physicians about ADRs is necessary since the lack of training is known to induce inadequate use of drugs. creator: Sandra Castillo-Guzman creator: Omar González-Santiago creator: Ismael A. Delgado-Leal creator: Gerardo E. Lozano-Luévano creator: Misael J. Reyes-Rodríguez creator: César V. Elizondo-Solis creator: Teresa A. Nava-Obregón creator: Dionicio Palacios-Ríos uri: https://doi.org/10.7717/peerj.2255 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Castillo-Guzman et al. title: A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model link: https://peerj.com/articles/2248 last-modified: 2016-07-28 description: Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software. creator: Watthanai Pinthong creator: Panya Muangruen creator: Prapat Suriyaphol creator: Dumrong Mairiang uri: https://doi.org/10.7717/peerj.2248 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pinthong et al. title: The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China link: https://peerj.com/articles/2185 last-modified: 2016-07-28 description: Many studies predict that climate change will cause species movement and turnover, but few have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change may cause a major shift in spatial patterns of amphibian diversity. Amphibians in China would lose 20% of their original ranges on average; the distribution outside current ranges would increase by 15%. Suitable habitats for over 90% of species will be located in the north of their current range, for over 95% of species in higher altitudes (from currently 137–4,124 m to 286–4,396 m in the 2050s or 314–4,448 m in the 2070s), and for over 75% of species in the west of their current range. Also, our results predict two different general responses to the climate change: some species contract their ranges while moving westwards, southwards and to higher altitudes, while others expand their ranges. Finally, our analyses indicate that range dynamics and fragmentation are related, which means that the effects of climate change on Chinese amphibians might be two-folded. creator: Ren-Yan Duan creator: Xiao-Quan Kong creator: Min-Yi Huang creator: Sara Varela creator: Xiang Ji uri: https://doi.org/10.7717/peerj.2185 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Duan et al. title: What are the probable predictors of urinary incontinence during pregnancy? link: https://peerj.com/articles/2283 last-modified: 2016-07-27 description: Objectives. The frequency, predisposing factors and impact of urinary incontinence (UI) on quality of life (QoL) during pregnancy were investigated.Materials and Method. A preliminary cross-sectional survey was studied among pregnant women between January and July of 2014. A total of 132 pregnant women were recruited using a questionnaire form for sociodemographic features, the Turkish version of the International Consultation on Incontinence-Short Form (ICIQ-SF), for the characteristics of UI and Wagner’s Quality of Life scale to assess impact on QoL. p < 0.05 was set significant.Results.Urinary incontinence was present in 56 out of 132 pregnant women (42.4%, UI-present group): mean age, 26.7 ± 5.4y(p = 0.780); median height, 160 cm (min–max: 153–176, p = 0.037); median BMI, 28.7 kg/m2(min–max: 22.4–50.0, p = 0.881); urine leakage occurred per week once (n = 18, 32.1%), twice or thrice (n = 8, 14.3%); per day few times (n = 14, 25%), once (n = 5, 8.9%) and always (n = 8, 14.3%) with mainly a small amount of urine leakage (n = 33, 58.9%) or a moderate (n = 4, 7.1%). There were statistically significant relationships between QoL scores and frequency of UI (p = 0.002) or amount of leakage (p = 0.002). Impact on QoL scores ranged from mild (n = 33, 58.9%), moderate (n = 4, 7.1%) to severe (n = 4, 7.1%) levels in daily life. UI impacted the daily life activities of women by making them less likely to undertake activities outside their homes (23.2%), by affecting their working performance and friendships (8.9%), their daily home activities (7.1%), their general health status (12.5%), their sexual relations (12.5%), by making them more nervous or anxious (10.7%) and by the need to wear pads or protectors (25%). ANOVA, Tukey, and Tamhane tests as the minimal important difference model yielded significant relevance between statistical analyses and clinical outcomes by using standard deviations (p = 0.001, 0.001 and 0.005 respectively). The following features favored the occurence of UI: Age (OR = 0.845, 95% CI [0.268–2.669]), being a housewife (OR = 1.800, 95% CI [0.850–3.810]), anemia (OR = 0.939, 95% CI [0.464–1.901]), parity (OR = 0.519, 95% CI [0.325–0.829]), miscarriage (OR = 1.219, 95% CI [0.588–2.825]) and living in rural areas (OR = 1.800, 95% CI [0.887–3.653]). Height (p = 0, 037), educational status (0.016), miscarriage (0.002), parity (0.006) and place of living (0.020) were significant factors.Conclusions.Many pregnant women are suffering from UI, which warrants a significant public health consideration in the region. Age, height, being a housewife or graduation level higher than primary school, living in rural, parity, miscarriage, and anemia were the factors in favor of the onset of UI. The authors plan a health promotion program in the region according to the results in order to provide information to health caregivers, especially family physicians, and to educate women about the predictors of UI and pelvic floor exercises for primary prevention and secondary relief of UI during and after pregnancy and provide some hygienic supplies to the poor in this aspect. creator: Nejat Demircan creator: Ülkü Özmen creator: Fürüzan Köktürk creator: Hamdi Küçük creator: Şevket Ata creator: Müge Harma creator: İnan İlker Arıkan uri: https://doi.org/10.7717/peerj.2283 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Demircan et al. title: Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles link: https://peerj.com/articles/2274 last-modified: 2016-07-27 description: The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCR-based studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals’ clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP. creator: Alonzo Alfaro-Núñez creator: Anders Miki Bojesen creator: Mads F. Bertelsen creator: Nathan Wales creator: George H. Balazs creator: M. Thomas P. Gilbert uri: https://doi.org/10.7717/peerj.2274 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Alfaro-Núñez et al. title: Medium-sized exotic prey create novel food webs: the case of predators and scavengers consuming lagomorphs link: https://peerj.com/articles/2273 last-modified: 2016-07-27 description: Food web interactions are key to community structure. The introduction of species can be seen as an uncontrolled experiment of the addition of species. Introduced species lead to multiple changes, frequently threatening the native biodiversity. However, little is known about their direct effect on the upper level of the food web. In this study we review empirical data on the predator–prey relationship between the introduced lagomorphs and their consumers, and use meta-analytical tools to quantify the strength of their interactions. We expect that exotic lagomorphs will destabilize food webs, affect ecological processes and compromise the conservation of the invaded regions. We found 156 studies on the diet of 43 species of predators that consume lagomorphs as exotic preys in South America and Oceania. We found an average exotic lagomorphs-predator link of 20% which indicates a strong interaction, given that the average for the strongest links with native prey (when lagomorphs are not included in the predator diet) is about 24%. Additionally, this last link decreases to 17% when lagomorphs are present. When lagomorphs arrive in a new environment they may become the most important resource for predators, producing an unstable equilibrium in the novel food web. Any disruption of this interaction could have catastrophic consequences for the native diversity by directly impacting predators or indirectly impacting native preys by apparent competition. Eradication or any change in their abundances should be carefully considered in conservation actions since those will have great impacts on predator populations and ultimately in the whole communities. creator: Facundo Barbar creator: Fernando Hiraldo creator: Sergio A. Lambertucci uri: https://doi.org/10.7717/peerj.2273 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Barbar et al. title: Competition-function tradeoffs in ectomycorrhizal fungi link: https://peerj.com/articles/2270 last-modified: 2016-07-27 description: Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function.Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus.Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest.Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining “high-quality” ectomycorrhizal fungal partners in natural systems. creator: Holly V. Moeller creator: Kabir G. Peay uri: https://doi.org/10.7717/peerj.2270 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Moeller and Peay title: Community shelter use in response to two benthic decapod predators in the Long Island Sound link: https://peerj.com/articles/2265 last-modified: 2016-07-27 description: To investigate community shelter effects of two invasive decapod species, Hemigrapsus sanguineus and Carcinus maenas, in the Long Island Sound (LIS), we deployed artificial shelters in the intertidal and immediate subtidal zones. These consisted of five groups during the summer: a control, a resident H. sanguineus male or female group, and a resident C. maenas male or female group. We quantified utilization of the shelters at 24 h by counting crabs and fish present. We found significant avoidance of H. sanguineus in the field by benthic hermit crabs (Pagurus spp.) and significant avoidance of C. maenas by the seaboard goby (Gobiosoma ginsburgi). The grubby (Myoxocephalus aenaeus) avoided neither treatment, probably since it tends to be a predator of invertebrates. H. sanguineus avoided C. maenas treatments, whereas C. maenas did not avoid any treatment. Seasonal deployments in the subtidal indicated cohabitation of a number of benthic species in the LIS, with peak shelter use corresponding with increased predation and likely reproductive activity in spring and summer for green crabs (C. maenas), hermit crabs (Pagurus spp.), seaboard gobies (G. ginsburgi), and grubbies (Myoxocephalus aenaeus). creator: David M. Hudson creator: Dugan Reagan creator: Joseph F. Crivello uri: https://doi.org/10.7717/peerj.2265 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hudson et al. title: Dropping behaviour of pea aphid nymphs increases their development time and reduces their reproductive capacity as adults link: https://peerj.com/articles/2236 last-modified: 2016-07-27 description: Background. Many aphid species, including the pea aphid Acyrthosiphon pisum, exhibit a behaviour where they drop or fall from their host plant, a commonly used strategy to avoid predation, parasitism or physical disturbance. We hypothesised that there was a physiological non-consumptive cost due to such dropping behaviour because aphids would expend energy re-establishing themselves on a host plant and also lose feeding time.Methods. We evaluated this non-consumptive cost by determining the development time and reproductive potential of pea aphids that whilst developing as nymphs had regularly dropped to the ground following dislodgment from their host plant. Using a microcosm approach, in a replicated and balanced laboratory experiment, we caused aphid dropping behaviour by tapping the plants on which they were feeding.Results. The results demonstrated that disturbance by dropping behaviour increased nymphal development time and reduced their subsequent reproductive capacity as adults.Discussion. We conclude that dropping behaviour had a strong negative effect on the development of nymphs and their subsequent reproductive capacity. This implies that the physiological cost of such a behaviour choice is substantial, and that such avoidance strategies require a trade-off which reduces the capacity of a population to increase. creator: Barbara Agabiti creator: Roxanne J. Wassenaar creator: Linton Winder uri: https://doi.org/10.7717/peerj.2236 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Agabiti et al. title: Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus link: https://peerj.com/articles/2200 last-modified: 2016-07-27 description: The blue and red shrimp, Aristeus antennatus, is a commercially important crustacean, in the Mediterranean Sea, which has been listed as a priority species for fishery management. Hypervariable microsatellite markers could be a useful tool to identify genetic stocks among geographically close fishing grounds. Potential microsatellite markers (97) identified from next-generation sequencing of an individual shrimp using a 454 GS Junior Pyrosequencer were tested on a preliminary panel of 15 individuals representing the four worldwide genetic stocks of the species from which 35 polymorphic loci were identified and used to characterize an additional 20 individuals from the Western Mediterranean Sea. In the Western Mediterranean sample, 32 out of 35 were polymorphic loci and the number of alleles per locus ranged from 2 to 14 and expected heterozygosity ranged from 0.050 to 0.968. No linkage disequilibrium was detected, indicating the independence of the loci. These novel microsatellites provide additional tools to address questions relating to genetic diversity, parentage studies and connectivity patterns of A. antennatus populations and help develop effective strategies to ensure long-term sustainability of this resource. creator: Sandra Heras creator: Laia Planella creator: Ilaria Caldarazzo creator: Manuel Vera creator: José-Luis García-Marín creator: Maria Ines Roldán uri: https://doi.org/10.7717/peerj.2200 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Heras et al. title: Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase link: https://peerj.com/articles/2272 last-modified: 2016-07-26 description: The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals. creator: Ming-Yue Ma creator: Xin-Ran Lan creator: Deng-Ke Niu uri: https://doi.org/10.7717/peerj.2272 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Ma et al. title: Construction and use of a Cupriavidus necator H16 soluble hydrogenase promoter (PSH) fusion to gfp (green fluorescent protein) link: https://peerj.com/articles/2269 last-modified: 2016-07-26 description: Hydrogenases are metalloenzymes that reversibly catalyse the oxidation or production of molecular hydrogen (H2). Amongst a number of promising candidates for application in the oxidation of H2 is a soluble [Ni–Fe] uptake hydrogenase (SH) produced by Cupriavidus necator H16. In the present study, molecular characterisation of the SH operon, responsible for functional SH synthesis, was investigated by developing a green fluorescent protein (GFP) reporter system to characterise PSH promoter activity using several gene cloning approaches. A PSH promoter-gfp fusion was successfully constructed and inducible GFP expression driven by the PSH promoter under de-repressing conditions in heterotrophic growth media was demonstrated in the recombinant C. necator H16 cells. Here we report the first successful fluorescent reporter system to study PSH promoter activity in C. necator H16. The fusion construct allowed for the design of a simple screening assay to evaluate PSH activity. Furthermore, the constructed reporter system can serve as a model to develop a rapid fluorescent based reporter for subsequent small-scale process optimisation experiments for SH expression. creator: Bat-Erdene Jugder creator: Jeffrey Welch creator: Nady Braidy creator: Christopher P. Marquis uri: https://doi.org/10.7717/peerj.2269 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jugder et al. title: Morphometric comparisons of plant-mimetic juvenile fish associated with plant debris observed in the coastal subtropical waters around Kuchierabu-jima Island, southern Japan link: https://peerj.com/articles/2268 last-modified: 2016-07-26 description: The general morphological shape of plant-resembling fish and plant parts were compared using a geometric morphometrics approach. Three plant-mimetic fish species, Lobotes surinamensis (Lobotidae), Platax orbicularis (Ephippidae) and Canthidermis maculata (Balistidae), were compared during their early developmental stages with accompanying plant debris (i.e., leaves of several taxa) in the coastal subtropical waters around Kuchierabu-jima Island, closely facing the Kuroshio Current. The degree of similarity shared between the plant parts and co-occurring fish species was quantified, however fish remained morphologically distinct from their plant models. Such similarities were corroborated by analysis of covariance and linear discriminant analysis, in which relative body areas of fish were strongly related to plant models. Our results strengthen the paradigm that morphological clues can lead to ecological evidence to allow predictions of behavioural and habitat choice by mimetic fish, according to the degree of similarity shared with their respective models. The resemblance to plant parts detected in the three fish species may provide fitness advantages via convergent evolutionary effects. creator: Alexya Cunha de Queiroz creator: Yoichi Sakai creator: Marcelo Vallinoto creator: Breno Barros uri: https://doi.org/10.7717/peerj.2268 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Queiroz et al. title: Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks link: https://peerj.com/articles/2261 last-modified: 2016-07-26 description: A major limitation with traditional phage preparations is the variability in titer, salts, and bacterial contaminants between successive propagations. Here we introduce the Phage On Tap (PoT) protocol for the quick and efficient preparation of homogenous bacteriophage (phage) stocks. This method produces homogenous, laboratory-scale, high titer (up to 1010–11 PFU·ml−1), endotoxin reduced phage banks that can be used to eliminate the variability between phage propagations and improve the molecular characterizations of phage. The method consists of five major parts, including phage propagation, phage clean up by 0.22 μm filtering and chloroform treatment, phage concentration by ultrafiltration, endotoxin removal, and the preparation and storage of phage banks for continuous laboratory use. From a starting liquid lysate of > 100 mL, the PoT protocol generated a clean, homogenous, laboratory phage bank with a phage recovery efficiency of 85% within just two days. In contrast, the traditional method took upwards of five days to produce a high titer, but lower volume phage stock with a recovery efficiency of only 4%. Phage banks can be further purified for the removal of bacterial endotoxins, reducing endotoxin concentrations by over 3,000-fold while maintaining phage titer. The PoT protocol focused on T-like phages, but is broadly applicable to a variety of phages that can be propagated to sufficient titer, producing homogenous, high titer phage banks that are applicable for molecular and cellular assays. creator: Natasha Bonilla creator: Maria Isabel Rojas creator: Giuliano Netto Flores Cruz creator: Shr-Hau Hung creator: Forest Rohwer creator: Jeremy J. Barr uri: https://doi.org/10.7717/peerj.2261 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bonilla et al. title: Emotion recognition based on customized smart bracelet with built-in accelerometer link: https://peerj.com/articles/2258 last-modified: 2016-07-26 description: Background: Recently, emotion recognition has become a hot topic in human-computer interaction. If computers could understand human emotions, they could interact better with their users. This paper proposes a novel method to recognize human emotions (neutral, happy, and angry) using a smart bracelet with built-in accelerometer.Methods: In this study, a total of 123 participants were instructed to wear a customized smart bracelet with built-in accelerometer that can track and record their movements. Firstly, participants walked two minutes as normal, which served as walking behaviors in a neutral emotion condition. Participants then watched emotional film clips to elicit emotions (happy and angry). The time interval between watching two clips was more than four hours. After watching film clips, they walked for one minute, which served as walking behaviors in a happy or angry emotion condition. We collected raw data from the bracelet and extracted a few features from raw data. Based on these features, we built classification models for classifying three types of emotions (neutral, happy, and angry).Results and Discussion: For two-category classification, the classification accuracy can reach 91.3% (neutral vs. angry), 88.5% (neutral vs. happy), and 88.5% (happy vs. angry), respectively; while, for the differentiation among three types of emotions (neutral, happy, and angry), the accuracy can reach 81.2%.Conclusions: Using wearable devices, we found it is possible to recognize human emotions (neutral, happy, and angry) with fair accuracy. Results of this study may be useful to improve the performance of human-computer interaction. creator: Zhan Zhang creator: Yufei Song creator: Liqing Cui creator: Xiaoqian Liu creator: Tingshao Zhu uri: https://doi.org/10.7717/peerj.2258 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang et al. title: Flower diversity and bee reproduction in an arid ecosystem link: https://peerj.com/articles/2250 last-modified: 2016-07-26 description: Background: Diverse flower communities are more stable in floral resource production along the flowering season, but the question about how the diversity and stability of resources affect pollinator reproduction remains open. High plant diversity could favor short foraging trips, which in turn would enhance bee fitness. In addition to plant diversity, greater temporal stability of floral resources in diverse communities could favor pollinator fitness because such communities are likely to occupy the phenological space more broadly, increasing floral availability for pollinators throughout the season. In addition, this potential effect of flower diversity on bee reproduction could be stronger for generalist pollinators because they can use a broader floral spectrum. Based on above arguments we predicted that pollinator reproduction would be positively correlated to flower diversity, and to temporal stability in flower production, and that this relationship would be stronger for the most generalized pollinator species.Materials and Methods: Using structural equation models, we evaluated the effect of these variables and other ecological factors on three estimates of bee reproduction (average number of brood cells per nest per site, total number of brood cells per site, and total number of nests per site), and whether such effects were modulated by bee generalization on floral resources.Results: Contrary to our expectations, flower diversity had no effect on bee reproduction, stability in flower production had a weakly negative effect on one of the bee reproductive variables, and the strength of the fitness-diversity relationship was unrelated to bee generalization. In contrast, elevation had a negative effect on bee reproduction, despite the narrow elevation range encompassed by our sites.Discussion: Flower diversity did not affect the reproduction of the solitary bees studied here. This result could stem from the context dependence of the diversity-stability relationship, given that elevation had a positive effect on flower diversity but a negative effect on bee reproduction. Although high temporal stability in flower production is expected to enhance pollinator reproduction, in our study it had a weakly negative—instead of positive—effect on the average number of brood cells per nest. Other environmental factors that vary with elevation could influence bee reproduction. Our study focused on a small group of closely-related bee species, which cautions against generalization of our findings to other groups of pollinators. More studies are clearly needed to assess the extent to which pollinator demography is influenced by the diversity of floral resources. creator: Jimena Dorado creator: Diego P. Vázquez uri: https://doi.org/10.7717/peerj.2250 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Dorado & Vázquez title: Human feeding biomechanics: performance, variation, and functional constraints link: https://peerj.com/articles/2242 last-modified: 2016-07-26 description: The evolution of the modern human (Homo sapiens) cranium is characterized by a reduction in the size of the feeding system, including reductions in the size of the facial skeleton, postcanine teeth, and the muscles involved in biting and chewing. The conventional view hypothesizes that gracilization of the human feeding system is related to a shift toward eating foods that were less mechanically challenging to consume and/or foods that were processed using tools before being ingested. This hypothesis predicts that human feeding systems should not be well-configured to produce forceful bites and that the cranium should be structurally weak. An alternate