title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2013-09 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Why do leaf-tying caterpillars abandon their leaf ties? link: https://peerj.com/articles/173 last-modified: 2013-09-26 description: Leaf-tying caterpillars act as ecosystem engineers by building shelters between overlapping leaves, which are inhabited by other arthropods. Leaf-tiers have been observed to leave their ties and create new shelters (and thus additional microhabitats), but the ecological factors affecting shelter fidelity are poorly known. For this study, we explored the effects of resource limitation and occupant density on shelter fidelity and assessed the consequences of shelter abandonment. We first quantified the area of leaf material required for a caterpillar to fully develop for two of the most common leaf-tiers that feed on white oak, Quercus alba. On average, Psilocorsis spp. caterpillars consumed 21.65 ± 0.67 cm2 leaf material to complete development. We also measured the area of natural leaf ties found in a Maryland forest, to determine the distribution of resources available to caterpillars in situ. Of 158 natural leaf ties examined, 47% were too small to sustain an average Psilocorsis spp. caterpillar for the entirety of its development. We also manipulated caterpillar densities within experimental ties on potted trees to determine the effects of cohabitants on the likelihood of a caterpillar to leave its tie. We placed 1, 2, or 4 caterpillars in ties of a standard size and monitored the caterpillars twice daily to track their movement. In ties with more than one occupant, caterpillars showed a significantly greater propensity to leave their tie, and left sooner and at a faster rate than those in ties as single occupants. To understand the consequences of leaf tie abandonment, we observed caterpillars searching a tree for a site to build a shelter in the field. This is a risky behavior, as 17% of the caterpillars observed died while searching for a shelter site. Caterpillars that successfully built a shelter traveled 110 ± 20 cm and took 28 ± 7 min to find a suitable site to build a shelter. In conclusion, leaf-tying caterpillars must frequently abandon their leaf tie due to food limitation and interactions with other caterpillars, but this is a costly behavior. creator: Michelle Sliwinski creator: Elisha Sigmon uri: https://doi.org/10.7717/peerj.173 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Sliwinski and Sigmon title: Mind the gaps: investigating the cause of the current range disjunction in the Cape Platanna, Xenopus gilli (Anura: Pipidae) link: https://peerj.com/articles/166 last-modified: 2013-09-26 description: Low-lying areas of the Cape at Africa’s south-westernmost tip have undergone dramatic marine-remodelling, with regular changes in sea-level following glacial cycles. Species for which marine barriers are impenetrable underwent concomitant radical distribution changes which may account for current range disjunctions. The Cape platanna, Xenopus gilli, is a frog distributed in only three disjunt areas within low-lying regions of the southwestern Cape. We determined the relationship between frogs from these three disjunct areas, by using a combination of morphometric analysis and mtDNA (ND2 and 16S fragments) sequences of 130 frogs from eight ponds. Coalescent analyses on molecular data dated the divergence in two major clades to around 4.6 Mya, a period during which major uplifting on the eastern side of the subcontinent caused climate changes throughout southern Africa. Principal components analysis showed significant morphometric differences between each clade on head and limb measurements. Consistent differences in ventral colouration and patterning were also observed. We report on increased levels of hybridisation with X. laevis throughout the range of X. gilli, which reaches at least 27% hybrids in some ponds. Urgent conservation actions are required to control habitat loss from alien invasive vegetation, and prevent introgression with the domestic-exotic, X. laevis. creator: Deborah J. Fogell creator: Krystal A. Tolley creator: G. John Measey uri: https://doi.org/10.7717/peerj.166 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Fogell et al. title: Goats favour personal over social information in an experimental foraging task link: https://peerj.com/articles/172 last-modified: 2013-09-24 description: Animals can use their environments more efficiently by selecting particular sources of information (personal or social), according to specific situations. Group-living animals may benefit from gaining information based on the behaviour of other individuals. Indeed, social information is assumed to be faster and less costly to use than personal information, thus increasing foraging efficiency. However, when food sources change seasonally or are randomly distributed, individual information may become more reliable than social information. The aim of this study was to test the use of conflicting personal versus social information in goats (Capra hircus), in a foraging task. We found that goats relied more on personal than social information, when both types of information were available and in conflict. No effect of social rank was found on the occasions when goats followed other demonstrator goats. Goats are selective browsers/grazers and