hypothesis, based on the observation that humans have mechanically efficient jaw adductors, states that the modern human face is adapted to generate and withstand high biting forces. We used finite element analysis (FEA) to test two opposing mechanical hypotheses: that compared to our closest living relative, chimpanzees (Pan troglodytes), the modern human craniofacial skeleton is (1) less well configured, or (2) better configured to generate and withstand high magnitude bite forces. We considered intraspecific variation in our examination of human feeding biomechanics by examining a sample of geographically diverse crania that differed notably in shape. We found that our biomechanical models of human crania had broadly similar mechanical behavior despite their shape variation and were, on average, less structurally stiff than the crania of chimpanzees during unilateral biting when loaded with physiologically-scaled muscle loads. Our results also show that modern humans are efficient producers of bite force, consistent with previous analyses. However, highly tensile reaction forces were generated at the working (biting) side jaw joint during unilateral molar bites in which the chewing muscles were recruited with bilateral symmetry. In life, such a configuration would have increased the risk of joint dislocation and constrained the maximum recruitment levels of the masticatory muscles on the balancing (non-biting) side of the head. Our results do not necessarily conflict with the hypothesis that anterior tooth (incisors, canines, premolars) biting could have been selectively important in humans, although the reduced size of the premolars in humans has been shown to increase the risk of tooth crown fracture. We interpret our results to suggest that human craniofacial evolution was probably not driven by selection for high magnitude unilateral biting, and that increased masticatory muscle efficiency in humans is likely to be a secondary byproduct of selection for some function unrelated to forceful biting behaviors. These results are consistent with the hypothesis that a shift to softer foods and/or the innovation of pre-oral food processing techniques relaxed selective pressures maintaining craniofacial features that favor forceful biting and chewing behaviors, leading to the characteristically small and gracile faces of modern humans. creator: Justin A. Ledogar creator: Paul C. Dechow creator: Qian Wang creator: Poorva H. Gharpure creator: Adam D. Gordon creator: Karen L. Baab creator: Amanda L. Smith creator: Gerhard W. Weber creator: Ian R. Grosse creator: Callum F. Ross creator: Brian G. Richmond creator: Barth W. Wright creator: Craig Byron creator: Stephen Wroe creator: David S. Strait uri: https://doi.org/10.7717/peerj.2242 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Ledogar et al. title: Computational fluid dynamics modelling of left valvular heart diseases during atrial fibrillation link: https://peerj.com/articles/2240 last-modified: 2016-07-26 description: Background: Although atrial fibrillation (AF), a common arrhythmia, frequently presents in patients with underlying valvular disease, its hemodynamic contributions are not fully understood. The present work aimed to computationally study how physical conditions imposed by pathologic valvular anatomy act on AF hemodynamics.Methods: We simulated AF with different severity grades of left-sided valvular diseases and compared the cardiovascular effects that they exert during AF, compared to lone AF. The fluid dynamics model used here has been recently validated for lone AF and relies on a lumped parameterization of the four heart chambers, together with the systemic and pulmonary circulation. The AF modelling involves: (i) irregular, uncorrelated and faster heart rate; (ii) atrial contractility dysfunction. Three different grades of severity (mild, moderate, severe) were analyzed for each of the four valvulopathies (AS, aortic stenosis, MS, mitral stenosis, AR, aortic regurgitation, MR, mitral regurgitation), by varying–through the valve opening angle–the valve area.Results: Regurgitation was hemodynamically more relevant than stenosis, as the latter led to inefficient cardiac flow, while the former introduced more drastic fluid dynamics variation. Moreover, mitral valvulopathies were more significant than aortic ones. In case of aortic valve diseases, proper mitral functioning damps out changes at atrial and pulmonary levels. In the case of mitral valvulopathy, the mitral valve lost its regulating capability, thus hemodynamic variations almost equally affected regions upstream and downstream of the valve. In particular, the present study revealed that both mitral and aortic regurgitation strongly affect hemodynamics, followed by mitral stenosis, while aortic stenosis has the least impact among the analyzed valvular diseases.Discussion: The proposed approach can provide new mechanistic insights as to which valvular pathologies merit more aggressive treatment of AF. Present findings, if clinically confirmed, hold the potential to impact AF management (e.g., adoption of a rhythm control strategy) in specific valvular diseases. creator: Stefania Scarsoglio creator: Andrea Saglietto creator: Fiorenzo Gaita creator: Luca Ridolfi creator: Matteo Anselmino uri: https://doi.org/10.7717/peerj.2240 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Scarsoglio et al. title: Flash visual evoked potentials in diurnal birds of prey link: https://peerj.com/articles/2217 last-modified: 2016-07-26 description: The objective of this pilot study was to evaluate the feasibility of Flash Visual Evoked Potentials (FVEPs) testing in birds of prey in a clinical setting and to describe the protocol and the baseline data for normal vision in this species. FVEP recordings were obtained from 6 normal adult birds of prey: n. 2 Harris’s Hawks (Parabuteo unicinctus), n. 1 Lanner Falcon (Falco biarmicus), n. 2 Gyrfalcons (Falco rusticolus) and n. 1 Saker Falcon (Falco cherrug). Before carrying out VEP tests, all animals underwent neurologic and ophthalmic routine examination. Waveforms were analysed to identify reproducible peaks from random variation of baseline. At least three positive and negative peaks were highlighted in all tracks with elevated repeatability. Measurements consisted of the absolute and relative latencies of these peaks (P1, N1, P2, N2, P3, and N3) and their peak-to-peak amplitudes. Both the peak latency and wave morphology achieved from normal animals were similar to those obtained previously in other animal species. This test can be easily and safely performed in a clinical setting in birds of prey and could be useful for an objective assessment of visual function. creator: Maurizio Dondi creator: Fabio Biaggi creator: Francesco Di Ianni creator: Pier Luigi Dodi creator: Fausto Quintavalla uri: https://doi.org/10.7717/peerj.2217 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dondi et al. title: Tissue mortality by Caribbean ciliate infection and white band disease in three reef-building coral species link: https://peerj.com/articles/2196 last-modified: 2016-07-26 description: Caribbean ciliate infection (CCI) and white band disease (WBD) are diseases that affect a multitude of coral hosts and are associated with rapid rates of tissue losses, thus contributing to declining coral cover in Caribbean reefs. In this study we compared tissue mortality rates associated to CCI in three species of corals with different growth forms: Orbicella faveolata (massive-boulder), O. annularis (massive-columnar) and Acropora cervicornis (branching). We also compared mortality rates in colonies of A. cervicornis bearing WBD and CCI. The study was conducted at two locations in Los Roques Archipelago National Park between April 2012 and March 2013. In A. cervicornis, the rate of tissue loss was similar between WBD (0.8 ± 1 mm/day, mean ± SD) and CCI (0.7 ± 0.9 mm/day). However, mortality rate by CCI in A. cervicornis was faster than in the massive species O. faveolata (0.5 ± 0.6 mm/day) and O. annularis (0.3 ± 0.3 mm/day). Tissue regeneration was at least fifteen times slower than the mortality rates for both diseases regardless of coral species. This is the first study providing coral tissue mortality and regeneration rates associated to CCI in colonies with massive morphologies, and it highlights the risks of further cover losses of the three most important reef-building species in the Caribbean. creator: Alejandra Verde creator: Carolina Bastidas creator: Aldo Croquer uri: https://doi.org/10.7717/peerj.2196 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Verde et al. title: Probiotic Bacillus coagulans GBI-30, 6086 reduces exercise-induced muscle damage and increases recovery link: https://peerj.com/articles/2276 last-modified: 2016-07-21 description: Objective. Probiotics have been reported to support healthy digestive and immune function, aid in protein absorption, and decrease inflammation. Further, a trend to increase vertical jump power has been observed following co-administration of protein and probiotics in resistance-trained subjects. However, to date the potential beneficial effect of probiotics on recovery from high intensity resistance exercise have yet to be explored. Therefore, this study examined the effect of co-administration of protein and probiotics on muscle damage, recovery and performance following a damaging exercise bout.Design. Twenty nine (n = 29) recreationally-trained males (mean ± SD; 21.5 ± 2.8 years; 89.7 ± 28.2 kg; 177.4 ± 8.0 cm) were assigned to consume either 20 g of casein (PRO) or 20 g of casein plus probiotic (1 billion CFU Bacillus coagulans GBI-30, 6086, PROBC) in a crossover, diet-controlled design. After two weeks of supplementation, perceptional measures, athletic performance, and muscle damage were analyzed following a damaging exercise bout.Results. The damaging exercise bout significantly increased muscle soreness, and reduced perceived recovery; however, PROBC significantly increased recovery at 24 and 72 h, and decreased soreness at 72 h post exercise in comparison to PRO. Perceptual measures were confirmed by increases in CK (PRO: +266.8%, p = 0.0002; PROBC: +137.7%, p = 0.01), with PROBC showing a trend towards reduced muscle damage (p = 0.08). The muscle-damaging exercise resulted in significantly increased muscle swelling and Blood Urea Nitrogen levels in both conditions with no difference between groups. The strenuous exercise significantly reduced athletic performance in PRO (Wingate Peak Power; PRO: (−39.8 watts, −5.3%, p = 0.03)), whereas PROBC maintained performance (+10.1 watts, +1.7%).Conclusions. The results provide evidence that probiotic supplementation in combination with protein tended to reduce indices of muscle damage, improves recovery, and maintains physical performance subsequent to damaging exercise. creator: Ralf Jäger creator: Kevin A. Shields creator: Ryan P. Lowery creator: Eduardo O. De Souza creator: Jeremy M. Partl creator: Chase Hollmer creator: Martin Purpura creator: Jacob M. Wilson uri: https://doi.org/10.7717/peerj.2276 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jäger et al. title: Article processing charges for open access publication—the situation for research intensive universities in the USA and Canada link: https://peerj.com/articles/2264 last-modified: 2016-07-21 description: Background. Open access (OA) publishing via article processing charges (APCs) is growing as an alternative to subscription publishing. The Pay It Forward (PIF) Project is exploring the feasibility of transitioning from paying subscriptions to funding APCs for faculty at research intensive universities. Estimating of the cost of APCs for the journals authors at research intensive universities tend to publish is essential for the PIF project and similar initiatives. This paper presents our research into this question.Methods. We identified APC prices for publications by authors at the 4 research intensive United States (US) and Canadian universities involved in the study. We also obtained APC payment records from several Western European universities and funding agencies. Both data sets were merged with Web of Science (WoS) metadata. We calculated the average APCs for articles and proceedings in 13 discipline categories published by researchers at research intensive universities. We also identified 41 journals published by traditionally subscription publishers which have recently converted to APC funded OA and recorded the APCs they charge.Results. We identified 7,629 payment records from the 4 European APC payment databases and 14,356 OA articles authored by PIF partner university faculty for which we had listed APC prices. APCs for full OA journals published by PIF authors averaged 1,775 USD; full OA journal APCs paid by Western European funders averaged 1,865 USD; hybrid APCs paid by Western European funders averaged 2,887 USD. The APC for converted journals published by major subscription publishers averaged 1,825 USD. APC funded OA is concentrated in the life and basic sciences. APCs funded articles in the social sciences and humanities are often multidisciplinary and published in journals such as PLOS ONE that largely publish in the life sciences.Conclusions. Full OA journal APCs average a little under 2,000 USD while hybrid articles average about 3,000 USD for publications by researchers at research intensive universities. There is a lack of information on discipline differences in APCs due to the concentration of APC funded publications in a few fields and the multidisciplinary nature of research. creator: David Solomon creator: Bo-Christer Björk uri: https://doi.org/10.7717/peerj.2264 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Solomon and Björk title: Non-invasive assessment of phosphate metabolism and oxidative capacity in working skeletal muscle in healthy young Chinese volunteers using 31P Magnetic Resonance Spectroscopy link: https://peerj.com/articles/2259 last-modified: 2016-07-21 description: Background. Generally, males display greater strength and muscle capacity than females while performing a task. Muscle biopsy is regarded as the reference method of evaluating muscle functions; however, it is invasive and has sampling errors, and is not practical for longitudinal studies and dynamic measurement during excise. In this study, we built an in-house force control and gauge system for quantitatively applying force to quadriceps while the subjects underwent 31P Magnetic Resonance Spectroscopy (31P-MRS); our aim was to investigate if there is a sex difference of phosphate metabolite change in working muscles in young heathy Chinese volunteers.Methods. Volunteers performed knee-extending excises using a force control and gauge system while lying prone in a Philips 3T Magnetic Resonance (MR) scanner. The 31P-MRS coil was firmly placed under the middle of the quadriceps . 31P-MRS measurements of inorganic phosphate (Pi), phosphocreatine (PCr) and adenosine triphosphate (ATP) were acquired from quadriceps while subjects were in a state of pre-, during- and post-exercise. The PCr, Pi, PCr/Pi, PCr/ATP, pH, work/energy cost ratio (WE), kPCr and oxidative capacity were compared between males and females.Results. A total of 17 volunteers underwent the study. Males: N = 10, age = 23.30 ± 1.25years; females: N = 7, age = 23.57 ± 0.79 years. In this study, males had significantly greater WE (16.33 ± 6.46 vs. 7.82 ± 2.16, p = 0.002) than females. Among PCr, Pi, PCr/Pi, PCr/ATP, pH, kPCr and oxidative capacity at different exercise status, only PCr/Pi (during-exercise, males = 5.630 ± 1.647, females = 4.014 ± 1.298, p = 0.047), PCr/ATP (during-exercise, males =1.273 ± 0.219, females = 1.523 ± 0.167, p = 0.025), and ATP (post-exercise, males = 24.469 ± 3.911 mmol/kg, females = 18.353 ± 4.818 mmol/kg, p = 0.035) had significant sex differences. Males had significantly greater PCr/Pi, but less PCr/ATP than females during exercise, suggesting males had higher energy transfer efficiency than females. At the post-exercise status, the recovery of PCr did not show sex difference.Conclusions. Our in-house force control and gauge system quantitatively applied force during the exercise for 31P-MRS experiments, and a sex difference of higher energy transfer efficiency and WE was detected in males with mild loaded exercising quadriceps. This noninvasive technology allows us to further study and understand the sex difference of high energy phosphate metabolism in the future. creator: Ming Li creator: Fei Chen creator: Huiting Wang creator: Wenbo Wu creator: Xin Zhang creator: Chuanshuai Tian creator: Haiping Yu creator: Renyuan Liu creator: Bin Zhu creator: Bing Zhang creator: Zhenyu Dai uri: https://doi.org/10.7717/peerj.2259 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Li et al. title: Impact of agricultural management on bacterial laccase-encoding genes with possible implications for soil carbon storage in semi-arid Mediterranean olive farming link: https://peerj.com/articles/2257 last-modified: 2016-07-21 description: Background: In this work, we aimed to gain insights into the contribution of soil bacteria to carbon sequestration in Mediterranean habitats. In particular, we aimed to use bacterial laccase-encoding genes as molecular markers for soil organic C cycling. Using rainfed olive farming as an experimental model, we determined the stability and accumulation levels of humic substances and applied these data to bacterial laccase-encoding gene expression and diversity in soils under four different agricultural management systems (bare soils under tillage/no tillage and vegetation cover under chemical/mechanical management).Materials and Methods: Humic C (> 104 Da) was subjected to isoelectric focusing. The GC-MS method was used to analyze aromatic hydrocarbons. Real-Time PCR quantification and denaturing gradient gel electrophoresis (DGGE) for functional bacterial laccase-like multicopper oxidase (LMCO)-encoding genes and transcripts were also carried out.Results: Soils under spontaneous vegetation, eliminated in springtime using mechanical methods for more than 30 years, showed the highest humic acid levels as well as the largest bacterial population rich in laccase genes and transcripts. The structure of the bacterial community based on LMCO genes also pointed to phylogenetic differences between these soils due to the impact of different management systems. Soils where herbicides were used to eliminate spontaneous vegetation once a year and those where pre-emergence herbicides resulted in bare soils clustered together for DNA-based DGGE analysis, which indicated a certain amount of microbial selection due to the application of herbicides. When LMCO-encoding gene expression was studied, soils where cover vegetation was managed either with herbicides or with mechanical methods showed less than 10% similarity, suggesting that the type of weed management strategy used can impact weed community composition and consequently laccase substrates derived from vegetation decay.Conclusions: We suggest that the low humic acid content retrieved in the herbicide-treated soils was mainly related to the type (due to vegetal cover specialization) and smaller quantity (due to lower vegetal biomass levels) of phenolic substrates for laccase enzymes involved in humification processes. We also found that spontaneous vegetal cover managed using mechanical methods could be the best option for achieving C stabilization in rainfed Mediterranean agroecosystems. creator: Beatriz Moreno creator: Emilio Benitez uri: https://doi.org/10.7717/peerj.2257 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Moreno & Benitez title: Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study link: https://peerj.com/articles/2253 last-modified: 2016-07-21 description: Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used 13C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the 13Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results. creator: Pablo G. Garay creator: Osvaldo A. Martin creator: Harold A. Scheraga creator: Jorge A. Vila uri: https://doi.org/10.7717/peerj.2253 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Garay et al. title: Simultaneous bilateral laser therapy accelerates recovery after noise-induced hearing loss in a rat model link: https://peerj.com/articles/2252 last-modified: 2016-07-21 description: Noise-induced hearing loss is a common type of hearing loss. The effects of laser therapy have been investigated from various perspectives, including in wound healing, inflammation reduction, and nerve regeneration, as well as in hearing research. A promising feature of the laser is its capability to penetrate soft tissue; depending on the wavelength, laser energy can penetrate into the deepest part of the body without damaging non-target soft tissues. Based on this idea, we developed bilateral transtympanic laser therapy, which uses simultaneous laser irradiation in both ears, and evaluated the effects of bilateral laser therapy on cochlear damage caused by noise overexposure. Thus, the purpose of this research was to assess the benefits of simultaneous bilateral laser therapy compared with unilateral laser therapy and a control. Eighteen Sprague-Dawley rats were exposed to narrow-band noise at 115 dB SPL for 6 h. Multiple auditory brainstem responses were measured after each laser irradiation, and cochlear hair cells were counted after the 15th such irradiation. The penetration depth of the 808 nm laser was also measured after sacrifice. Approximately 5% of the laser energy reached the contralateral cochlea. Both bilateral and unilateral laser therapy decreased the hearing threshold after noise overstimulation in the rat model. The bilateral laser therapy group showed faster functional recovery at all tested frequencies compared with the unilateral laser therapy group. However, there was no difference in the endpoint ABR results or final hair cell survival, which was analyzed histologically. creator: Jae-Hun Lee creator: So-Young Chang creator: Wesley J. Moy creator: Connie Oh creator: Se-Hyung Kim creator: Chung-Ku Rhee creator: Jin-Chul Ahn creator: Phil-Sang Chung creator: Jae Yun Jung creator: Min Young Lee uri: https://doi.org/10.7717/peerj.2252 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lee et al. title: Neural and endocranial anatomy of Triassic phytosaurian reptiles and convergence with fossil and modern crocodylians link: https://peerj.com/articles/2251 last-modified: 2016-07-21 description: Phytosaurs are a clade of large, carnivorous pseudosuchian archosaurs from the Late Triassic with a near cosmopolitan distribution. Their superficial resemblance to longirostrine (long-snouted) crocodylians, such as gharials, has often been used in the past to infer ecological and behavioural convergence between the two groups. Although more than thirty species of phytosaur are currently recognised, little is known about the endocranial anatomy of this clade. Here, we describe the endocranial anatomy (including the brain, inner ear, neurovascular structures and sinus systems) of the two non-mystriosuchine phytosaurs Parasuchus angustifrons (=“Paleorhinus angustifrons”) and Ebrachosuchus neukami from the Late Triassic of Germany based on digital reconstructions. Results show that the endocasts of both taxa are very similar to each other in their rostrocaudally elongate morphology, with long olfactory tracts, weakly demarcated cerebral regions and dorsoventrally short endosseous labyrinths. In addition, several sinuses, including large antorbital sinuses and prominent dural venous sinuses, were reconstructed. Comparisons with the endocranial anatomy of derived phytosaurs indicate that Phytosauria is united by the presence of elongate olfactory tracts and longitudinally arranged brain architecture—characters which are also shared with Crocodyliformes. However, a substantial morphological variability is observed in the cephalic and pontine flexure and the presence of a pineal organ across the different phytosaur species. These results suggest that the endocranial anatomy in Phytosauria generally follows a plesiomorphic pattern, with moderate variation within the clade likely resulting from divergent sensory and behavioural adaptations. creator: Stephan Lautenschlager creator: Richard J. Butler uri: https://doi.org/10.7717/peerj.2251 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lautenschlager and Butler title: Percentile curves for skinfold thickness for Canadian children and youth link: https://peerj.com/articles/2247 last-modified: 2016-07-21 description: Background. Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objective of the present study was to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) in a representative population of Canadian children and youth.Methods. We analyzed data from 3,938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for SFT were calculated using the GAMLSS method.Results. Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak.Conclusions. The current study has presented for the first time percentile curves for five SFT measures in a representative sample of Canadian children and youth. creator: Stefan Kuhle creator: Jillian Ashley-Martin creator: Bryan Maguire creator: David C. Hamilton uri: https://doi.org/10.7717/peerj.2247 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kuhle et al. title: Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator? link: https://peerj.com/articles/2246 last-modified: 2016-07-21 description: Background. This work examines the relationship between emotional intelligence (EI) and depressive symptomatology in institutionalized older adults, delving into the mechanisms underlying this relationship. Considering that previous evidence of the variation of the EI-depression relationship depending on whether the emotional ability or the perception of that ability is evaluated, a model of multiple mediation was tested in which the dimensions of emotional self-efficacy (ESE) act as mediators in the relationship between ability EI and depressive symptomatology.Methods. The sample consisted of 115 institutionalized older adults (47.82% women; 80.3 ± 7.9 years of age) from the province of Jaén (Spain) who completed a test of ESE, a measure of ability EI, and a self-administered questionnaire of depressive symptoms.Results. The results showed a positive association between older adults’ emotional performance and depressive symptomatology, finding stronger associations with ESE than with EI abilities. In addition, multiple mediation analyses showed that two of the four dimensions of ESE fully mediated the relationship between ability EI and depressive symptoms.Discussion. These findings suggest that older adults’ high levels of emotional competence generate a feeling of ESE which can protect them against depressive symptoms. This work supports the predictive validity of emotional abilities and ESE for the mental health of a group that is particularly vulnerable to depression, institutionalized older adults. The limitations of the work are discussed, and future lines of research were considered. creator: Octavio Luque-Reca creator: José María Augusto-Landa creator: Manuel Pulido-Martos uri: https://doi.org/10.7717/peerj.2246 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Luque-Reca et al. title: Fast men slow more than fast women in a 10 kilometer road race link: https://peerj.com/articles/2235 last-modified: 2016-07-21 description: Background. Previous studies have demonstrated that men are more likely than women to slow in the marathon (footrace). This study investigated whether the sex difference in pacing occurs for a shorter race distance.Materials &Methods. Data were acquired from the Bolder Boulder 10 km road race for the years 2008–2013, which encompassed 191,693 performances. There were two pacing measures, percentage change in pace of the first 3 miles relative to the final 3.2 miles and percentage change in pace of the first mile relative to the final 5.2 miles. Pacing was analyzed as a continuous variable and as two categorical variables, as follows: “maintain the pace,” defined as slowing <5% and “marked slowing,” defined as slowing ≥10%.Results. Among the fastest (men < 48:40; women < 55:27) and second fastest (men < 53:54; women < 60:28) sex-specific finishing time sextiles, men slowed significantly more than women with both pacing measures, but there were no consistently significant sex differences in pacing among the slower four sextiles. For the fastest sextile, the odds for women were 1.96 (first pacing measure) and 1.36 (second measure) times greater than men to maintain the pace. For the fastest sextile, the odds for women were 0.46 (first measure) and 0.65 (second measure) times that of men to exhibit marked slowing. Multiple regression indicated that being older was associated with lesser slowing, but the sex difference among faster runners persisted when age was controlled.Conclusions. There was a sex difference in pacing during a 10 km race where glycogen depletion is not typically relevant. These results support the hypothesis that the sex difference in pacing partly reflects a sex difference in decision making. creator: Robert O. Deaner creator: Vittorio Addona creator: Rickey E. Carter creator: Michael J. Joyner creator: Sandra K. Hunter uri: https://doi.org/10.7717/peerj.2235 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Deaner et al. title: Computer-assisted initial diagnosis of rare diseases link: https://peerj.com/articles/2211 last-modified: 2016-07-21 description: Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial diagnosis of rare diseases by clinicians. In this work we aimed at developing a computational approach to aid in that initial diagnosis. We also aimed at implementing this approach in a user friendly web prototype. We call this tool Rare Disease Discovery. Finally, we also aimed at testing the performance of the prototype.Methods. Rare Disease Discovery uses the publicly available ORPHANET data set of association between rare diseases and their symptoms to automatically predict the most likely rare diseases based on a patient’s symptoms. We apply the method to retrospectively diagnose a cohort of 187 rare disease patients with confirmed diagnosis. Subsequently we test the precision, sensitivity, and global performance of the system under different scenarios by running large scale Monte Carlo simulations. All settings account for situations where absent and/or unrelated symptoms are considered in the diagnosis.Results. We find that this expert system has high diagnostic precision (≥80%) and sensitivity (≥99%), and is robust to both absent and unrelated symptoms.Discussion. The Rare Disease Discovery prediction engine appears to provide a fast and robust method for initial assisted differential diagnosis of rare diseases. We coupled this engine with a user-friendly web interface and it can be freely accessed at http://disease-discovery.udl.cat/. The code and most current database for the whole project can be downloaded from https://github.com/Wrrzag/DiseaseDiscovery/tree/no_classifiers. creator: Rui Alves creator: Marc Piñol creator: Jordi Vilaplana creator: Ivan Teixidó creator: Joaquim Cruz creator: Jorge Comas creator: Ester Vilaprinyo creator: Albert Sorribas creator: Francesc Solsona uri: https://doi.org/10.7717/peerj.2211 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Alves et al. title: A century of ecosystem change: human and seabird impacts on plant species extirpation and invasion on islands link: https://peerj.com/articles/2208 last-modified: 2016-07-21 description: We used 116 years of floral and faunal records from Mandarte Island, British Columbia, Canada, to estimate the indirect effects of humans on plant communities via their effects on the population size of a surface-nesting, colonial seabird, the Glaucous-winged gull (Larus glaucescens). Comparing current to historical records revealed 18 extirpations of native plant species (32% of species historically present), 31 exotic species introductions, and one case of exotic introduction followed by extirpation. Contemporary surveys indicated that native species cover declined dramatically from 1986 to 2006, coincident with the extirpation of ‘old-growth’ conifers. Because vegetation change co-occurred with an increasing gull population locally and regionally, we tested several predictions from the hypothesis that the presence and activities of seabirds help to explain those changes. Specifically, we predicted that on Mandarte and nearby islands with gull colonies, we should observe higher nutrient loading and exotic plant species richness and cover than on nearby islands without gull colonies, as a consequence of competitive dominance in species adapted to high soil nitrogen and trampling. As predicted, we found that native plant species cover and richness were lower, and exotic species cover and richness higher, on islands with versus without gull colonies. In addition, we found that soil carbon and nitrogen on islands with nesting gulls were positively related to soil depth and exotic species richness and cover across plots and islands. Our results support earlier suggestions that nesting seabirds can drive rapid change in insular plant communities by increasing nutrients and disturbing vegetation, and that human activities that affect seabird abundance may therefore indirectly affect plant community composition on islands with seabird colonies. creator: Thomas K. Lameris creator: Joseph R. Bennett creator: Louise K. Blight creator: Marissa Giesen creator: Michael H. Janssen creator: Joop J.H.J. Schaminée creator: Peter Arcese uri: https://doi.org/10.7717/peerj.2208 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Lameris et al. title: Proteomic indicators of oxidation and hydration state in colorectal cancer link: https://peerj.com/articles/2238 last-modified: 2016-07-20 description: New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer. Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (ZC) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue (${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$n¯H2O) is computed by writing the overall formation reactions of proteins from basis species. Using results reported in proteomic studies of clinical samples, many datasets exhibit higher mean ZC or ${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$n¯H2O of proteins in carcinoma or adenoma compared to normal tissue. In contrast, average protein compositions in bacterial genomes often have lower ZC for bacteria enriched in fecal samples from cancer patients compared to healthy donors. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H2O and fugacity of O2 that reflect the compositional differences. The compositional analysis suggests that a systematic change in chemical composition is an essential feature of cancer proteomes, and the thermodynamic descriptions show that the observed proteomic transformations in host tissue could be promoted by relatively high microenvironmental oxidation and hydration states. creator: Jeffrey M. Dick uri: https://doi.org/10.7717/peerj.2238 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dick title: The relationship between different exercise modes and visuospatial working memory in older adults: a cross-sectional study link: https://peerj.com/articles/2254 last-modified: 2016-07-20 description: The purpose of the study was to investigate the relationship between different exercise modes and visuospatial working memory in healthy older adults. A cross-sectional design was adopted. A total of 111 healthy older adults were enrolled in the study. They were classified by the exercise-related questionnaire to be in an open-skill group, closed-skill group or sedentary group. In experiment 1, the participants performed a visuospatial working memory task. The results indicated that both closed-skill (p < 0.05) and open-skill (p < 0.01) groups reached a higher accuracy than the sedentary group. Experiment 2 examined whether the exercise-induced benefit of working memory was manifested in passive maintenance or active manipulation of working memory which was assessed by visuospatial short-term memory task and visuospatial mental rotation task, respectively. The results showed that the open-skill (p < 0.01) group was more accurate than the sedentary group in the visuospatial short-term memory task, whereas the group difference in the visuospatial mental rotation task was not significant. These findings combined to suggest that physical exercise was associated with better visuospatial working memory in older adults. Furthermore, open-skill exercises that demand higher cognitive processing showed selective benefit for passive maintenance of working memory. creator: Wei Guo creator: Biye Wang creator: Yue Lu creator: Qin Zhu creator: Zhihao Shi creator: Jie Ren uri: https://doi.org/10.7717/peerj.2254 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Guo et al. title: Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci link: https://peerj.com/articles/2220 last-modified: 2016-07-20 description: The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting the monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the Late Miocene/Tortonian age. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice—during the mid-Miocene and Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south–central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia. creator: Tilottama Roy creator: Nathan S. Catlin creator: Drake M.G. Garner creator: Philip D. Cantino creator: Anne-Cathrine Scheen creator: Charlotte Lindqvist uri: https://doi.org/10.7717/peerj.2220 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Roy et al. title: Morphological analysis of dendrites and spines by hybridization of ridge detection with twin support vector machine link: https://peerj.com/articles/2207 last-modified: 2016-07-20 description: Dendritic spines are described as neuronal protrusions. The morphology of dendritic spines and dendrites has a strong relationship to its function, as well as playing an important role in understanding brain function. Quantitative analysis of dendrites and dendritic spines is essential to an understanding of the formation and function of the nervous system. However, highly efficient tools for the quantitative analysis of dendrites and dendritic spines are currently undeveloped. In this paper we propose a novel three-step cascaded algorithm–RTSVM— which is composed of ridge detection as the curvature structure identifier for backbone extraction, boundary location based on differences in density, the Hu moment as features and Twin Support Vector Machine (TSVM) classifiers for spine classification. Our data demonstrates that this newly developed algorithm has performed better than other available techniques used to detect accuracy and false alarm rates. This algorithm will be used effectively in neuroscience research. creator: Shuihua Wang creator: Mengmeng Chen creator: Yang Li creator: Ying Shao creator: Yudong Zhang creator: Sidan Du creator: Jane Wu uri: https://doi.org/10.7717/peerj.2207 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: DNA barcode data accurately assign higher spider taxa link: https://peerj.com/articles/2201 last-modified: 2016-07-20 description: The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades. creator: Jonathan A. Coddington creator: Ingi Agnarsson creator: Ren-Chung Cheng creator: Klemen Čandek creator: Amy Driskell creator: Holger Frick creator: Matjaž Gregorič creator: Rok Kostanjšek creator: Christian Kropf creator: Matthew Kweskin creator: Tjaša Lokovšek creator: Miha Pipan creator: Nina Vidergar creator: Matjaž Kuntner uri: https://doi.org/10.7717/peerj.2201 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Coddington et al. title: Commercial fishing gear modifications to reduce interactions between Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and the southern flounder (Paralichthys lethostigma) fishery in North Carolina (USA) link: https://peerj.com/articles/2192 last-modified: 2016-07-20 description: Bycatch of protected species in commercial fishing operations is a primary concern to fishery managers because it threatens the conservation, protection, and recovery of fragile species, such as the Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus). One potential solution to reduce the risk associated with commercial fishing operations is to design commercial fishing gear that is more selective in terms of interactions between Atlantic sturgeon and commercial fisheries. Given this conservation and management need, the overarching goal was to reduce Atlantic sturgeon fishery interactions and maintain southern flounder (Paralichthys lethostigma) catch in North Carolina. The specific objectives of this study were to design and evaluate the effectiveness of a modified gillnet. Overall, the results proved that lowering the profile and amount of webbing had a beneficial impact at reducing Atlantic sturgeon incidental encounters and bycatch. The modified gillnet reduced bycatch and Atlantic sturgeon encounters by 39.6% and 60.9%, respectively. Our design entangled 51.6% fewer southern flounder, which corresponded to a 48.9% reduction in total weight; the modified gear entangled slightly larger southern flounder than the control gear. Our findings showed the number of Atlantic sturgeon encounters was positively associated with mean water depth, with more Atlantic sturgeon encountered in deeper (5.1–6.3 m) than shallower waters; 75% were encountered at depths between 4.6 and 6.1 m. Most southern flounder (n = 518, 39.7%) were taken at a water depth between 3.76 and 5.0 m. This observation suggests that southern flounder prefer slightly shallower waters than Atlantic sturgeon. creator: Juan C. Levesque creator: Christian Hager creator: Eric Diaddorio creator: R. Jason Dickey uri: https://doi.org/10.7717/peerj.2192 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Levesque et al. title: Artificial reefs and marine protected areas: a study in willingness to pay to access Folkestone Marine Reserve, Barbados, West Indies link: https://peerj.com/articles/2175 last-modified: 2016-07-20 description: Artificial reefs in marine protected areas provide additional habitat for biodiversity viewing, and therefore may offer an innovative management solution for managing for coral reef recovery and resilience. Marine park user fees can generate revenue to help manage and maintain natural and artificial reefs. Using a stated preference survey, this study investigates the present consumer surplus associated with visitor use of a marine protected area in Barbados. Two hypothetical markets were presented to differentiate between respondents use values of either: (a) natural reefs within the marine reserve or (b) artificial reef habitat for recreational enhancement. Information was also collected on visitors’ perceptions of artificial reefs, reef material preferences and reef conservation awareness. From a sample of 250 visitors on snorkel trips, we estimate a mean willingness to pay of US$18.33 (median—US$15) for natural reef use and a mean value of US$17.58 (median—US$12.50) for artificial reef use. The number of marine species viewed, age of respondent, familiarity with the Folkestone Marine Reserve and level of environmental concern were statistically significant in influencing willingness to pay. Regression analyses indicate visitors are willing to pay a significant amount to view marine life, especially turtles. Our results suggest that user fees could provide a considerable source of income to aid reef conservation in Barbados. In addition, the substantial use value reported for artificial reefs indicates a reef substitution policy may be supported by visitors to the Folkestone Marine Reserve. We discuss our findings and highlight directions for future research that include the need to collect data to establish visitors’ non-use values to fund reef management. creator: Anne E. Kirkbride-Smith creator: Philip M. Wheeler creator: Magnus L. Johnson uri: https://doi.org/10.7717/peerj.2175 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kirkbride-Smith et al. title: Remote sensing of land use/cover changes and its effect on wind erosion potential in southern Iran link: https://peerj.com/articles/1948 last-modified: 2016-07-20 description: Wind erosion is a complex process influenced by different factors. Most of these factors are stable over time, but land use/cover and land management practices are changing gradually. Therefore, this research investigates the impact of changing land use/cover and land management on wind erosion potential in southern Iran. We used remote sensing data (Landsat ETM+ and Landsat 8 imagery of 2004 and 2013) for land use/cover mapping and employed the Iran Research Institute of Forest and Rangeland (IRIFR) method to estimate changes in wind erosion potential. For an optimal mapping, the performance of different classification algorithms and input layers was tested. The amount of changes in wind erosion and land use/cover were quantified using cross-tabulation between the two years. To discriminate land use/cover related to wind erosion, the best results were obtained by combining the original spectral bands with synthetic bands and using Maximum Likelihood classification algorithm (Kappa Coefficient of 0.8 and 0.9 for Landsat ETM+ and Landsat 8, respectively). The IRIFR modelling results indicate that the wind erosion potential has increased over the last decade. The areas with a very high sediment yield potential have increased, whereas the areas with a low, medium, and high sediment yield potential decreased. The area with a very low sediment yield potential have remained constant. When comparing the change in erosion potential with land use/cover change, it is evident that soil erosion potential has increased mostly in accordance with the increase of the area of agricultural practices. The conversion of rangeland to agricultural land was a major land-use change which lead to more agricultural practices and associated soil loss. Moreover, results indicate an increase in sandification in the study area which is also a clear evidence of increasing in soil erosion. creator: Mahrooz Rezaei creator: Abdolmajid Sameni creator: Seyed Rashid Fallah Shamsi creator: Harm Bartholomeus uri: https://doi.org/10.7717/peerj.1948 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rezaei et al. title: New holostean fishes (Actinopterygii: Neopterygii) from the Middle Triassic of the Monte San Giorgio (Canton Ticino, Switzerland) link: https://peerj.com/articles/2234 last-modified: 2016-07-19 description: The new neopterygian genus Ticinolepis, including two new species T. longaeva and T. crassidens is described from Middle Triassic carbonate platform deposits of the Monte San Giorgio. The anatomy of this fish shows a mosaic of halecomorph and ginglymodian characters and, thus, the new taxon probably represents a basal holostean. During the latest Anisian to earliest Ladinian the two new species coexisted in the intraplatform basin represented by the uppermost Besano Formation, but only T. longaeva sp. nov. inhabited the more restricted basin represented by the Ladinian Meride Limestone (except for the Kalkschieferzone). The more widely distributed type species shows interesting patterns of intraspecific variation including ontogenetic changes and morphological variation over time. The second species presents anatomical features that strongly indicate a strictly durophagous diet. The different distribution of the species is interpreted as a result of habitat partitioning and different adaptability to palaeoenvironmental changes. creator: Adriana López-Arbarello creator: Toni Bürgin creator: Heinz Furrer creator: Rudolf Stockar uri: https://doi.org/10.7717/peerj.2234 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 López-Arbarello et al. title: Correlations between personality traits and specific groups of alpha waves in the human EEG link: https://peerj.com/articles/2245 last-modified: 2016-07-19 description: Background. Different individuals have alpha waves with different wavelengths. The distribution of the wavelengths is assumed to be bell-shaped and smooth. Although this view is generally accepted, it is still just an assumption and has never been critically tested. When exploring the relationship between alpha waves and personality traits, it makes a huge difference if the distribution of the alpha waves is smooth or if specific groups of alpha waves can be demonstrated. Previous studies have not considered the possibility that specific groups of alpha waves may exist.Methods. Computerized EEGs have become standard, but wavelength measurements are problematic when based on averaging procedures using the Fourier transformation because such procedures cause a large systematic error. If the actual wavelength is of interest, it is necessary to go back to basic physiology and use raw EEG signals. In the present study, measurements were made directly from sequences of alpha waves where every wave could be identified. Personality dimensions were measured using an inventory derived from the International Personality Item Pool.Results. Recordings from 200 healthy individuals revealed that there are three main groups of alpha waves. These groups had frequencies around 8, 10, and 12 waves per second. The middle group had a bimodal distribution, and a subdivision gave a total of four alpha groups. In the center of each group, the degree of extraversion was high and the degree of neuroticism was low. Many small differences in personality traits were found when the centers were compared with one another. This gave four personality profiles that resemble the four classical temperaments. When people in the surrounding zones were compared with those in the centers, relatively large differences in personality traits were found.Conclusions. Specific groups of alpha waves exist, and these groups have to be taken into account when correlations are made to personality dimensions and temperament types. There is a link between alpha waves and personality traits, and this link implies that there is an underlying relationship. To explain the nature of this relationship, there are two hypotheses that can be applied. One of these deals with the general organization of the forebrain and the other explains why the brain generates alpha waves. creator: Tomas Johannisson uri: https://doi.org/10.7717/peerj.2245 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Johannisson