therefore relying on personal rather than social information could be the most efficient way to find patchily distributed resources in highly variable environments. Studies testing specific assumptions regarding the use of different sources of information can extend our understanding of decision making, including observed patterns of social learning. creator: Luigi Baciadonna creator: Alan G. McElligott creator: Elodie F. Briefer uri: https://doi.org/10.7717/peerj.172 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Baciadonna et al. title: MiR-184 regulates insulin secretion through repression of Slc25a22 link: https://peerj.com/articles/162 last-modified: 2013-09-24 description: Insulin secretion from pancreatic β-cells plays an essential role in blood glucose homeostasis and type 2 diabetes. Many genes are involved in the secretion of insulin and most of these genes can be targeted by microRNAs (miRNAs). However, the role of miRNAs in insulin secretion and type 2 diabetes has not been exhaustively studied. The expression miR-184, a miRNA enriched in pancreatic islets, negatively correlates with insulin secretion, suggesting that it is a good candidate for miRNA-mediated regulation of insulin secretion. Here we report that miR-184 inhibits insulin secretion in the MIN6 pancreatic β-cell line through the repression of its target Slc25a22, a mitochondrial glutamate carrier. Our study provides new insight into the regulation of insulin secretion by glutamate transport in mitochondria. creator: Sumiyo Morita creator: Takuro Horii creator: Mika Kimura creator: Izuho Hatada uri: https://doi.org/10.7717/peerj.162 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Morita et al. title: The controlled imitation task: a new paradigm for studying self-other control link: https://peerj.com/articles/161 last-modified: 2013-09-19 description: In the automatic imitation task (AIT) participants make a cued response during simultaneous exposure to a congruent or incongruent action made by another agent. Participants are slower to make the cued response on incongruent trials, which is thought to reflect conflict between the motor representation activated by the cue and the motor representation activated by the observed action. On incongruent trials, good performance requires the capacity to suppress the imitative action, in favor of producing the cued response. Here, we introduce a new experimental paradigm that complements the AIT, and is therefore a useful task for studying the control of self and other activated representations. In what we term the “Controlled Imitation Task (CIT)”, participants are cued to make an action, but on 50% of trials, within 100 ms of this cue, an on-screen hand makes a congruent or incongruent action. If the onscreen hand moves, the participant must suppress the cued response, and instead imitate the observed action as quickly and accurately as possible. In direct contrast to the AIT, the CIT requires suppression of a self-activated motor representation, and prioritization of an imitative response. In experiment 1, we report a robust pattern of interference effects in the CIT, such that participants are slower to make the imitative response on incongruent compared to congruent trials. In experiment 2, we replicate this effect while including a non-imitative spatial-cue control condition to show that the effect is particularly robust for imitative response tendencies per se. Owing to the essentially opposite control requirements of the CIT versus the AIT (i.e., suppression of self-activated motor representations instead of suppression of other-activated motor representations), we propose that this new task is a potentially informative complementary paradigm to the AIT that can be used in studies of self-other control processes. creator: Sukhvinder S. Obhi creator: Jeremy Hogeveen uri: https://doi.org/10.7717/peerj.161 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Obhi and Hogeveen title: Publication trends in neuroimaging of minimally conscious states link: https://peerj.com/articles/155 last-modified: 2013-09-19 description: We used existing and customized bibliometric and scientometric methods to analyze publication trends in neuroimaging research of minimally conscious states and describe the domain in terms of its geographic, contributor, and content features. We considered publication rates for the years 2002–2011, author interconnections, the rate at which new authors are added, and the domains that inform the work of author contributors. We also provided a content analysis of clinical and ethical themes within the relevant literature. We found a 27% growth in the number of papers over the period of study, professional diversity among a wide range of peripheral author contributors but only few authors who dominate the field, and few new technical paradigms and clinical themes that would fundamentally expand the landscape. The results inform both the science of consciousness as well as parallel ethics and policy studies of the potential for translational challenges of neuroimaging in research and health care of people with disordered states of consciousness. creator: Alex Garnett creator: Grace Lee creator: Judy Illes uri: https://doi.org/10.7717/peerj.155 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Garnett et al. title: Between tide and wave marks: a unifying