title: Lateral presentation of faces alters overall viewing strategy link: https://peerj.com/articles/2241 last-modified: 2016-07-19 description: Eye tracking has been used during face categorisation and identification tasks to identify perceptually salient facial features and infer underlying cognitive processes. However, viewing patterns are influenced by a variety of gaze biases, drawing fixations to the centre of a screen and horizontally to the left side of face images (left-gaze bias). In order to investigate potential interactions between gaze biases uniquely associated with facial expression processing, and those associated with screen location, face stimuli were presented in three possible screen positions to the left, right and centre. Comparisons of fixations between screen locations highlight a significant impact of the screen centre bias, pulling fixations towards the centre of the screen and modifying gaze biases generally observed during facial categorisation tasks. A left horizontal bias for fixations was found to be independent of screen position but interacting with screen centre bias, drawing fixations to the left hemi-face rather than just to the left of the screen. Implications for eye tracking studies utilising centrally presented faces are discussed. creator: Christopher J. Luke creator: Petra M.J. Pollux uri: https://doi.org/10.7717/peerj.2241 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Luke and Pollux title: Equivalent intraperitoneal doses of ibuprofen supplemented in drinking water or in diet: a behavioral and biochemical assay using antinociceptive and thromboxane inhibitory dose–response curves in mice link: https://peerj.com/articles/2239 last-modified: 2016-07-19 description: Background. Ibuprofen is used chronically in different animal models of inflammation by administration in drinking water or in diet due to its short half-life. Though this practice has been used for years, ibuprofen doses were never assayed against parenteral dose–response curves. This study aims at identifying the equivalent intraperitoneal (i.p.) doses of ibuprofen, when it is administered in drinking water or in diet.Methods. Bioassays were performed using formalin test and incisional pain model for antinociceptive efficacy and serum TXB2 for eicosanoid inhibitory activity. The dose–response curve of i.p. administered ibuprofen was constructed for each test using 50, 75, 100 and 200 mg/kg body weight (b.w.). The dose–response curves were constructed of phase 2a of the formalin test (the most sensitive phase to COX inhibitory agents), the area under the ‘change in mechanical threshold’-time curve in the incisional pain model and serum TXB2 levels. The assayed ibuprofen concentrations administered in drinking water were 0.2, 0.35, 0.6 mg/ml and those administered in diet were 82, 263, 375 mg/kg diet.Results. The 3 concentrations applied in drinking water lay between 73.6 and 85.5 mg/kg b.w., i.p., in case of the formalin test; between 58.9 and 77.8 mg/kg b.w., i.p., in case of the incisional pain model; and between 71.8 and 125.8 mg/kg b.w., i.p., in case of serum TXB2 levels. The 3 concentrations administered in diet lay between 67.6 and 83.8 mg/kg b.w., i.p., in case of the formalin test; between 52.7 and 68.6 mg/kg b.w., i.p., in case of the incisional pain model; and between 63.6 and 92.5 mg/kg b.w., i.p., in case of serum TXB2 levels.Discussion. The increment in pharmacological effects of different doses of continuously administered ibuprofen in drinking water or diet do not parallel those of i.p. administered ibuprofen. It is therefore difficult to assume the equivalent parenteral daily doses based on mathematical calculations. creator: Raghda A.M. Salama creator: Nesreen H. El Gayar creator: Sonia S. Georgy creator: May Hamza uri: https://doi.org/10.7717/peerj.2239 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Salama et al. title: The final spawning ground of Tachypleus gigas (Müller, 1785) on the east Peninsular Malaysia is at risk: a call for action link: https://peerj.com/articles/2232 last-modified: 2016-07-19 description: Tanjung Selongor and Pantai Balok (State Pahang) are the only two places known for spawning activity of the Malaysian horseshoe crab - Tachypleus gigas (Müller, 1785) on the east coast of Peninsular Malaysia. While the former beach has been disturbed by several anthropogenic activities that ultimately brought an end to the spawning activity of T. gigas, the status of the latter remains uncertain. In the present study, the spawning behavior of T. gigas at Pantai Balok (Sites I-III) was observed over a period of thirty six months, in three phases, between 2009 and 2013. Every year, the crab’s nesting activity was found to be high during Southwest monsoon (May–September) followed by Northeast (November–March) and Inter monsoon (April and October) periods. In the meantime, the number of female T. gigas in 2009–2010 (Phase-1) was higher (38 crabs) than in 2010–2011 (Phase-2: 7 crabs) and 2012–2013 (Phase-3: 9 crabs) for which both increased overexploitation (for edible and fishmeal preparations) as well as anthropogenic disturbances in the vicinity (sand mining since 2009, land reclamation for wave breaker/parking lot constructions in 2011 and fishing jetty construction in 2013) are responsible. In this context, the physical infrastructure developments have altered the sediment close to nesting sites to be dominated by fine sand (2.5Xφ ) with moderately-well sorted (0.6–0.7σφ), very-coarse skewed (−2.4SKφ), and extremely leptokurtic (12.6Kφ) properties. Also, increased concentrations of Cadmium (from 4.2 to 13.6 mg kg−1) and Selenium (from 11.5 to 23.3 mg kg−1) in the sediment, and Sulphide (from 21 to 28 µg l−1) in the water were observed. In relation to the monsoonal changes affecting sheltered beach topography and sediment flux, the spawning crabs have shown a seasonal nest shifting behaviour in-between Sites I-III during 2009–2011. However, in 2012–2013, the crabs were mostly restricted to the areas (i.e., Sites I and II) with high oxygen (5.5–8.0 mg l−1) and moisture depth (6.2–10.2 cm). In view of the sustained anthropogenic pressure on the coastal habitats on one hand and decreasing horseshoe crabs population on the other, it is crucial to implement both conservation and management measures for T. gigas at Pantai Balok. Failing that may lead to the loss of this final spawning ground on the east coast of P. Malaysia. creator: Bryan Raveen Nelson creator: Behara Satyanarayana creator: Julia Hwei Zhong Moh creator: Mhd Ikhwanuddin creator: Anil Chatterji creator: Faizah Shaharom uri: https://doi.org/10.7717/peerj.2232 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nelson et al. title: Reconstitution of the complete rupture in musculotendinous junction using skeletal muscle-derived multipotent stem cell sheet-pellets as a “bio-bond” link: https://peerj.com/articles/2231 last-modified: 2016-07-19 description: Background. Significant and/or complete rupture in the musculotendinous junction (MTJ) is a challenging lesion to treat because of the lack of reliable suture methods. Skeletal muscle-derived multipotent stem cell (Sk-MSC) sheet-pellets, which are able to reconstitute peripheral nerve and muscular/vascular tissues with robust connective tissue networks, have been applied as a “bio-bond”.Methods. Sk-MSC sheet-pellets, derived from GFP transgenic-mice after 7 days of expansion culture, were detached with EDTA to maintain cell–cell connections. A completely ruptured MTJ model was prepared in the right tibialis anterior (TA) of the recipient mice, and was covered with sheet-pellets. The left side was preserved as a contralateral control. The control group received the same amount of the cell-free medium. The sheet-pellet transplantation (SP) group was further divided into two groups; as the short term (4–8 weeks) and long term (14–18 weeks) recovery group. At each time point after transplantation, tetanic tension output was measured through the electrical stimulation of the sciatic nerve. The behavior of engrafted GFP+ tissues and cells was analyzed by fluorescence immunohistochemistry.Results. The SP short term recovery group showed average 64% recovery of muscle mass, and 36% recovery of tetanic tension output relative to the contralateral side. Then, the SP long term recovery group showed increased recovery of average muscle mass (77%) and tetanic tension output (49%). However, the control group showed no recovery of continuity between muscle and tendon, and demonstrated increased muscle atrophy, with coalescence to the tibia during 4–8 weeks after operation. Histological evidence also supported the above functional recovery of SP group. Engrafted Sk-MSCs primarily formed the connective tissues and muscle fibers, including nerve-vascular networks, and bridged the ruptured tendon–muscle fiber units, with differentiation into skeletal muscle cells, Schwann cells, vascular smooth muscle, and endothelial cells.Discussion. This bridging capacity between tendon and muscle fibers of the Sk-MSC sheet-pellet, as a “bio-bond,” represents a possible treatment for various MTJ ruptures following surgery. creator: Hiroyuki Hashimoto creator: Tetsuro Tamaki creator: Maki Hirata creator: Yoshiyasu Uchiyama creator: Masato Sato creator: Joji Mochida uri: https://doi.org/10.7717/peerj.2231 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hashimoto et al. title: Love the one you’re with: replicate viral adaptations converge on the same phenotypic change link: https://peerj.com/articles/2227 last-modified: 2016-07-19 description: Parallelism is important because it reveals how inherently stochastic adaptation is. Even as we come to better understand evolutionary forces, stochasticity limits how well we can predict evolutionary outcomes. Here we sought to quantify parallelism and some of its underlying causes by adapting a bacteriophage (ID11) with nine different first-step mutations, each with eight-fold replication, for 100 passages. This was followed by whole-genome sequencing five isolates from each endpoint. A large amount of variation arose—281 mutational events occurred representing 112 unique mutations. At least 41% of the mutations and 77% of the events were adaptive. Within wells, populations generally experienced complex interference dynamics. The genome locations and counts of mutations were highly uneven: mutations were concentrated in two regulatory elements and three genes and, while 103 of the 112 (92%) of the mutations were observed in ≤4 wells, a few mutations arose many times. 91% of the wells and 81% of the isolates had a mutation in the D-promoter. Parallelism was moderate compared to previous experiments with this system. On average, wells shared 27% of their mutations at the DNA level and 38% when the definition of parallel change is expanded to include the same regulatory feature or residue. About half of the parallelism came from D-promoter mutations. Background had a small but significant effect on parallelism. Similarly, an analyses of epistasis between mutations and their ancestral background was significant, but the result was mostly driven by four individual mutations. A second analysis of epistasis focused on de novo mutations revealed that no isolate ever had more than one D-promoter mutation and that 56 of the 65 isolates lacking a D-promoter mutation had a mutation in genes D and/or E. We assayed time to lysis in four of these mutually exclusive mutations (the two most frequent D-promoter and two in gene D) across four genetic backgrounds. In all cases lysis was delayed. We postulate that because host cells were generally rare (i.e., high multiplicity of infection conditions developed), selection favored phage that delayed lysis to better exploit their current host (i.e., ‘love the one you’re with’). Thus, the vast majority of wells (at least 64 of 68, or 94%) arrived at the same phenotypic solution, but through a variety of genetic changes. We conclude that answering questions about the range of possible adaptive trajectories, parallelism, and the predictability of evolution requires attention to the many biological levels where the process of adaptation plays out. creator: Craig R. Miller creator: Anna C. Nagel creator: LuAnn Scott creator: Matt Settles creator: Paul Joyce creator: Holly A. Wichman uri: https://doi.org/10.7717/peerj.2227 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Miller et al. title: Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures link: https://peerj.com/articles/2223 last-modified: 2016-07-19 description: Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products. creator: Kok-Gan Chan creator: Kumutha Priya creator: Chien-Yi Chang creator: Ahmad Yamin Abdul Rahman creator: Kok Keng Tee creator: Wai-Fong Yin uri: https://doi.org/10.7717/peerj.2223 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chan et al. title: Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria link: https://peerj.com/articles/2222 last-modified: 2016-07-19 description: Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/. creator: Edward W. Davis II creator: Alexandra J. Weisberg creator: Javier F. Tabima creator: Niklaus J. Grunwald creator: Jeff H. Chang uri: https://doi.org/10.7717/peerj.2222 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Davis II et al. title: Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics link: https://peerj.com/articles/2214 last-modified: 2016-07-19 description: Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties.Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic).Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering.Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species. creator: Juan J. Martinez-Nicolas creator: Pablo Melgarejo creator: Pilar Legua creator: Francisco Garcia-Sanchez creator: Francisca Hernández uri: https://doi.org/10.7717/peerj.2214 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Martinez-Nicolas et al. title: Enhanced functional connectivity properties of human brains during in-situ nature experience link: https://peerj.com/articles/2210 last-modified: 2016-07-19 description: In this study, we investigated the impacts of in-situ nature and urban exposure on human brain activities and their dynamics. We randomly assigned 32 healthy right-handed college students (mean age = 20.6 years, SD = 1.6; 16 males) to a 20 min in-situ sitting exposure in either a nature (n = 16) or urban environment (n = 16) and measured their Electroencephalography (EEG) signals. Analyses revealed that a brief in-situ restorative nature experience may induce more efficient and stronger brain connectivity with enhanced small-world properties compared with a stressful urban experience. The enhanced small-world properties were found to be correlated with “coherent” experience measured by Perceived Restorativeness Scale (PRS). Exposure to nature also induces stronger long-term correlated activity across different brain regions with a right lateralization. These findings may advance our understanding of the functional activities during in-situ environmental exposures and imply that a nature or nature-like environment may potentially benefit cognitive processes and mental well-being. creator: Zheng Chen creator: Yujia He creator: Yuguo Yu uri: https://doi.org/10.7717/peerj.2210 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chen et al. title: fluff: exploratory analysis and visualization of high-throughput sequencing data link: https://peerj.com/articles/2209 last-modified: 2016-07-19 description: Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org.Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff. creator: Georgios Georgiou creator: Simon J. van Heeringen uri: https://doi.org/10.7717/peerj.2209 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Georgiou and Van Heeringen title: Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes link: https://peerj.com/articles/2204 last-modified: 2016-07-19 description: Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along with demographic parameters in sensitivity routines. GRIP 2.0 is an important decision-support tool that can be used to prioritize research, identify habitat-based thresholds and management intervention points to improve probability of species persistence, and evaluate trade-offs of alternative management options. creator: Ilona Naujokaitis-Lewis creator: Janelle M.R. Curtis uri: https://doi.org/10.7717/peerj.2204 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Naujokaitis-Lewis and Curtis title: Data mining in conservation research using Latin and vernacular species names link: https://peerj.com/articles/2202 last-modified: 2016-07-19 description: In conservation science, assessments of trends and priorities for actions often focus on species as the management unit. Studies on species coverage in online media are commonly conducted by using species vernacular names. However, the use of species vernacular names for web-based data search is problematic due to the high risk of mismatches in results. While the use of Latin names may produce more consistent results, it is uncertain whether a search using Latin names will produce unbiased results as compared to vernacular names. We assessed the potential of Latin names to be used as an alternative to vernacular names for the data mining within the field of conservation science. By using Latin and vernacular names, we searched for species from four species groups: diurnal birds of prey, Carnivora, Primates and marine mammals. We assessed the relationship of the results obtained within different online sources, such as Internet pages, newspapers and social media networks. Results indicated that the search results based on Latin and vernacular names were highly correlated, and confirmed that one may be used as an alternative for the other. We also demonstrated the potential of the number of images posted on the Internet to be used as an indication of the public attention towards different species. creator: Ivan Jarić creator: Franck Courchamp creator: Jörn Gessner creator: David L. Roberts uri: https://doi.org/10.7717/peerj.2202 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jarić et al. title: Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice link: https://peerj.com/articles/2187 last-modified: 2016-07-19 description: Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain. creator: Julie M. Allen creator: J. Gordon Burleigh creator: Jessica E. Light creator: David L. Reed uri: https://doi.org/10.7717/peerj.2187 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Allen et al. title: The diagnostic accuracy of acute phase proteins and proinflammatory cytokines in sheep with pneumonic pasteurellosis link: https://peerj.com/articles/2161 last-modified: 2016-07-19 description: The goal of this study was to assess the diagnostic accuracy of acute phase proteins and proinflammatory cytokines in sheep with pneumonic pasteurellosis. Blood samples were collected from 56 sheep (36 naturally infected with Pasteurella multocida and 20 healthy controls) belonging to one farm in Eastern region, Saudi Arabia. Serum samples were evaluated for acute phase proteins (Haptoglobin (Hp), serum amyloid A (SAA) and fibrinogen (Fb)), and the proinflammatory cytokines (interleukins (IL-1α, IL-1β, and IL-6), tumor necrosis factor-alpha (TNF-α), and interferon-gamma (IFN-ϒ)). Additionally, nasopharyngeal swabs and bronchoalveolar lavages were collected from all animals for bacteriological examinations. Receiver operating characteristic curve was used to assess the diagnostic performance of each parameter. All parameters showed moderate to high degree of positive correlation with case-control status. There was no significant difference in the area under the curve (AUC) among acute phase proteins; however, both Hp and SAA showed better sensitivity and specificity than Fb. The proinflammatory cytokines (IL1-α, IL1-β, and IL6) showed similar and highly accurate diagnostic performance (AUC > 0.9), whereas IFN-ϒ was moderately accurate (AUC = 0.79). In conclusion, this study confirms the value of acute phase proteins and cytokines as diagnostic biomarkers of naturally occuring pneumonic pasteurellosis in sheep. creator: Wael M. El-Deeb creator: Ahmed M. Elmoslemany uri: https://doi.org/10.7717/peerj.2161 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 El-Deeb and Elmoslemany title: Preferred temperature and thermal breadth of birds wintering in peninsular Spain: the limited effect of temperature on species distribution link: https://peerj.com/articles/2156 last-modified: 2016-07-19 description: Background. The availability of environmental energy, as measured by temperature, is expected to limit the abundance and distribution of endotherms wintering at temperate latitudes. A prediction of this hypothesis is that birds should attain their highest abundances in warmer areas. However, there may be a spatial mismatch between species preferred habitats and species preferred temperatures, so some species might end-up wintering in sub-optimal thermal environments.Methods. We model the influence of minimum winter temperature on the relative abundance of 106 terrestrial bird species wintering in peninsular Spain, at 10 ×10 km2 resolution, using 95%-quantile regressions. We analyze general trends across species on the shape of the response curves, the environmental preferred temperature (at which the species abundance is maximized), the mean temperature in the area of distribution and the thermal breadth (area under the abundance-temperature curve).Results. Temperature explains a low proportion of variation in abundance. The most significant effect is on limiting the maximum potential abundance of species. Considering this upper-limit response, there is a large interspecific variability on the thermal preferences and specialization of species. Overall, there is a preponderance of positive relationships between species abundance and temperature; on average, species attain their maximum abundances in areas 1.9 °C warmer than the average temperature available in peninsular Spain. The mean temperature in the area of distribution is lower than the thermal preferences of the species.Discussion. Many species prefer the warmest areas to overwinter, which suggests that temperature imposes important restrictions to birds wintering in the Iberian Peninsula. However, one third of species overwinter in locations colder than their thermal preferences, probably reflecting the interaction between habitat and thermal requirements. There is a high inter-specific variation in the versatility of species using the available thermal space, and the limited effect of temperature highlights the role of other environmental factors determining species abundance. creator: Luis M. Carrascal creator: Sara Villén-Pérez creator: David Palomino uri: https://doi.org/10.7717/peerj.2156 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Carrascal et al. title: Pleistocene phylogeography and cryptic diversity of a tiger beetle, Calomera littoralis, in North-Eastern Mediterranean and Pontic regions inferred from mitochondrial COI gene sequences link: https://peerj.com/articles/2128 last-modified: 2016-07-19 description: Background.Calomera littoralis is a Palearctic species, widely distributed in Europe; inhabiting predominantly its Atlantic, Mediterranean and Black Sea coastlines.Methods. Its phylogeography on the Balkan Peninsula and on the north-western Black Sea coast was inferred using a 697 bp long portion of the mitochondrial COI gene, amplified from 169 individuals collected on 43 localities.Results. The results revealed two genetically divergent groups/lineages, the southern one inhabiting both the Balkan Peninsula and the Pontic Region and the northern one found exclusively in the Pontic Region. Species delimitation based on DNA barcoding gap suggested an interspecific level of divergence between these groups. Multivariate analysis of eight male and female morphometric traits detected no difference between the groups, implying they may represent cryptic species. The Bayesian time-calibrated reconstruction of phylogeny suggested that the lineages diverged ca. 2.3 Ma, in early Pleistocene.Discussion. The presence of the two genetically divergent groups results most likely from contemporary isolation of the Pontic basin from the Mediterranean that broke the continuous strip of coastal habitats inhabited by C. littoralis. Demographic analyses indicated that both lineages have been in demographic and spatial expansion since ca. 0.15 Ma. It coincides with the terminal stage of MIS-6, i.e., Wartanian/Saalian glaciation, and beginning of MIS-5e, i.e., Eemian interglacial, during which, due to eustatic sea level rise, a wide connection between Mediterranean and the Pontic basin was re-established. This, along with re-appearance of coastal habitats could initiate north-east expansion of the southern lineage and its secondary contact with the northern one. The isolation of the Pontic basin from the Mediterranean during the Weichselian glaciation most likely did not have any effect on their phylogeography. creator: Radomir Jaskuła creator: Tomasz Rewicz creator: Mateusz Płóciennik creator: Michał Grabowski uri: https://doi.org/10.7717/peerj.2128 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jaskuła et al. title: Constant and seasonal drivers of bird communities in a wind farm: implications for conservation link: https://peerj.com/articles/2105 last-modified: 2016-07-19 description: Background. One of the most difficult challenges for conservation biology is to reconcile growing human demands for resources with the rising need for protecting nature. Wind farms producing renewable energy have been recognised to be a threat for birds, but clear directives for environmental planning are still missing.Methods. Point counts were performed to study the relationship between eight environmental variables and bird populations in different parts of a year on the largest Polish wind farm between March 2011 and February 2013. Variables potentially related to species richness (Chao 1 estimator) and the abundance of the entire bird community as well as five selected farmland species were analysed with the use of generalized linear mixed models.Results. Some associations between the studied variables and bird populations were season/year specific, while others had a constant direction (positive or negative) across seasons and/or years. The latter were distance to the nearest turbine, field size, number of wind turbines, proximity of settlements and water bodies. Spatial autocorrelation and counting time were significantly correlated with bird population estimates but the directions of these relationships varied among seasons and years. Associations between abundance of individual species and environmental variables were species-specific.Conclusions. The results demonstrated a constant negative relationship between wind turbine proximity and bird numbers. Other environmental variables, such as field size, proximity of settlements and water bodies that also had constant associations with bird populations across seasons may be taken into account when minimizing adverse effects of wind farm development on birds or choosing optimal locations of new turbines. creator: Zuzanna M. Rosin creator: Piotr Skórka creator: Paweł Szymański creator: Marcin Tobolka creator: Andrzej Luczak creator: Piotr Tryjanowski uri: https://doi.org/10.7717/peerj.2105 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rosin et al. title: Acceptance of the German e-mental health portal www.psychenet.de: an online survey link: https://peerj.com/articles/2093 last-modified: 2016-07-19 description: Background. Taking into account the high prevalence of mental disorders and the multiple barriers to the use of mental health services, new forms of fostering patient information, involvement, and self-management are needed to complement existing mental health services. The study aimed at investigating acceptance regarding design and content of the e-mental health portal www.psychenet.de.Methods. An online cross-sectional survey was conducted between May 2013 and May 2015 using a self-administered questionnaire including items on perceived ease of use, perceived usefulness, attitude towards using, and perceived trust. Effects of different participants’ characteristics on the portals’ acceptance were analyzed.Results. The majority of the N = 252 respondents suffered from mental disorders (n = 139) or were relatives from persons with mental disorders (n = 65). The portal was assessed as “good” or “very good” by 71% of the respondents. High levels of agreement (89–96%) were shown for statements on the perceived ease of use, the behavioral intention to use the portal, and the trustworthiness of the portal. Lower levels of agreement were shown for some statements on the perceived usefulness of the portals’ content. There were no effects of different participants’ characteristics on the perceived ease of use, the perceived usefulness, the attitude towards using the website and the perceived trust.Discussion. This survey provides preliminary evidence that the e-mental health portal www.psychenet.de appears to be a usable, useful and trustworthy information resource for a broad target group. The behavioral usefulness of the portals’ content might be improved by integrating more activating patient decision aids. creator: Lisa Tlach creator: Juliane Thiel creator: Martin Härter creator: Sarah Liebherz creator: Jörg Dirmaier uri: https://doi.org/10.7717/peerj.2093 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tlach et al. title: A simple, sufficient, and consistent method to score the status of threats and demography of imperiled species link: https://peerj.com/articles/2230 last-modified: 2016-07-14 description: Managers of large, complex wildlife conservation programs need information on the conservation status of each of many species to help strategically allocate limited resources. Oversimplifying status data, however, runs the risk of missing information essential to strategic allocation. Conservation status consists of two components, the status of threats a species faces and the species’ demographic status. Neither component alone is sufficient to characterize conservation status. Here we present a simple key for scoring threat and demographic changes for species using detailed information provided in free-form textual descriptions of conservation status. This key is easy to use (simple), captures the two components of conservation status without the cost of more detailed measures (sufficient), and can be applied by different personnel to any taxon (consistent). To evaluate the key’s utility, we performed two analyses. First, we scored the threat and demographic status of 37 species recently recommended for reclassification under the Endangered Species Act (ESA) and 15 control species, then compared our scores to two metrics used for decision-making and reports to Congress. Second, we scored the threat and demographic status of all non-plant ESA-listed species from Florida (54 spp.), and evaluated scoring repeatability for a subset of those. While the metrics reported by the U.S. Fish and Wildlife Service (FWS) are often consistent with our scores in the first analysis, the results highlight two problems with the oversimplified metrics. First, we show that both metrics can mask underlying demographic declines or threat increases; for example, ∼40% of species not recommended for reclassification had changes in threats or demography. Second, we show that neither metric is consistent with either threats or demography alone, but conflates the two. The second analysis illustrates how the scoring key can be applied to a substantial set of species to understand overall patterns of ESA implementation. The scoring repeatability analysis shows promise, but indicates thorough training will be needed to ensure consistency. We propose that large conservation programs adopt our simple scoring system for threats and demography. By doing so, program administrators will have better information to monitor program effectiveness and guide their decisions. creator: Jacob W. Malcom creator: Whitney M. Webber creator: Ya-Wei Li uri: https://doi.org/10.7717/peerj.2230 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Malcom et al. title: Comparison of buckwheat, red clover, and purple tansy as potential surrogate plants for use in semi-field pesticide risk assessments with Bombus impatiens link: https://peerj.com/articles/2228 last-modified: 2016-07-14 description: Background. Bumble bees (Bombus spp.) are important wild and managed pollinators. There is increased interest in incorporating data on bumble bees into risk assessments for pesticides, but standardized methods for assessing hazards of pesticides in semi-field and field settings have not yet been established for bumble bees. During semi-field studies, colonies are caged with pesticide-treated flowering surrogate plants, which must be attractive to foragers to ensure colony exposure to the test compound, and must produce an ample nectar and pollen to sustain colonies during testing. However, it is not known which plant(s) are suitable for use in semi-field studies with bumble bees.Materials and Methods. We compared B. impatiens foraging activity and colony development on small plots of flowering buckwheat (Fagopyrum esculentum, var. common), red clover (Trifolium pratense), and purple tansy (Phacelia tanacetifolia) under semi-field conditions to assess their suitability as surrogate plants for pesticide risk assessment studies with bumble bees. We also compared the growth characteristics and input requirements of each plant type.Results. All three plant types generally established and grew well. Red clover and purple tansy experienced significant weed pressure and/or insect pest damage. In contrast, pest pressure was extremely low in buckwheat. Overall, B. impatiens foraging activity was significantly greater on buckwheat plots than red clover or purple tansy, but plant type had no effect on number of individuals produced per colony or colony weight.Discussion. Because of the consistently high foraging activity and successful colony development observed on buckwheat plots, combined with its favourable growth characteristics and low maintenance requirements, we recommend buckwheat as a surrogate plant for use in semi-field pesticide toxicity assessments with B. impatiens. creator: Angela E. Gradish creator: G. Christopher Cutler creator: Andrew J. Frewin creator: Cynthia D. Scott-Dupree uri: https://doi.org/10.7717/peerj.2228 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gradish et al. title: Meter scale variation in shrub dominance and soil moisture structure Arctic arthropod communities link: https://peerj.com/articles/2224 last-modified: 2016-07-14 description: The Arctic is warming at twice the rate of the rest of the world. This impacts Arctic species both directly, through increased temperatures, and indirectly, through structural changes in their habitats. Species are expected to exhibit idiosyncratic responses to structural change, which calls for detailed investigations at the species and community level. Here, we investigate how arthropod assemblages of spiders and beetles respond to variation in habitat structure at small spatial scales. We sampled transitions in shrub dominance and soil moisture between three different habitats (fen, dwarf shrub heath, and tall shrub tundra) at three different sites along a fjord gradient in southwest Greenland, using yellow pitfall cups. We identified 2,547 individuals belonging to 47 species. We used species richness estimation, indicator species analysis and latent variable modeling to examine differences in arthropod community structure in response to habitat variation at local (within site) and regional scales (between sites). We estimated species responses to the environment by fitting species-specific generalized linear models with environmental covariates. Species assemblages were segregated at the habitat and site level. Each habitat hosted significant indicator species, and species richness and diversity were significantly lower in fen habitats. Assemblage patterns were significantly linked to changes in soil moisture and vegetation height, as well as geographic location. We show that meter-scale variation among habitats affects arthropod community structure, supporting the notion that the Arctic tundra is a heterogeneous environment. To gain sufficient insight into temporal biodiversity change, we require studies of species distributions detailing species habitat preferences. creator: Rikke Reisner Hansen creator: Oskar Liset Pryds Hansen creator: Joseph J. Bowden creator: Urs A. Treier creator: Signe Normand creator: Toke Høye uri: https://doi.org/10.7717/peerj.2224 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hansen et al. title: Molecular characterization of an adiponectin receptor homolog in the white leg shrimp, Litopenaeus vannamei link: https://peerj.com/articles/2221 last-modified: 2016-07-14 description: Adiponectin (AdipoQ) and its receptors (AdipoRs) are strongly related to growth and development of skeletal muscle, as well as glucose and lipid metabolism in vertebrates. Herein we report the identification of the first full-length cDNA encoding an AdipoR homolog (Liv-AdipoR) from the decapod crustacean Litopenaeus vannamei using a combination of next generation sequencing (NGS) technology and bioinformatics analysis. The full-length Liv-AdipoR (1,245 bp) encoded a protein that exhibited the canonical seven transmembrane domains (7TMs) and the inversed topology that characterize members of the progestin and adipoQ receptor (PAQR) family. Based on the obtained sequence information, only a single orthologous AdipoR gene appears to exist in arthropods, whereas two paralogs, AdipoR1 and AdipoR2, have evolved in vertebrates. Transcriptional analysis suggested that the single Liv-AdipoR gene appears to serve the functions of two mammalian AdipoRs. At 72 h after injection of 50 pmol Liv-AdipoR dsRNA (340 bp) into L. vannamei thoracic muscle and deep abdominal muscle, transcription levels of Liv-AdipoR decreased by 93% and 97%, respectively. This confirmed optimal conditions for RNAi of Liv-AdipoR. Knockdown of Liv-AdipoR resulted in significant changes in the plasma levels of ammonia, 3-methylhistine, and ornithine, but not plasma glucose, suggesting that that Liv-AdipoR is important for maintaining muscle fibers. The chronic effect of Liv-AdipoR dsRNA injection was increased mortality. Transcriptomic analysis showed that 804 contigs were upregulated and 212 contigs were downregulated by the knockdown of Liv-AdipoR in deep abdominal muscle. The significantly upregulated genes were categorized as four main functional groups: RNA-editing and transcriptional regulators, molecular chaperones, metabolic regulators, and channel proteins. creator: Ah Ran Kim creator: Md Jobaidul Alam creator: Tae-ho Yoon creator: Soo Rin Lee creator: Hyun Park creator: Doo-Nam Kim creator: Doo-Hae An creator: Jae-Bong Lee creator: Chung Il Lee creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.2221 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kim et al. title: ­A practical application of reduced-copper antifouling paint in marine biological research link: https://peerj.com/articles/2213 last-modified: 2016-07-14 description: Biofouling of experimental cages and other field apparatuses can be problematic for scientists and has traditionally been addressed using frequent manual removal (e.g., scraping, scrubbing). Recent environmental restrictions and legislative changes have driven the development of less hazardous antifouling products, making antifouling paint a potential alternative option to manual removal. Consequently, the viability of using these newly developed products as a replacement for the manual cleaning of exclusion cages was experimentally investigated. There were six treatments tested, comprising three with settlement tiles in experimental cages coated with antifouling paint, two with settlement tiles in unpainted experimental cages, and one cage-free suspended tile. The three antifouling treatments comprised two reduced-copper paints (21% Cu2O and 40% Cu2O) and one copper-free, Econea™-based paint (labeled “ecofriendly”). Antifouling paints were assessed for performance of preventing fouling of the cages and whether they elicited local effects on settlement tiles contained within them. All three paints performed well to reduce fouling of the cages during the initial six weeks of the experiment, but the efficacy of “ecofriendly” paint began to decrease during an extended deployment that lasted 14 weeks. The macro-community composition, biomass, and percent cover of settled organism on tiles within cages treated with copper-based paints (21% and 40% concentrations) were indistinguishable from tiles within the manually scrubbed cages. In contrast, settlement to tiles from the “ecofriendly” treatment was different in composition of macro-community and lower in biomass, suggesting the presence of local effects and therefore rendering it unsuitable for use in settlement experiments. The results of this study suggest that reduced-copper paints have the potential to serve as an alternative to manual maintenance, which may be useful for deployments in locations that are difficult to access on a frequent schedule. creator: Andrea S. Jerabek creator: Kara R. Wall creator: Christopher D. Stallings uri: https://doi.org/10.7717/peerj.2213 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jerabek et al. title: Human population and socioeconomic modulators of conservation performance in 788 Amazonian and Atlantic Forest reserves link: https://peerj.com/articles/2206 last-modified: 2016-07-14 description: Protected areas form a quintessential component of the global strategy to perpetuate tropical biodiversity within relatively undisturbed wildlands, but they are becoming increasingly isolated by rapid agricultural encroachment. Here we consider a network of 788 forest protected areas (PAs) in the world’s largest tropical country to examine the degree to which they remain intact, and their responses to multiple biophysical and socioeconomic variables potentially affecting natural habitat loss under varying contexts of rural development. PAs within the complex Brazilian National System of Conservation Units (SNUC) are broken down into two main classes—strictly protected and sustainable use. Collectively, these account for 22.6% of the forest biomes within Brazil’s national territory, primarily within the Amazon and the Atlantic Forest, but are widely variable in size, ecoregional representation, management strategy, and the degree to which they are threatened by human activities both within and outside reserve boundaries. In particular, we examine the variation in habitat conversion rates in both strictly protected and sustainable use reserves as a function of the internal and external human population density, and levels of land-use revenue in adjacent human-dominated landscapes. Our results show that PAs surrounded by heavily settled agro-pastoral landscapes face much greater challenges in retaining their natural vegetation, and that strictly protected areas are considerably less degraded than sustainable use reserves, which can rival levels of habitat degradation within adjacent 10-km buffer areas outside. creator: Ana Alice B. de Marques creator: Mauricio Schneider creator: Carlos A. Peres uri: https://doi.org/10.7717/peerj.2206 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 De Marques et al. title: Association between aberrant APC promoter methylation and breast cancer pathogenesis: a meta-analysis of 35 observational studies link: https://peerj.com/articles/2203 last-modified: 2016-07-14 description: Background. Adenomatous polyposis coli (APC) is widely known as an antagonist of the Wnt signaling pathway via the inactivation of β-catenin. An increasing number of studies have reported that APC methylation contributes to the predisposition to breast cancer (BC). However, recent studies have yielded conflicting results.Methods. Herein, we systematically carried out a meta-analysis to assess the correlation between APC methylation and BC risk. Based on searches of the Cochrane Library, PubMed, Web of Science and Embase databases, the odds ratio (OR) with 95% confidence interval (CI) values were pooled and summarized.Results. A total of 31 articles involving 35 observational studies with 2,483 cases and 1,218 controls met the inclusion criteria. The results demonstrated that the frequency of APC methylation was significantly higher in BC cases than controls under a random effect model (OR = 8.92, 95% CI [5.12–15.52]). Subgroup analysis further confirmed the reliable results, regardless of the sample types detected, methylation detection methods applied and different regions included. Interestingly, our results also showed that the frequency of APC methylation was significantly lower in early-stage BC patients than late-stage ones (OR = 0.62, 95% CI [0.42–0.93]).Conclusion. APC methylation might play an indispensable role in the pathogenesis of BC and could be regarded as a potential biomarker for the diagnosis of BC. creator: Dan Zhou creator: Weiwei Tang creator: Wenyi Wang creator: Xiaoyan Pan creator: Han-Xiang An creator: Yun Zhang uri: https://doi.org/10.7717/peerj.2203 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhou et al. title: Transcription factor organic cation transporter 1 (OCT-1) affects the expression of porcine Klotho (KL) gene link: https://peerj.com/articles/2186 last-modified: 2016-07-14 description: Klotho (KL), originally discovered as an aging suppressor, is a membrane protein that shares sequence similarity with the β-glucosidase enzymes. Recent reports showed Klotho might play a role in adipocyte maturation and systemic glucose metabolism. However, little is known about the transcription factors involved in regulating the expression of porcine KL gene. Deletion fragment analysis identified KL-D2 (−418 bp to −3 bp) as the porcine KL core promoter. MARC0022311SNP (A or G) in KL intron 1 was detected in Landrace × DIV pigs using the Porcine SNP60 BeadChip. The pGL-D2-A and pGL-D2-G were constructed with KL-D2 and the intron fragment of different alleles and relative luciferase activity of pGL3-D2-G was significantly higher than that of pGL3-D2-A in the PK cells and ST cells. This was possibly the result of a change in KL binding ability with transcription factor organic cation transporter 1 (OCT-1), which was confirmed using electrophoretic mobility shift assays (EMSA) and chromatin immune-precipitation (ChIP). Moreover, OCT-1 regulated endogenous KL expression by RNA interference experiments. Our study indicates SNP MARC0022311 affects porcine KL expression by regulating its promoter activity via OCT-1. creator: Yan Li creator: Lei Wang creator: Jiawei Zhou creator: Fenge Li uri: https://doi.org/10.7717/peerj.2186 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Li et al. title: Quantification of coral sperm collected during a synchronous spawning event link: https://peerj.com/articles/2180 last-modified: 2016-07-14 description: Most studies of coral reproductive biology to date have focused on oocyte numbers and sizes. Only one (ex situ) study has enumerated sperm numbers, even though these data have multiple potential applications. We quantified total coral sperm and eggs per gamete bundle collected from six species in situ during a synchronous spawning event in Singapore. Egg-sperm bundles were captured midwater as they floated towards the surface after being released by the colony. For each sample, a semi-transparent soft plastic bottle was squeezed and released to create a small suction force that was used to ‘catch’ the bundles. This technique provided several advantages over traditional methods, including low cost, ease of use, no diving prior to the night of collection needed, and the ability to target specific areas of the colony. The six species sampled were Echinophyllia aspera, Favites abdita, F. chinensis, Merulina ampliata, M. scabricula and Platygyra pini. The mean number of sperm packaged within one egg-sperm bundle ranged from 2.04 × 106 to 1.93 × 107. The mean number of eggs per egg-sperm bundle ranged from 26.67 (SE ± 3.27) to 85.33 (SE ± 17.79). These data are critical for fertilisation success models, but the collection technique described could also be applied to studies requiring in situ spawning data at the polyp level. creator: Aaron Teo creator: James R. Guest creator: Mei Lin Neo creator: Kareen Vicentuan creator: Peter A. Todd uri: https://doi.org/10.7717/peerj.2180 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Teo et al. title: Characterization of a biofilm-forming Shigella flexneri phenotype due to deficiency in Hep biosynthesis link: https://peerj.com/articles/2178 last-modified: 2016-07-14 description: Deficiency in biosynthesis of inner core of lipopolysaccharide (LPS) rendered a characteristic biofilm-forming phenotype in E. coli. The pathological implications of this new phenotype in Shigella flexneri, a highly contagious enteric Gram-negative bacteria that is closely related to E. coli, were investigated in this study. The ΔrfaC (also referred as waaC) mutant, with incomplete inner core of LPS due to deficiency in Hep biosynthesis, was characteristic of strong biofilm formation ability and exhibited much more pronounced adhesiveness and invasiveness to human epithelial cells than the parental strain and other LPS mutants, which also showed distinct pattern of F-actin recruitment. Failure to cause keratoconjunctivitis and colonize in the intestine in guinea pigs revealed that the fitness gain on host adhesion resulted from biofilm formation is not sufficient to offset the loss of fitness on survivability caused by LPS deletion. Our study suggests a clear positive relationship between increased surface hydrophobicity and adhesiveness of Shigella flexneri, which should be put into consideration of virulence of Shigella, especially when therapeutic strategy targeting the core oligosaccharide (OS) is considered an alternative to deal with bacterial antibiotics-resistance. creator: Dan Xu creator: Wei Zhang creator: Bing Zhang creator: Chongbing Liao creator: Yongping Shao uri: https://doi.org/10.7717/peerj.2178 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Xu et al. title: A preliminary case study of the effect of shoe-wearing on the biomechanics of a horse’s foot link: https://peerj.com/articles/2164 last-modified: 2016-07-14 description: Horse racing is a multi-billion-dollar industry that has raised welfare concerns due to injured and euthanized animals. Whilst the cause of musculoskeletal injuries that lead to horse morbidity and mortality is multifactorial, pre-existing pathologies, increased speeds and substrate of the racecourse are likely contributors to foot disease. Horse hooves have the ability to naturally deform during locomotion and dissipate locomotor stresses, yet farriery approaches are utilised to increase performance and protect hooves from wear. Previous studies have assessed the effect of different shoe designs on locomotor performance; however, no biomechanical study has hitherto measured the effect of horseshoes on the stresses of the foot skeleton in vivo. This preliminary study introduces a novel methodology combining three-dimensional data from biplanar radiography with inverse dynamics methods and finite element analysis (FEA) to evaluate the effect of a stainless steel shoe on the function of a Thoroughbred horse’s forefoot during walking. Our preliminary results suggest that the stainless steel shoe shifts craniocaudal, mediolateral and vertical GRFs at mid-stance. We document a similar pattern of flexion-extension in the PIP (pastern) and DIP (coffin) joints between the unshod and shod conditions, with slight variation in rotation angles throughout the stance phase. For both conditions, the PIP and DIP joints begin in a flexed posture and extend over the entire stance phase. At mid-stance, small differences in joint angle are observed in the PIP joint, with the shod condition being more extended than the unshod horse, whereas the DIP joint is extended more in the unshod than the shod condition. We also document that the DIP joint extends more than the PIP after mid-stance and until the end of the stance in both conditions. Our FEA analysis, conducted solely on the bones, shows increased von Mises and Maximum principal stresses on the forefoot phalanges in the shod condition at mid-stance, consistent with the tentative conclusion that a steel shoe might increase mechanical loading. However, because of our limited sample size none of these apparent differences have been tested for statistical significance. Our preliminary study illustrates how the shoe may influence the dynamics and mechanics of a Thoroughbred horse’s forefoot during slow walking, but more research is needed to quantify the effect of the shoe on the equine forefoot during the whole stance phase, at faster speeds/gaits and with more individuals as well as with a similar focus on the hind feet. We anticipate that our preliminary analysis using advanced methodological approaches will pave the way for new directions in research on the form/function relationship of the equine foot, with the ultimate goal to minimise foot injuries and improve animal health and welfare. creator: Olga Panagiotopoulou creator: Jeffery W. Rankin creator: Stephen M. Gatesy creator: John R. Hutchinson uri: https://doi.org/10.7717/peerj.2164 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Panagiotopoulou et al. title: Characterizing abnormal behavior in a large population of zoo-housed chimpanzees: prevalence and potential influencing factors link: https://peerj.com/articles/2225 last-modified: 2016-07-13 description: Abnormal behaviors in captive animals are generally defined as behaviors that are atypical for the species and are often considered to be indicators of poor welfare. Although some abnormal behaviors have been empirically linked to conditions related to elevated stress and compromised welfare in primates, others have little or no evidence on which to base such a relationship. The objective of this study was to investigate a recent claim that abnormal behavior is endemic in the captive population by surveying a broad sample of chimpanzees (Pan troglodytes), while also considering factors associated with the origins of these behaviors. We surveyed animal care staff from 26 accredited zoos to assess the prevalence of abnormal behavior in a large sample of chimpanzees in the United States for which we had information on origin and rearing history. Our results demonstrated that 64% of this sample was reported to engage in some form of abnormal behavior in the past two years and 48% of chimpanzees engaged in abnormal behavior other than coprophagy. Logistic regression models were used to analyze the historical variables that best predicted the occurrence of all abnormal behavior, any abnormal behavior that was not coprophagy, and coprophagy. Rearing had opposing effects on the occurrence of coprophagy and the other abnormal behaviors such that mother-reared individuals were more likely to perform coprophagy, whereas non-mother-reared individuals were more likely to perform other abnormal behaviors. These results support the assertion that coprophagy may be classified separately when assessing abnormal behavior and the welfare of captive chimpanzees. This robust evaluation of the prevalence of abnormal behavior in our sample from the U.S. zoo population also demonstrates the importance of considering the contribution of historical variables to present behavior, in order to better understand the causes of these behaviors and any potential relationship to psychological wellbeing. creator: Sarah L. Jacobson creator: Stephen R. Ross creator: Mollie A. Bloomsmith uri: https://doi.org/10.7717/peerj.2225 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Jacobson et al. title: Dominant forest tree species are potentially vulnerable to climate change over large portions of their range even at high latitudes link: https://peerj.com/articles/2218 last-modified: 2016-07-13 description: Projecting suitable conditions for a species as a function of future climate provides a reasonable, although admittedly imperfect, spatially explicit estimate of species vulnerability associated with climate change. Projections emphasizing range shifts at continental scale, however, can mask contrasting patterns at local or regional scale where management and policy decisions are made. Moreover, models usually show potential for areas to become climatically unsuitable, remain suitable, or become suitable for a particular species with climate change, but each of these outcomes raises markedly different ecological and management issues. Managing forest decline at sites where climatic stress is projected to increase is likely to be the most immediate challenge resulting from climate change. Here we assess habitat suitability with climate change for five dominant tree species of eastern North American forests, focusing on areas of greatest vulnerability (loss of suitability in the baseline range) in Quebec (Canada) rather than opportunities (increase in suitability). Results show that these species are at risk of maladaptation over a remarkably large proportion of their baseline range. Depending on species, 5–21% of currently climatically suitable habitats are projected to be at risk of becoming unsuitable. This suggests that species that have traditionally defined whole regional vegetation assemblages could become less adapted to these regions, with significant impact on ecosystems and forest economy. In spite of their well-recognised limitations and the uncertainty that remains, regionally-explicit risk assessment approaches remain one of the best options to convey that message and the need for climate policies and forest management adaptation strategies. creator: Catherine Périé creator: Sylvie de Blois uri: https://doi.org/10.7717/peerj.2218 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Périé and De Blois title: HIV/STIs risks between migrant MSM and local MSM: a cross-sectional comparison study in China link: https://peerj.com/articles/2169 last-modified: 2016-07-13 description: Background. Internal migration plays a significant role in China’s HIV epidemic. However, few studies have directly compared migrant men who have sex with men (MSM) with local MSM with regard to HIV/sexually transmitted infections (STIs) risks.Methods. We conducted a study in Guangzhou, China, with the aim of understanding the differences in HIV/STIs risks between migrant MSM and local MSM. A cross-sectional study was conducted among 273 migrant MSM and 249 local MSM in Guangzhou, China. Their behavioral and serologic data on HIV/syphilis were collected and compared between the two groups. A multivariate logistic regression was used to estimate the associations between HIV/STIs risks and migratory status.Results. Migrant MSM, compared to local MSM, have higher odds of reporting unprotected anal intercourse (UAI) (OR = 1.4; 95% CI [0.9–2.0]) and having multiple homosexual partners (OR = 1.2; 95% CI [0.8–1.8]). A lower rate of condom use at homosexual debut was reported in migrant MSM than in local MSM (OR = 0.7; 95% CI [0.5–0.9]). Migrant MSM have less odds of reporting HIV/STIs testing in the previous 6 months relative to local MSM (OR = 0.5; 95% CI [0.4–0.8]). In addition, migrant MSM demonstrated a lower level of HIV knowledge than local MSM (OR = 0.4; 95% CI [0.2–0.8]).Conclusion. Migrant MSM are more likely to engage in sexual risk behaviors, report a lower level of HIV knowledge and have less access to HIV/STIs testing. Further comprehensive interventions targeting migrant MSM are urged. creator: Jie Wu creator: Hong Wu creator: Pengsheng Li creator: Ciyong Lu uri: https://doi.org/10.7717/peerj.2169 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wu et al. title: New insight into the role of MMP14 in metabolic balance link: https://peerj.com/articles/2142 last-modified: 2016-07-13 description: Membrane-anchored matrix metalloproteinase 14 (MMP14) is involved broadly in organ development through both its proteolytic and signal-transducing functions. Knockout of Mmp14 (KO) in mice results in a dramatic reduction of body size and wasting followed by premature death, the mechanism of which is poorly understood. Since the mammary gland develops after birth and is thus dependent for its functional progression on systemic and local cues, we chose it as an organ model for understanding why KO mice fail to thrive. A global analysis of the mammary glands’ proteome in the wild type (WT) and KO mice provided insight into an unexpected role of MMP14 in maintaining metabolism and homeostasis. We performed mass spectrometry and quantitative proteomics to determine the protein signatures of mammary glands from 7 to 11 days old WT and KO mice and found that KO rudiments had a significantly higher level of rate-limiting enzymes involved in catabolic pathways. Glycogen and lipid levels in KO rudiments were reduced, and the circulating levels of triglycerides and glucose were lower. Analysis of the ultrastructure of mammary glands imaged by electron microscopy revealed a significant increase in autophagy signatures in KO mice. Finally, Mmp14 silenced mammary epithelial cells displayed enhanced autophagy. Applied to a systemic level, these findings indicate that MMP14 is a crucial regulator of tissue homeostasis. If operative on a systemic level, these findings could explain how Mmp14KO litter fail to thrive due to disorder in metabolism. creator: Hidetoshi Mori creator: Ramray Bhat creator: Alexandre Bruni-Cardoso creator: Emily I. Chen creator: Danielle M. Jorgens creator: Kester Coutinho creator: Katherine Louie creator: Benjamin Ben Bowen creator: Jamie L. Inman creator: Victoria Tecca creator: Sarah J. Lee creator: Sabine Becker-Weimann creator: Trent Northen creator: Motoharu Seiki creator: Alexander D. Borowsky creator: Manfred Auer creator: Mina J. Bissell uri: https://doi.org/10.7717/peerj.2142 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Mori et al. title: Applicability of the ReproQ client experiences questionnaire for quality improvement in maternity care link: https://peerj.com/articles/2092 last-modified: 2016-07-13 description: Background. The ReproQuestionnaire (ReproQ) measures the client’s experience with maternity care, following the WHO responsiveness model. In 2015, the ReproQ was appointed as national client experience questionnaire and will be added to the national list of indicators in maternity care. For using the ReproQ in quality improvement, the questionnaire should be able to identify best and worst practices. To achieve this, ReproQ should be reliable and able to identify relevant differences.Methods and Findings. We sent questionnaires to 17,867 women six weeks after labor (response 32%). Additionally, we invited 915 women for the retest (response 29%). Next we determined the test–retest reliability, the Minimally Important Difference (MID) and six known group comparisons, using two scorings methods: the percentage women with at least one negative experience and the mean score. The reliability for the percentage negative experience and mean score was both ‘good’ (Absolute agreement = 79%; intraclass correlation coefficient = 0.78). The MID was 11% for the percentage negative and 0.15 for the mean score. Application of the MIDs revealed relevant differences in women’s experience with regard to professional continuity, setting continuity and having travel time.Conclusions. The measurement characteristics of the ReproQ support its use in quality improvement cycle. Test–retest reliability was good, and the observed minimal important difference allows for discrimination of good and poor performers, also at the level of specific features of performance. creator: Marisja Scheerhagen creator: Henk F. van Stel creator: Dominique J.C. Tholhuijsen creator: Erwin Birnie creator: Arie Franx creator: Gouke J. Bonsel uri: https://doi.org/10.7717/peerj.2092 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Scheerhagen et al. title: Behavioral flexibility in an invasive bird is independent of other behaviors link: https://peerj.com/articles/2215 last-modified: 2016-07-12 description: Behavioral flexibility is considered important for a species to adapt to environmental change. However, it is unclear how behavioral flexibility works: it relates to problem solving ability and speed in unpredictable ways, which leaves an open question of whether behavioral flexibility varies with differences in other behaviors. If present, such correlations would mask which behavior causes individuals to vary. I investigated whether behavioral flexibility (reversal learning) performances were linked with other behaviors in great-tailed grackles, an invasive bird. I found that behavioral flexibility did not significantly correlate with neophobia, exploration, risk aversion, persistence, or motor diversity. This suggests that great-tailed grackle performance in behavioral flexibility tasks reflects a distinct source of individual variation. Maintaining multiple distinct sources of individual variation, and particularly variation in behavioral flexibility, may be a mechanism for coping with the diversity of novel elements in their environments and facilitate this species’ invasion success. creator: Corina J. Logan uri: https://doi.org/10.7717/peerj.2215 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Logan title: Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau link: https://peerj.com/articles/2226 last-modified: 2016-07-12 description: Background: The Qinghai-Tibet Plateau (QTP) is home to the vast grassland in China. The QTP grassland ecosystem has been seriously degraded by human land use practices and climate change. Fertilization is used in this region to increase vegetation yields for grazers. The impact of long-term fertilization on plant and microbial communities has been studied extensively. However, the influence of short-term fertilization on arbuscular mycorrhizal fungal (AMF) communities in the QTP is largely unknown, despite their important functional role in grassland ecosystems.Methods: We investigated AMF community responses to three years of N and/or P addition at an experimental field site on the QTP, using the Illumina MiSeq platform (PE 300).Results: Fertilization resulted in a dramatic shift in AMF community composition and NP addition significantly increased AMF species richness and phylogenetic diversity. Aboveground biomass, available phosphorus, and NO3− were significantly correlated with changes in AMF community structure. Changes in these factors were driven by fertilization treatments. Thus, fertilization had a large impact on AMF communities, mediated by changes in aboveground productivity and soil chemistry.Discussion: Prior work has shown how plants often lower their reliance on AMF symbioses following fertilization, leading to decrease AMF abundance and diversity. However, our study reports a rise in AMF diversity with fertilization treatment. Because AMF can provide stress tolerance to their hosts, we suggest that extreme weather on the QTP may help drive a positive relationship between fertilizer amendment and AMF diversity. creator: Xingjia Xiang creator: Sean M. Gibbons creator: Jin-Sheng He creator: Chao Wang creator: Dan He creator: Qian Li creator: Yingying Ni creator: Haiyan Chu uri: https://doi.org/10.7717/peerj.2226 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Xiang et al. title: Shades of yellow: interactive effects of visual and odour cues in a pest beetle link: https://peerj.com/articles/2219 last-modified: 2016-07-12 description: Background: The visual ecology of pest insects is poorly studied compared to the role of odour cues in determining their behaviour. Furthermore, the combined effects of both odour and vision on insect orientation are frequently ignored, but could impact behavioural responses.Methods: A locomotion compensator was used to evaluate use of different visual stimuli by a major coleopteran pest of stored grains (Sitophilus zeamais), with and without the presence of host odours (known to be attractive to this species), in an open-loop setup.Results: Some visual stimuli—in particular, one shade of yellow, solid black and high-contrast black-against-white stimuli—elicited positive orientation behaviour from the beetles in the absence of odour stimuli. When host odours were also present, at 90° to the source of the visual stimulus, the beetles presented with yellow and vertical black-on-white grating patterns changed their walking course and typically adopted a path intermediate between the two stimuli. The beetles presented with a solid black-on-white target continued to orient more strongly towards the visual than the odour stimulus.Discussion: Visual stimuli can strongly influence orientation behaviour, even in species where use of visual cues is sometimes assumed to be unimportant, while the outcomes from exposure to multimodal stimuli are unpredictable and need to be determined under differing conditions. The importance of the two modalities of stimulus (visual and olfactory) in food location is likely to depend upon relative stimulus intensity and motivational state of the insect. creator: Sarah E.J. Arnold creator: Philip C. Stevenson creator: Steven R. Belmain uri: https://doi.org/10.7717/peerj.2219 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Arnold et al. title: Hierarchical organization of a Sardinian sand dune plant community link: https://peerj.com/articles/2199 last-modified: 2016-07-12 description: Coastal sand dunes have attracted the attention of plant ecologists for over a century, but they have largely relied on correlations to explain dune plant community organization. We examined long-standing hypotheses experimentally that sand binding, inter-specific interactions, abiotic factors and seedling recruitment are drivers of sand dune plant community structure in Sardinia, Italy. Removing foundation species from the fore-, middle- and back-dune habitats over three years led to erosion and habitat loss on the fore-dune and limited plant recovery that increased with dune elevation. Reciprocal species removals in all zones suggested that inter-specific competition is common, but that dominance is transient, particularly due to sand burial disturbance in the middle-dune. A fully factorial 2-year manipulation of water, nutrient availability and substrate stability revealed no significant proximate response to these physical factors in any dune zone. In the fore- and middle-dune, plant seeds are trapped under adult plants during seed germination, and seedling survivorship and growth generally increase with dune height in spite of increased herbivory in the back-dune. Sand and seed erosion leads to limited seed recruitment on the fore-dune while high summer temperatures and preemption of space lead to competitive dominance of woody plants in the back-dune. Our results suggest that Sardinian sand dune plant communities are organized hierarchically, structured by sand binding foundation species on the fore-dune, sand burial in the middle-dune and increasingly successful seedling recruitment, growth and competitive dominance in the back-dune. creator: Valentina Cusseddu creator: Giulia Ceccherelli creator: Mark Bertness uri: https://doi.org/10.7717/peerj.2199 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Cusseddu et al. title: How smartphone usage correlates with social anxiety and loneliness link: https://peerj.com/articles/2197 last-modified: 2016-07-12 description: Introduction: Early detection of social anxiety and loneliness might be useful to prevent substantial impairment in personal relationships. Understanding the way people use smartphones can be beneficial for implementing an early detection of social anxiety and loneliness. This paper examines different types of smartphone usage and their relationships with people with different individual levels of social anxiety or loneliness.Methods: A total of 127 Android smartphone volunteers participated in this study, all of which have agreed to install an application (MobileSens) on their smartphones, which can record user’s smartphone usage behaviors and upload the data into the server. They were instructed to complete an online survey, including the Interaction Anxiousness Scale (IAS) and the University of California Los Angeles Loneliness Scale (UCLA-LS). We then separated participants into three groups (high, middle and low) based on their scores of IAS and UCLA-LS, respectively. Finally, we acquired digital records of smartphone usage from MobileSens and examined the differences in 105 types of smartphone usage behaviors between high-score and low-score group of IAS/UCLA-LS.Results: Individuals with different scores on social anxiety or loneliness might use smartphones in different ways. For social anxiety, compared with users in low-score group, users in high-score group had less number of phone calls (incoming and outgoing) (Mann-Whitney U = 282.50∼409.00, p < 0.05), sent and received less number of text messages in the afternoon (Mann-Whitney U = 391.50∼411.50, p < 0.05), used health & fitness apps more frequently (Mann-Whitney U = 493.00, p < 0.05) and used camera apps less frequently (Mann-Whitney U = 472.00, p < 0.05). For loneliness, users in low-score group, users in high-score group had less number of phone calls (incoming and outgoing) (Mann-Whitney U = 305.00∼407.50, p < 0.05) and used following apps more frequently: health & fitness (Mann-Whitney U = 510.00, p < 0.05), system (Mann-Whitney U = 314.00, p < 0.01), phone beautify (Mann-Whitney U = 385.00, p < 0.05), web browser (Mann-Whitney U = 416.00, p < 0.05) and social media (RenRen) (Mann-Whitney >U = 388.50, p < 0.01).Discussion: The results show that individuals with social anxiety or loneliness receive less incoming calls and use healthy applications more frequently, but they do not show differences in outgoing-call-related features. Individuals with higher levels of social anxiety also receive less SMSs and use camera apps less frequently, while lonely individuals tend to use system, beautify, browser and social media (RenRen) apps more frequently.Conclusion: This paper finds that there exists certain correlation among smartphone usage and social anxiety and loneliness. The result may be useful to improve social interaction for those who lack social interaction in daily lives and may be insightful for recognizing individual levels of social anxiety and loneliness through smartphone usage behaviors. creator: Yusong Gao creator: Ang Li creator: Tingshao Zhu creator: Xiaoqian Liu creator: Xingyun Liu uri: https://doi.org/10.7717/peerj.2197 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Gao et al. title: Different patterns of pfcrt and pfmdr1 polymorphism in Plasmodium falciparum isolates from Tehama region, Yemen link: https://peerj.com/articles/2191 last-modified: 2016-07-12 description: Introduction. Despite the efforts of the malaria control programme, malaria morbidity is still a common health problem in Yemen, with 60% of the population at risk. Plasmodium falciparum is responsible for 99% of malaria cases. The emergence in Yemen of parasite resistance to chloroquine (CQ) prompted the adoption of artemisinin combination therapy (ACT) in 2009, which involves the use of artesunate plus sulphadoxine-pyrimethamine (AS + SP). However, CQ was retained as the drug of choice for vivax