model of physical zonation on littoral shores link: https://peerj.com/articles/154 last-modified: 2013-09-19 description: The effects of tides on littoral marine habitats are so ubiquitous that shorelines are commonly described as ‘intertidal’, whereas waves are considered a secondary factor that simply modifies the intertidal habitat. However mean significant wave height exceeds tidal range at many locations worldwide. Here we construct a simple sinusoidal model of coastal water level based on both tidal range and wave height. From the patterns of emergence and submergence predicted by the model, we derive four vertical shoreline benchmarks which bracket up to three novel, spatially distinct, and physically defined zones. The (1) emergent tidal zone is characterized by tidally driven emergence in air; the (2) wave zone is characterized by constant (not periodic) wave wash; and the (3) submergent tidal zone is characterized by tidally driven submergence. The decoupling of tidally driven emergence and submergence made possible by wave action is a critical prediction of the model. On wave-dominated shores (wave height ≫ tidal range), all three zones are predicted to exist separately, but on tide-dominated shores (tidal range ≫ wave height) the wave zone is absent and the emergent and submergent tidal zones overlap substantially, forming the traditional “intertidal zone”. We conclude by incorporating time and space in the model to illustrate variability in the physical conditions and zonation on littoral shores. The wave:tide physical zonation model is a unifying framework that can facilitate our understanding of physical conditions on littoral shores whether tropical or temperate, marine or lentic. creator: Christopher E. Bird creator: Erik C. Franklin creator: Celia M. Smith creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.154 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Bird et al. title: Behavioral niche partitioning in a sympatric tiger beetle assemblage and implications for the endangered Salt Creek tiger beetle link: https://peerj.com/articles/169 last-modified: 2013-09-17 description: How behavioral patterns are related to niche partitioning is an important question in understanding how closely related species within ecological communities function. Behavioral niche partitioning associated with thermoregulation is well documented in tiger beetles as a group. Co-occurring species of salt flat tiger beetles have adapted many thermoregulatory behaviors to cope with this harsh ecosystem. On first examination these beetles appear to occur in overlapping microhabitats and therefore compete for resources. To determine if behavioral niche partitioning is allowing multiple species to occur within the same harsh salt flat ecosystem we observed Cicindela nevadica lincolniana, Cicindela circumpicta, Cicindela fulgida, and Cicindela togata between 8:00 h and 21:00 h and recorded all behaviors related to thermoregulation using a digital voice recorder. Results of this study strongly indicate that competition among these species for resources has been reduced by the adaptation of different thermoregulatory behaviors such as spending time in shallow water, avoiding the sun during the hottest parts of the day, and by positioning their body against or away from the soil. The endangered C. n. lincolniana appears to rely most heavily on the shallow water of seeps for their diurnal foraging behavior (potentially limiting their foraging habitat), but with the advantage of allowing foraging during the hottest times of the day when potential competitors are less frequent. Ironically, this association also may help explain C. n. lincolniana’s susceptibility to extinction: beyond the loss of saline wetlands generally, limited seeps and pools even within remaining saline habitat may represent a further habitat limitation within an already limited habitat. creator: Tierney R. Brosius creator: Leon G. Higley uri: https://doi.org/10.7717/peerj.169 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Brosius et al. title: Prescribing of psychotropic medications to the elderly population of a Canadian province: a retrospective study using administrative databases link: https://peerj.com/articles/168 last-modified: 2013-09-17 description: Background. Psychotropic medications, in particular second-generation antipsychotics (SGAs) and benzodiazepines, have been associated with harm in elderly populations. Health agencies around the world have issued warnings about the risks of prescribing such medications to frail individuals affected by dementia and current guidelines recommend their use only in cases where the benefits clearly outweigh the risks. This study documents the use of psychotropic medications in the entire elderly population of a Canadian province in the context of current clinical guidelines for the treatment of behavioural disturbances.Methods. Prevalent and incident utilization of antipsychotics, benzodiazepines and related medications (zopiclone and zaleplon) were determined in the population of Manitobans over age 65 in the time period 1997/98 to 2008/09 fiscal years. Comparisons between patients living in the community and those living in personal care (nursing) homes (PCH) were conducted. Influence of sociodemographic characteristics on prescribing was assessed by generalized estimating equations. Non-optimal