malaria. To assess the impact of the change in the malaria treatment policy five years after its introduction, the present study investigated the mutations in the CQ resistance transporter (pfcrt) and multidrug resistance 1 (pfmdr1) genes.Method. A molecular investigation of 10 codons of pfcrt (72–76, 220, 271, 326, 356, and 371) and five codons of pfmdr1 (86, 184, 1034, 1042, and 1246) was conducted on P. falciparum isolates from districts with the highest malaria endemicity in the Hodeidah and Al-Mahwit governorates in Tehama region, Yemen. A total of 86 positive cases of falciparum monoinfection were investigated for the presence of mutations related to CQ and other antimalarials using a PCR-RFLP assay.Results. There was a wide prevalence of pfcrt gene mutations with the pfcrt 76T CQ resistance marker being predominant (97.7%). The prevalence of other pfcrt mutations varied from high (75E: 88%) to moderate (74I: 79.1%, 220S: 69.8%, 271E and 371I: 53.5%) or low (326S: 36%, 72S: 10.5%). Mutated pfcrt 72–76 amino acids haplotypes were highly prevalent (98.8%). Among these, the CVIET classic, old-world African/Southeast Asian haplotype was the most predominant, and was mostly found in the isolates from the Khamis Bani Saad district of Al-Mahwit (93.1%) and the AdDahi district of Hodeidah (88.9%). However, it was only found in 26.3% of the isolates from the Bajil district of Hodeidah. Surprisingly, the SVMNT new-world South American haplotype was exclusively detected in 9.3% of the isolates from the Bajil district of Hodeidah. Mutations at Y184F of pfmdr1 were found in all isolates (100%) from all districts. The mutation for codons 1034C and 86Y were found only in the isolates from the AdDahi and Khamis Bani Saad districts. Overall, the AdDahi and Khamis Bani Saad districts were similar in terms of carrying most of the mutations in the pfcrt and pfmdr1 genes, while there was a lower prevalence of mutation in the isolates from the Bajil district.Conclusion. The high prevalence of mutations in pfcrt 5 years after the official cessation of CQ use against P. falciparum suggests that there is sustained CQ pressure on P. falciparum isolates in the study area. Moreover, the low prevalence of mutations in the pfmdr1 gene could be a good indicator of the high susceptibility of P. falciparum isolates to antimalarials other than CQ. A new strategy to ensure the complete nationwide withdrawal of CQ from the private drug market is recommended. creator: Wahib M. Atroosh creator: Hesham M. Al-Mekhlafi creator: Adel Al-Jasari creator: Hany Sady creator: Salwa S. Dawaki creator: Fatin N. Elyana creator: Mona A. Al-Areeqi creator: Nabil A. Nasr creator: Awatif M. Abdulsalam creator: Lahvanya R. Subramaniam creator: Meram Azzani creator: Init Ithoi creator: Yee Ling Lau creator: Johari Surin uri: https://doi.org/10.7717/peerj.2191 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Atroosh et al. title: Members of the methanotrophic genus Methylomarinum inhabit inland mud pots link: https://peerj.com/articles/2116 last-modified: 2016-07-12 description: Proteobacteria capable of converting the greenhouse gas methane to biomass, energy, and carbon dioxide represent a small but important sink in global methane inventories. Currently, 23 genera of methane oxidizing (methanotrophic) proteobacteria have been described, although many are represented by only a single validly described species. Here we describe a new methanotrophic isolate that shares phenotypic characteristics and phylogenetic relatedness with the marine methanotroph Methylomarinum vadi. However, the new isolate derives from a terrestrial saline mud pot at the northern terminus of the Eastern Pacific Rise (EPR). This new cultivar expands our knowledge of the ecology of Methylomarinum, ultimately towards a fuller understanding of the role of this genus in global methane cycling. creator: Danielle T. Fradet creator: Patricia L. Tavormina creator: Victoria J. Orphan uri: https://doi.org/10.7717/peerj.2116 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Fradet et al. title: Food and nutritional security requires adequate protein as well as energy, delivered from whole-year crop production link: https://peerj.com/articles/2100 last-modified: 2016-07-12 description: Human food security requires the production of sufficient quantities of both high-quality protein and dietary energy. In a series of case-studies from New Zealand, we show that while production of food ingredients from crops on arable land can meet human dietary energy requirements effectively, requirements for high-quality protein are met more efficiently by animal production from such land. We present a model that can be used to assess dietary energy and quality-corrected protein production from various crop and crop/animal production systems, and demonstrate its utility. We extend our analysis with an accompanying economic analysis of commercially-available, pre-prepared or simply-cooked foods that can be produced from our case-study crop and animal products. We calculate the per-person, per-day cost of both quality-corrected protein and dietary energy as provided in the processed foods. We conclude that mixed dairy/cropping systems provide the greatest quantity of high-quality protein per unit price to the consumer, have the highest food energy production and can support the dietary requirements of the highest number of people, when assessed as all-year-round production systems. Global food and nutritional security will largely be an outcome of national or regional agroeconomies addressing their own food needs. We hope that our model will be used for similar analyses of food production systems in other countries, agroecological zones and economies. creator: Graeme D. Coles creator: Stephen D. Wratten creator: John R. Porter uri: https://doi.org/10.7717/peerj.2100 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Coles et al. title: Identification of 4-aminoquinoline core for the design of new cholinesterase inhibitors link: https://peerj.com/articles/2140 last-modified: 2016-07-07 description: Inhibition of acetylcholinesterase (AChE) using small molecules is still one of the most successful therapeutic strategies in the treatment of Alzheimer’s disease (AD). Previously we reported compound T5369186 with a core of quinolone as a new cholinesterase inhibitor. In the present study, in order to identify new cores for the designing of AChE inhibitors, we screened different derivatives of this core with the aim to identify the best core as the starting point for further optimization. Based on the results, we confirmed that only 4-aminoquinoline (compound 04 and 07) had cholinesterase inhibitory effects. Considering the simple structure and high inhibitory potency against AChE, 4-aminoquinoline provides a good starting core for further designing novel multifunctional AChEIs. creator: Yao Chen creator: Yaoyao Bian creator: Yuan Sun creator: Chen Kang creator: Sheng Yu creator: Tingming Fu creator: Wei Li creator: Yuqiong Pei creator: Haopeng Sun uri: https://doi.org/10.7717/peerj.2140 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chen et al. title: The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents link: https://peerj.com/articles/2159 last-modified: 2016-07-07 description: Background: Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping.Methods: Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground truthed using extant avians we seek to test if an incipient flight stroke may have contributed sufficient force to permit flap running, WAIR, or leaping takeoff along the phylogenetic lineage from Coelurosauria to birds.Results: None of these behaviours were found to meet the biomechanical threshold requirements before Paraves. Neither was there a continuous trend of refinement for any of these biomechanical performances across phylogeny nor a signal of universal applicability near the origin of birds. None of these flap-based locomotory models appear to have been a major influence on pre-flight character acquisition such as pennaceous feathers, suggesting non-locomotory behaviours, and less stringent locomotory behaviours such as balancing and braking, played a role in the evolution of the maniraptoran wing and nascent flight stroke. We find no support for widespread prevalence of WAIR in non-avian theropods, but can’t reject its presence in large winged, small-bodied taxa like Microraptor and Archaeopteryx.Discussion: Using our first principles approach we find that “near flight” locomotor behaviors are most sensitive to wing area, and that non-locomotory related selection regimes likely expanded wing area well before WAIR and other such behaviors were possible in derived avians. These results suggest that investigations of the drivers for wing expansion and feather elongation in theropods need not be intrinsically linked to locomotory adaptations, and this separation is critical for our understanding of the origin of powered flight and avian evolution. creator: T. Alexander Dececchi creator: Hans C.E. Larsson creator: Michael B. Habib uri: https://doi.org/10.7717/peerj.2159 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Dececchi et al. title: Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering link: https://peerj.com/articles/2031 last-modified: 2016-07-07 description: Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists’ efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15–20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global ‘do-it-yourself’ research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrickTM standard and finally, (iii) that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools.Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrickTM formatted plasmid.Results. All species were stable over 11 weeks of glycerol cryopreservation, sensitive to 17 µg/mL chloramphenicol and resistant to transformation using the conditions and plasmids tested. An incubator-shaker device, ‘UCLHack-12’ was assembled and used to cultivate sufficient quantity of Oceanobulbus indolifexcells to enable isolation of the anf1 gene and its subcloning into a plasmid to generate the BioBrickTM BBa_K729016.Conclusion.The process of ‘de-skilling’ biomolecular techniques, particularly for relatively under-investigated organisms, is still on-going. However, our successful cell growth and DNA manipulation experiments serve to indicate the types of capabilities that are now available to citizen scientists. Science democratised in this way can make a positive contribution to the debate around the use of bio-geoengineering to address oceanic pollution or climate change. creator: Yanika Borg creator: Aurelija Marija Grigonyte creator: Philipp Boeing creator: Bethan Wolfenden creator: Patrick Smith creator: William Beaufoy creator: Simon Rose creator: Tonderai Ratisai creator: Alexey Zaikin creator: Darren N. Nesbeth uri: https://doi.org/10.7717/peerj.2031 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Borg et al. title: Dugong dugon feeding in tropical Australian seagrass meadows: implications for conservation planning link: https://peerj.com/articles/2194 last-modified: 2016-07-07 description: Dugongs (Dugong dugon) are listed as vulnerable to extinction due to rapid population reductions caused in part by loss of seagrass feeding meadows. Understanding dugong feeding behaviour in tropical Australia, where the majority of dugongs live, will assist conservation strategies. We examined whether feeding patterns in intertidal seagrass meadows in tropical north-eastern Australia were related to seagrass biomass, species composition and/or nitrogen content. The total biomass of each seagrass species removed by feeding dugongs was measured and compared to its relative availability. Nitrogen concentrations were also determined for each seagrass species present at the sites. Dugongs consumed seagrass species in proportion to their availability, with biomass being the primary determining factor. Species composition and/or nitrogen content influenced consumption to a lesser degree. Conservation plans focused on protecting high biomass intertidal seagrass meadows are likely to be most effective at ensuring the survival of dugong in tropical north-eastern Australia. creator: Samantha J. Tol creator: Rob G. Coles creator: Bradley C. Congdon uri: https://doi.org/10.7717/peerj.2194 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tol et al. title: New information on the Wukongopteridae (Pterosauria) revealed by a new specimen from the Jurassic of China link: https://peerj.com/articles/2177 last-modified: 2016-07-07 description: The Wukongopteridae is an important pterosaur group discovered from Yanliao Biota, because it combines character states seen in non-pterodactyloid and pterodactyloid pterosaurs. So far, the Wukongopteridae contains three genera: Wukongopterus, Darwinopterus and Kunpengopterus; representing five species. Here we report on a new specimen, IVPP V 17959, that can be undoubtedly referred to the Wukongopteridae based on the presence of a confluent nasoantorbital fenestra, elongated cervical vertebrae (convergent with Pterodactyloidea) and a long tail enclosed by rod-like bony extensions of the zygapophyses. Traits distinguishing this new specimen from other wukongopterid pterosaurs include a premaxilla with a low ossified anterodorsal crest, a nasal bearing the most elongated process known in the Wukongopteridae, and a lacrimal that has a foramen in its middle portion. The new kind of premaxillary crest preserved in IVPP V 17959 suggests that the presence or absence of a premaxillary crest might be an interspecific feature within the Wukongopteridae. A phylogenetic analysis including all wukongopterid pterosaurs recovers IVPP V 17959 in a polytomy with Wukongopterus and the species of Darwinopterus, having Kunpengopterus in a more basal position. The postcranial skeleton of IVPP V 17959 has ontogenetically mature characteristics including a completely fused scapula and coracoid, fused proximal and distal carpal series, and an ossified extensor tendon process of the first wing phalanx, allowing its classification as ontogenetic stage five. Furthermore, the atlas and axis are separated in IVPP V 17959, which indicates that these two bones probably are not fused in skeletally mature wukongopterid individuals. creator: Xin Cheng creator: Shunxing Jiang creator: Xiaolin Wang creator: Alexander W.A. Kellner uri: https://doi.org/10.7717/peerj.2177 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cheng et al. title: Association between the HTR2C rs1414334 C/G gene polymorphism and the development of the metabolic syndrome in patients treated with atypical antipsychotics link: https://peerj.com/articles/2163 last-modified: 2016-07-07 description: Few studies have assessed the association between the rs1414334 C/G polymorphism in the HTR2C gene and the development of the metabolic syndrome in patients treated with atypical antipsychotics. To provide further evidence, a cross-sectional study was conducted in Spain between 2012 and 2013 in 166 patients with these characteristics. In these patients, the association between the polymorphism and the presence of the metabolic syndrome was determined by implementing binary logistic regression models adjusted for variables associated with the metabolic syndrome. We did not confirm previous claims that the C allele of the polymorphism was linked to the metabolic syndrome: the association was in the opposite direction and non-significant. This conclusion held after taking gender and lifestyle variables into account. creator: José María Rico-Gomis creator: Antonio Palazón-Bru creator: Irene Triano-García creator: Luis Fabián Mahecha-García creator: Ana García-Monsalve creator: Andrés Navarro-Ruiz creator: Berta Villagordo-Peñalver creator: Jessica Jiménez-Abril creator: Alicia Martínez-Hortelano creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.2163 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rico-Gomis et al. title: Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing link: https://peerj.com/articles/2147 last-modified: 2016-07-07 description: River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically important buffalo breeds namely: Banni, Jafrabadi and Mehsani, belonging to either high or low milk-yield group. Blood samples were collected from the milk-yield/breed balanced group of 12 buffaloes, and whole exome sequencing was performed using Roche 454 GS-FLX Titanium sequencer. Using an innovative approach namely, MultiCom; we have identified high-quality SNPs specific for high and low-milk yield buffaloes. Almost 70% of the reported genes in QTL regions of milk-yield and milk-fat in cattle were present among the buffalo milk-yield gene candidates. Functional analysis highlighted transcriptional regulation category in the low milk-yield group, and several new pathways in the two groups. Further, the discovered SNP candidates may account for more than half of mammary transcriptome changes in high versus low-milk yielding cattle. Thus, starting from the design of a reliable strategy, we identified reliable genomic markers specific for high and low-milk yield buffalo breeds and addressed possible downstream effects. creator: Ramesh Menon creator: Anand B. Patel creator: Chaitanya Joshi uri: https://doi.org/10.7717/peerj.2147 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Menon et al. title: The modulatory effect of Moringa oleifera leaf extract on endogenous antioxidant systems and inflammatory markers in an acetaminophen-induced nephrotoxic mice model link: https://peerj.com/articles/2127 last-modified: 2016-07-07 description: N-Acetyl-p-Aminophenol (APAP), also known as acetaminophen, is the most commonly used over-the counter analgesic and antipyretic medication. However, its overdose leads to both liver and kidney damage. APAP-induced toxicity is considered as one of the primary causes of acute liver failure; numerous scientific reports have focused majorly on APAP hepatotoxicity. Alternatively, not many works approach APAP nephrotoxicity focusing on both its mechanisms of action and therapeutic exploration. Moringa oleifera (MO) is pervasive in nature, is reported to possess a surplus amount of nutrients, and is enriched with several bioactive candidates including trace elements that act as curatives for various clinical conditions. In this study, we evaluated the nephro-protective potential of MO leaf extract against APAP nephrotoxicity in male Balb/c mice. A single-dose acute oral toxicity design was implemented in this study. Group 2, 3, 4 and 5 received a toxic dose of APAP (400 mg/kg of bw, i.p) and after an hour, these groups were administered with saline (10 mL/kg), silymarin—positive control (100 mg/kg of bw, i.p), MO leaf extract (100 mg/kg of bw, i.p), and MO leaf extract (200 mg/kg bw, i.p) respectively. Group 1 was administered saline (10 mL/kg) during both the sessions. APAP-treated mice exhibited a significant elevation of serum creatinine, blood urea nitrogen, sodium, potassium and chloride levels. A remarkable depletion of antioxidant enzymes such as SOD, CAT and GSH-Px with elevated MDA levels has been observed in APAP treated kidney tissues. They also exhibited a significant rise in pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) and decreased anti-inflammatory (IL-10) cytokine level in the kidney tissues. Disorganized glomerulus and dilated tubules with inflammatory cell infiltration were clearly observed in the histology of APAP treated mice kidneys. All these pathological changes were reversed in a dose-dependent manner after MO leaf extract treatment. Therefore, MO leaf extract has demonstrated some therapeutic effectiveness against APAP-induced nephrotoxicity through enhancement of the endogenous antioxidant system and a modulatory effect on specific inflammatory cytokines in kidney tissues. creator: Govindarajan Karthivashan creator: Aminu Umar Kura creator: Palanisamy Arulselvan creator: Norhaszalina Md. Isa creator: Sharida Fakurazi uri: https://doi.org/10.7717/peerj.2127 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Karthivashan et al. title: Differential nest-defense to perceived danger in urban and rural areas by female Eurasian sparrowhawk (Accipiter nisus) link: https://peerj.com/articles/2070 last-modified: 2016-07-07 description: The reaction of wildlife to humans is known to differ with surroundings. In urban environments that provide suitable habitats for breeding birds, animals adapt to humans and their response is accordingly altered. This study examined the nest defense behavior of female Eurasian sparrowhawks (Accipiter nisus) during the breeding season in urban and rural areas of Prague. The females showed four different types of reaction to humans that approached the nest and differed significantly between the two study areas. Contrary to expectations, urban nesting females were more aggressive than rural conspecifics. The intensity of response increased as the season progressed, and females defended their broods to a much greater degree than their clutches in both urban and rural habitats, suggesting a differential effort as a function of their relative investment in the breeding attempt conforming with the parental investment hypothesis. creator: Tomas Kunca creator: Reuven Yosef uri: https://doi.org/10.7717/peerj.2070 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kunca and Yosef title: Contribution of prosthetic treatment considerations for dental extractions of permanent teeth link: https://peerj.com/articles/2015 last-modified: 2016-07-07 description: Background. Tooth loss is an easily identifiable outcome that summarizes a complex suite of factors in an individual’s history of dental disease and its treatment by dental services over a lifetime. Assessment of overall tooth loss data is essential for epidemiologically evaluating the adequacy of dental care provided at a systems level, as well as for placing in context tooth loss for non-disease causes. For example, when derived from prosthetic treatment planning, the latter may unfortunately lead to some teeth being extracted (pulled) for the sake of better comprehensive clinical results. The objective of the present manuscript was to identify the contribution to overall tooth loss, by extraction of permanent teeth because of prosthetic treatment reasons.Material and Methods. A cross-sectional study included sex, age, total number of extractions performed by subject, sextant (anterior vs. posterior), group of teeth (incisors, canines, premolars and molars), upper or lower arch, and the main reason underlying extraction (extraction for any reason vs. prosthetic treatment), in patients 18 years of age and older seeking care at a dental school clinic in Mexico. A multivariate logistic regression model was generated.Results. A total of 749 teeth were extracted in 331 patients; 161 teeth (21.5% of total) were extracted for explicit prosthetic treatment indications. As age increased, the likelihood of having an extraction for prosthetic reasons increased 3% (OR = 1.03, p < 0.001). Women (OR = 1.57, p < 0.05) were more likely to be in this situation, and molars (OR = 2.70, p < 0.001) were most at risk. As the total number of extractions increased, the risk of having an extraction for prosthetic reasons decreased (OR = 0.94, p < 0.05).Conclusions. A significant amount (21.5%) of the extractions of permanent teeth were performed for prosthetic reasons in this dental school clinical environment; age, sex, type of tooth, and the total number of extractions moderated such pattern. creator: Miguel Ángel Fernández-Barrera creator: Carlo Eduardo Medina-Solís creator: Juan Fernando Casanova-Rosado creator: Martha Mendoza-Rodríguez creator: Mauricio Escoffié-Ramírez creator: Alejandro José Casanova-Rosado creator: José de Jesús Navarrete-Hernández creator: Gerardo Maupomé uri: https://doi.org/10.7717/peerj.2015 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Fernández-Barrera et al. title: New occurrences of fossilized feathers: systematics and taphonomy of the Santana Formation of the Araripe Basin (Cretaceous), NE, Brazil link: https://peerj.com/articles/1916 last-modified: 2016-07-07 description: Here we describe three fossil feathers from the Early Cretaceous Santana Formation of the Araripe Basin, Brazil. Feathers are the most complex multiform vertebrate integuments; they perform different functions, occurring in both avian and non-avian dinosaurs. Despite their rarity, fossil feathers have been found across the world. Most of the Brazilian feather fossil record comes from the Santana Formation. This formation is composed of two members: Crato (lake) and Romualdo (lagoon); both of which are predominantly reduced deposits, precluding bottom dwelling organisms, resulting in exceptional preservation of the fossils. Despite arid and hot conditions during the Cretaceous, life teemed in the adjacency of this paleolake. Feathered non-avian dinosaurs have not yet been described from the Crato Member, even though there are suggestions of their presence in nearby basins. Our description of the three feathers from the Crato laminated limestone reveals that, despite the small sample size, they can be referred to coelurosaurian theropods. Moreover, based on comparisons with extant feather morphotypes they can be identified as one contour feather and two downy feathers. Despite their rareness and low taxonomic potential, fossilized feathers can offer insights about the paleobiology of its owners and the paleoecology of the Araripe Basin. creator: Gustavo M.E.M. Prado creator: Luiz Eduardo Anelli creator: Setembrino Petri creator: Guilherme Raffaeli Romero uri: https://doi.org/10.7717/peerj.1916 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Prado et al. title: The implementation of rare events logistic regression to predict the distribution of mesophotic hard corals across the main Hawaiian Islands link: https://peerj.com/articles/2189 last-modified: 2016-07-06 description: Predictive habitat suitability models are powerful tools for cost-effective, statistically robust assessment of the environmental drivers of species distributions. The aim of this study was to develop predictive habitat suitability models for two genera of scleractinian corals (Leptoserisand Montipora) found within the mesophotic zone across the main Hawaiian Islands. The mesophotic zone (30–180 m) is challenging to reach, and therefore historically understudied, because it falls between the maximum limit of SCUBA divers and the minimum typical working depth of submersible vehicles. Here, we implement a logistic regression with rare events corrections to account for the scarcity of presence observations within the dataset. These corrections reduced the coefficient error and improved overall prediction success (73.6% and 74.3%) for both original regression models. The final models included depth, rugosity, slope, mean current velocity, and wave height as the best environmental covariates for predicting the occurrence of the two genera in the mesophotic zone. Using an objectively selected theta (“presence”) threshold, the predicted presence probability values (average of 0.051 for Leptoseris and 0.040 for Montipora) were translated to spatially-explicit habitat suitability maps of the main Hawaiian Islands at 25 m grid cell resolution. Our maps are the first of their kind to use extant presence and absence data to examine the habitat preferences of these two dominant mesophotic coral genera across Hawai‘i. creator: Lindsay M. Veazey creator: Erik C. Franklin creator: Christopher Kelley creator: John Rooney creator: L. Neil Frazer creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.2189 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Veazey et al. title: The effects of gamelike features and test location on cognitive test performance and participant enjoyment link: https://peerj.com/articles/2184 last-modified: 2016-07-06 description: Computerised cognitive assessments are a vital tool in the behavioural sciences, but participants often view them as effortful and unengaging. One potential solution is to add gamelike elements to these tasks in order to make them more intrinsically enjoyable, and some researchers have posited that a more engaging task might produce higher quality data. This assumption, however, remains largely untested. We investigated the effects of gamelike features and test location on the data and enjoyment ratings from a simple cognitive task. We tested three gamified variants of the Go-No-Go task, delivered both in the laboratory and online. In the first version of the task participants were rewarded with points for performing optimally. The second version of the task was framed as a cowboy shootout. The third version was a standard Go-No-Go task, used as a control condition. We compared reaction time, accuracy and subjective measures of enjoyment and engagement between task variants and study location. We found points to be a highly suitable game mechanic for gamified cognitive testing because they did not disrupt the validity of the data collected but increased participant enjoyment. However, we found no evidence that gamelike features could increase engagement to the point where participant performance improved. We also found that while participants enjoyed the cowboy themed task, the difficulty of categorising the gamelike stimuli adversely affected participant performance, increasing No-Go error rates by 28% compared to the non-game control. Responses collected online vs. in the laboratory had slightly longer reaction times but were otherwise very similar, supporting other findings that online crowdsourcing is an acceptable method of data collection for this type of research. creator: Jim Lumsden creator: Andy Skinner creator: Andy T. Woods creator: Natalia S. Lawrence creator: Marcus Munafò uri: https://doi.org/10.7717/peerj.2184 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lumsden et al. title: On the relationship between enamel band complexity and occlusal surface area in Equids (Mammalia, Perissodactyla) link: https://peerj.com/articles/2181 last-modified: 2016-07-06 description: Enamel patterns on the occlusal surfaces of equid teeth are asserted to have tribal-level differences. The most notable example compares the Equini and Hipparionini, where Equini have higher crowned teeth with less enamel-band complexity and less total occlusal enamel than Hipparionini. Whereas previous work has successfully quantified differences in enamel band shape by dividing the length of enamel band by the square root of the occlusal surface area (Occlusal Enamel Index, OEI), it was clear that OEI only partially removes the effect of body size. Because enamel band length scales allometrically, body size still has an influence on OEI, with larger individuals having relatively longer enamel bands than smaller individuals. Fractal dimensionality (D) can be scaled to any level, so we have used it to quantify occlusal enamel complexity in a way that allows us to get at an accurate representation of the relationship between complexity and body size. To test the hypothesis of tribal-level complexity differences between Equini and Hipparionini, we digitally traced a sample of 98 teeth, one tooth per individual; 31 Hipparionini and 67 Equini. We restricted our sampling to the P3-M2 to reduce the effect of tooth position. After calculating the D of these teeth with the fractal box method which uses the number of boxes of various sizes to calculate the D of a line, we performed a t-test on the individual values of D for each specimen, comparing the means between the two tribes, and a phylogenetically informed generalized least squares regression (PGLS) for each tribe with occlusal surface area as the independent variable and D as the dependent variable. The slopes of both PGLS analyses were compared using a t-test to determine if the same linear relationship existed between the two tribes. The t-test between tribes was significant (p < 0.0001), suggesting different D populations for each lineage. The PGLS for Hipparionini was a positive but not significant (p = 0.4912) relationship between D and occlusal surface area, but the relationship for Equini was significantly negative (p = 0.0177). λ was 0 for both tests, indicating no important phylogenetic signal is present in the relationship between these two characters, thus the PGLS collapses down to a non-phylogenetic generalized least squares (GLS) model. The t-test comparing the slopes of the regressions was not significant, indicating that the two lineages could have the same relationship between D and occlusal surface area. Our results suggest that the two tribes have the same negative relationship between D and occlusal surface area but the Hipparionini are offset to higher values than the Equini. This offset reflects the divergence between the two lineages since their last common ancestor and may have constrained their ability to respond to environmental change over the Neogene, leading to the differential survival of the Equini. creator: Nicholas A. Famoso creator: Edward Byrd Davis uri: https://doi.org/10.7717/peerj.2181 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Famoso and Davis title: Dental microwear reveals mammal-like chewing in the neoceratopsian dinosaur Leptoceratops gracilis link: https://peerj.com/articles/2132 last-modified: 2016-07-06 description: Extensive oral processing of food through dental occlusion and orbital mandibular movement is often cited as a uniquely mammalian trait that contributed to their evolutionary success. Save for mandibular translation, these adaptations are not seen in extant archosaurs or lepidosaurs. In contrast, some ornithischian dinosaurs show evidence of precise dental occlusion, habitual intraoral trituration and complex jaw motion. To date, however, a robust understanding of the diversity of jaw mechanics within non-avian dinosaurs, and its comparison with other vertebrates, remains unrealized. Large dental batteries, well-developed dental wear facets, and robust jaws suggests that neoceratopsian (horned) dinosaurs were capable chewers. But, biomechanical analyses have assumed a relatively simple, scissor-like (orthal) jaw mechanism for these animals. New analyses of dental microwear, presented here, show curvilinear striations on the teeth of Leptoceratops. These features indicate a rostral to caudal orbital motion of the mandible during chewing. A rostrocaudal mandibular orbit is seen in multituberculates, haramiyid allotherians, and some rodents, and its identification in Leptoceratops gracilis is the first evidence of complex, mammal-like chewing in a ceratopsian dinosaur. The term circumpalinal is here proposed to distinguish this new style of chewing from other models of ceratopsian mastication that also involve a palinal component. This previously unrecognized complexity in dinosaurian jaw mechanics indicates that some neoceratopsian dinosaurs achieved a mammalian level of masticatory efficiency through novel adaptive solutions. creator: Frank J. Varriale uri: https://doi.org/10.7717/peerj.2132 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Varriale title: Gene expression analysis of overwintering mountain pine beetle larvae suggests multiple systems involved in overwintering stress, cold hardiness, and preparation for spring development link: https://peerj.com/articles/2109 last-modified: 2016-07-06 description: Cold-induced mortality has historically been a key aspect of mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae), population control, but little is known about the molecular basis for cold tolerance in this insect. We used RNA-seq analysis to monitor gene expression patterns of mountain pine beetle larvae at four time points during their overwintering period—early-autumn, late-autumn, early-spring, and late-spring. Changing transcript profiles over the winter indicates a multipronged physiological response from larvae that is broadly characterized by gene transcripts involved in insect immune responses and detoxification during the autumn. In the spring, although transcripts associated with developmental process are present, there was no particular biological process dominating the transcriptome. creator: Jeanne A. Robert creator: Tiffany Bonnett creator: Caitlin Pitt creator: Luke J. Spooner creator: Jordie Fraser creator: Macaire M.S. Yuen creator: Christopher I. Keeling creator: Jörg Bohlmann creator: Dezene P.W. Huber uri: https://doi.org/10.7717/peerj.2109 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Robert et al. title: Characterisation of an atypical manifestation of black band disease on Porites lutea in the Western Indian Ocean link: https://peerj.com/articles/2073 last-modified: 2016-07-06 description: Recent surveys conducted on Reunion Island coral reefs revealed an atypical manifestation of black band disease on the main framework building coral, Porites lutea. This BBD manifestation (PorBBD) presented a thick lighter-colored band, which preceded the typical BBD lesion. Whilst BBD aetiology has been intensively described worldwide, it remains unclear if corals with apparently similar lesions across coral reefs are affected by the same pathogens. Therefore, a multidisciplinary approach involving field surveys, gross lesion monitoring, histopathology and 454-pyrosequencing was employed to provide the first comprehensive characterization of this particular manifestation. Surveys conducted within two geomorphological zones over two consecutive summers and winters showed spatial and seasonal patterns consistent with those found for typical BBD. Genetic analyses suggested an uncharacteristically high level of Vibrio spp. bacterial infection within PorBBD. However, microscopic analysis revealed high densities of cyanobacteria, penetrating the compromised tissue as well as the presence of basophilic bodies resembling bacterial aggregates in the living tissue, adjacent to the bacterial mat. Additionally, classical BBD-associated cyanobacterial strains, genetically related to Pseudoscillatoria coralii and Roseofilum reptotaenium were identified and isolated and the presence of sulfate-reducers or sulfide-oxidizers such as Desulfovibrio and Arcobacter, previously shown to be associated with anoxic microenvironment within typical BBD was also observed, confirming that PorBBD is a manifestation of classical BBD. creator: Mathieu Séré creator: David A. Wilkinson creator: Michael H. Schleyer creator: Pascale Chabanet creator: Jean-Pascal Quod creator: Pablo Tortosa uri: https://doi.org/10.7717/peerj.2073 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Séré et al. title: Altered expression profile of glycolytic enzymes during testicular ischemia reperfusion injury is associated with the p53/TIGAR pathway: effect of fructose 1,6-diphosphate link: https://peerj.com/articles/2195 last-modified: 2016-07-05 description: Background. Testicular ischemia reperfusion injury (tIRI) is considered the mechanism underlying the pathology of testicular torsion and detorsion. Left untreated, tIRI can induce testis dysfunction, damage to spermatogenesis and possible infertility. In this study, we aimed to assess the activities and expression of glycolytic enzymes (GEs) in the testis and their possible modulation during tIRI. The effect of fructose 1,6-diphosphate (FDP), a glycolytic intermediate, on tIRI was also investigated.Methods. Male Sprague-Dawley rats were divided into three groups: sham, unilateral tIRI, and tIRI + FDP (2 mg/kg). tIRI was induced by occlusion of the testicular artery for 1 h followed by 4 h of reperfusion. FDP was injected peritoneally 30 min prior to reperfusion. Histological and biochemical analyses were used to assess damage to spermatogenesis, activities of major GEs, and energy and oxidative stress markers. The relative mRNA expression of GEs was evaluated by real-time PCR. ELISA and immunohistochemistry were used to evaluate the expression of p53 and TP53-induced glycolysis and apoptosis regulator (TIGAR).Results. Histological analysis revealed tIRI-induced spermatogenic damage as represented by a significant decrease in the Johnsen biopsy score. In addition, tIRI reduced the activities of hexokinase 1, phosphofructokinase-1, glyceraldehyde 3-phosphate dehydrogenase, and lactate dehydrogenase C. However, mRNA expression downregulation was detected only for hexokinase 1, phosphoglycerate kinase 2, and lactate dehydrogenase C. ATP and NADPH depletion was also induced by tIRI and was accompanied by an increased Malondialdehyde concentration, reduced glutathione level, and reduced superoxide dismutase and catalase enzyme activities. The immunoexpression of p53 and TIGAR was markedly increased after tIRI. The above tIRI-induced alterations were attenuated by FDP treatment.Discussion. Our findings indicate that tIRI-induced spermatogenic damage is associated with dysregulation of GE activity and gene expression, which were associated with activation of the TIGAR/p53 pathway. FDP treatment had a beneficial effect on alleviating the damaging effects of tIRI. This study further emphasizes the importance of metabolic regulation for proper spermatogenesis. creator: May Al-Maghrebi creator: Waleed M. Renno uri: https://doi.org/10.7717/peerj.2195 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Al-Maghrebi and Renno title: Functional morphology of parasitic isopods: understanding morphological adaptations of attachment and feeding structures in Nerocila as a pre-requisite for reconstructing the evolution of Cymothoidae link: https://peerj.com/articles/2188 last-modified: 2016-07-05 description: Parasites significantly influence food webs and ecosystems and occur all over the world in almost every animal group. Within crustaceans there are numerous examples of ectoparasites; for example, representatives of the isopod group Cymothoidae. These obligatory parasitic isopods are relatively poorly studied regarding their functional morphology. Here we present new details of the morphological adaptations to parasitism of the cymothoiid ingroup Nerocila with up-to-date imaging methods (macro photography, stereo imaging, fluorescence photography, micro CT, and histology). Central aspects of the study were (1) the morphology of the mouthparts and (2) the attachment on the host, hence the morphology of the thoracopods. The mouthparts (labrum, mandibles, paragnaths, maxillulae, maxillae, maxillipeds) form a distinct mouth cone and are most likely used for true sucking. The mouthparts are tightly “folded” around each other and provide functional rails for the only two moving mouthparts, mandible and maxillula. Both are not moving in an ancestral-type median-lateral movement, but are strongly tilted to move more in a proximal-distal axis. New details concerning the attachment demonstrate that the angular arrangement of the thoracopods is differentiated to impede removal by the host. The increased understanding of morphological adaptation to parasitism of modern forms will be useful in identifying disarticulated (not attached to the host) fossil parasites. creator: Christina Nagler creator: Joachim T. Haug uri: https://doi.org/10.7717/peerj.2188 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nagler and Haug title: Global patterns of conservation research importance in different countries of the world link: https://peerj.com/articles/2173 last-modified: 2016-07-05 description: Conservation research is essential to help inform the science-based management of environments that support threatened and endangered wildlife; however, research effort is not necessarily uniform across countries globally. Here, we assessed how the research importance of conservation is distributed globally across different countries and what drives this variation. Specifically, we compared the number of conservation/ecological articles versus all scientific articles published for each country in relation to the number of endangered species, the protection status and number of ecosystems, and the economic status of each country (gross domestic product (GDP) per capita). We observed a significant and positive relationship between the proportion of conservation and ecology articles to all scientific articles with respect to the number of endangered species and the proportion of endangered species that are protected in a country, as well as GDP per capita. In conclusion, knowledge about the conservation and economic status of countries should be accounted for when predicting the research importance of conservation and ecology. creator: Hideyuki Doi creator: Teruhiko Takahara uri: https://doi.org/10.7717/peerj.2173 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Doi and Takahara title: Differences in meiofauna communities with sediment depth are greater than habitat effects on the New Zealand continental margin: implications for vulnerability to anthropogenic disturbance link: https://peerj.com/articles/2154 last-modified: 2016-07-05 description: Studies of deep-sea benthic communities have largely focused on particular (macro) habitats in isolation, with few studies considering multiple habitats simultaneously in a comparable manner. Compared to mega-epifauna and macrofauna, much less is known about habitat-related variation in meiofaunal community attributes (abundance, diversity and community structure). Here, we investigated meiofaunal community attributes in slope, canyon, seamount, and seep habitats in two regions on the continental slope of New Zealand (Hikurangi Margin and Bay of Plenty) at four water depths (700, 1,000, 1,200 and 1,500 m). We found that patterns were not the same for each community attribute. Significant differences in abundance were consistent across regions, habitats, water and sediment depths, while diversity and community structure only differed between sediment depths. Abundance was higher in canyon and seep habitats compared with other habitats, while between sediment layer, abundance and diversity were higher at the sediment surface. Our findings suggest that meiofaunal community attributes are affected by environmental factors that operate on micro- (cm) to meso- (0.1–10 km), and regional scales (> 100 km). We also found a weak, but significant, correlation between trawling intensity and surface sediment diversity. Overall, our results indicate that variability in meiofaunal communities was greater at small scale than at habitat or regional scale. These findings provide new insights into the factors controlling meiofauna in these deep-sea habitats and their potential vulnerability to anthropogenic activities. creator: Norliana Rosli creator: Daniel Leduc creator: Ashley A. Rowden creator: Malcolm R. Clark creator: P. Keith Probert creator: Katrin Berkenbusch creator: Carlos Neira uri: https://doi.org/10.7717/peerj.2154 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Rosli et al. title: Scarcity of ecosystem services: an experimental manipulation of declining pollination rates and its economic consequences for agriculture link: https://peerj.com/articles/2099 last-modified: 2016-07-05 description: Ecosystem services (ES) such as pollination are vital for the continuous supply of food to a growing human population, but the decline in populations of insect pollinators worldwide poses a threat to food and nutritional security. Using a pollinator (honeybee) exclusion approach, we evaluated the impact of pollinator scarcity on production in four brassica fields, two producing hybrid seeds and two producing open-pollinated ones. There was a clear reduction in seed yield as pollination rates declined. Open-pollinated crops produced significantly higher yields than did the hybrid ones at all pollination rates. The hybrid crops required at least 0.50 of background pollination rates to achieve maximum yield, whereas in open-pollinated crops, 0.25 pollination rates were necessary for maximum yield. The total estimated economic value of pollination services provided by honeybees to the agricultural industry in New Zealand is NZD $1.96 billion annually. This study indicates that loss of pollination services can result in significant declines in production and have serious implications for the market economy in New Zealand. Depending on the extent of honeybee population decline, and assuming that results in declining pollination services, the estimated economic loss to New Zealand agriculture could be in the range of NZD $295–728 million annually. creator: Harpinder Sandhu creator: Benjamin Waterhouse creator: Stephane Boyer creator: Steve Wratten uri: https://doi.org/10.7717/peerj.2099 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sandhu et al. title: The effect of blow flies (Diptera: Calliphoridae) on the size and weight of mangos (Mangifera indica L.) link: https://peerj.com/articles/2076 last-modified: 2016-07-05 description: Background: Pollination has a great effect on the yield of fruit trees. Blow flies are considered as an effective pollinator compared to hand pollination in fruit orchards. Therefore, this study was designed to evaluate the effect of different pollination methods in mango orchards.Methodology: The impact of pollination on quantity and quality of mango yield by blow flies was estimated by using three treatments, i.e., open pollinated trees, trees were covered by a net in the presence of blow flies for pollination, and trees were covered with a net but without insects.Results: The maximum number of flowers was recorded in irregular types of inflorescence, i.e., 434.80 flowers/inflorescence. Fruit setting (bud) was higher in open pollinated mango trees (i.e. 37.00/inflorescence) than enclosed pollination by blow flies (i.e. 22.34/inflorescence). The size of the mango fruit was the highest (5.06 mm) in open pollinated tree than those pollinated by blow flies (3.93 mm) and followed by without any pollinator (3.18 mm) at marble stage. We found that the maximum weight of mango fruit (201.19 g) was in open pollinated trees.Discussion: The results demonstrated that blow flies can be used as effective mango pollinators along with other flies and bees. The blow flies have shown a positive impact on the quality and quantity of mango. This study will be helpful in future and also applicable at farm level to use blow flies as pollinators that are cheap and easy to rear. creator: Shafqat Saeed creator: Muhammad Nadir Naqqash creator: Waqar Jaleel creator: Qamar Saeed creator: Fozia Ghouri uri: https://doi.org/10.7717/peerj.2076 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Saeed et al.