use was defined as the prescribing of high dose of antipsychotic medications and the use of combination therapy of a benzodiazepine (or zopiclone/zaleplon) with an antipsychotic. A decrease in intensity of use over time and lower proportions of patients treated with antipsychotics at high dose or in combination with benzodiazepines (or zopiclone/zaleplon) was considered a trend toward better prescribing. Multiple regression analysis determined predictors of non-optimal use in the elderly population.Results. A 20-fold greater prevalent utilization of SGAs was observed in PCH-dwelling elderly persons compared to those living in the community. In 2008/09, 27% of PCH-dwelling individuals received a prescription for an SGA. Patient characteristics, such as younger age, male gender, diagnoses of dementia (or use of an acetylcholinesterase inhibitor) or psychosis in the year prior the prescription, were predictors of non-optimal prescribing (e.g., high dose antipsychotics). During the period 2002/3 and 2007/8, amongst new users of SGAs, 10.2% received high doses. Those receiving high dose antipsychotics did not show high levels of polypharmacy.Conclusions. Despite encouraging trends, the use of psychotropic medications remains high in elderly individuals, especially in residents of nursing homes. Clinicians caring for such patients need to carefully assess risks and benefits. creator: Silvia Alessi-Severini creator: Matthew Dahl creator: Jennifer Schultz creator: Colleen Metge creator: Colette Raymond uri: https://doi.org/10.7717/peerj.168 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Alessi-Severini et al. title: Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology link: https://peerj.com/articles/167 last-modified: 2013-09-17 description: The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology.This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols.The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu). creator: Peter J.A. Cock creator: Björn A. Grüning creator: Konrad Paszkiewicz creator: Leighton Pritchard uri: https://doi.org/10.7717/peerj.167 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Cock et al. title: When given the opportunity, chimpanzees maximize personal gain rather than “level the playing field” link: https://peerj.com/articles/165 last-modified: 2013-09-17 description: We provided chimpanzees (Pan troglodytes) with the ability to improve the quality of food rewards they received in a dyadic test of inequity. We were interested to see if this provision influenced their responses and, if so, whether it was mediated by a social partner’s outcomes. We tested eight dyads using an exchange paradigm in which, depending on the condition, the chimpanzees were rewarded with either high-value (a grape) or low-value (a piece of celery) food rewards for each completed exchange. We included four conditions. In the first, “Different” condition, the subject received different, less-preferred, rewards than their partner for each exchange made (a test of inequity). In the “Unavailable” condition, high-value rewards were shown, but not given, to both chimpanzees prior to each exchange and the chimpanzees were rewarded equally with low-value rewards (a test of individual contrast). The final two conditions created equity. In these High-value and Low-value “Same” conditions both chimpanzees received the same food rewards for each exchange. Within each condition, the chimpanzees first completed ten trials in the Baseline Phase, in which the experimenter determined the rewards they received, and then ten trials in the Test Phase. In the Test Phase, the chimpanzees could exchange tokens through the aperture of a small wooden picture frame hung on their cage mesh in order to receive the high-value reward. Thus, in the Test Phase, the chimpanzees were provided with an opportunity to improve the quality of the rewards they received, either absolutely or relative to what their partner received. The chimpanzees responded in a targeted manner; in the Test Phase they attempted to maximize their returns in all conditions in which they had received low-value rewards during the Baseline Phase. Thus, the chimpanzees were apparently motivated to increase their reward regardless of their partners’, but they only used the mechanism provided when it afforded the opportunity for them to increase their rewards. We also found evidence that the chimpanzees’ responses were enhanced by social facilitation. Specifically, the chimpanzees were more likely to exchange their tokens through the frame when their test partner also did so, even in circumstances in which their reward value could not be improved. Our paradigm provided the chimpanzees with the possibility to improve the quality of rewards they received in the Test Phase. We found that refusals – to exchange tokens or to eat rewards – decreased significantly in the Test Phase compared to the Baseline Phase, where no such opportunity for improvement of outcomes existed. Thus, the chimpanzees participated more when they could improve the rewards they received. creator: Lydia M. Hopper creator: Susan P. Lambeth creator: Steven J. Schapiro creator: Sarah F. Brosnan uri: https://doi.org/10.7717/peerj.165 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Hopper et al. title: Using cloud-based mobile technology for assessment of competencies among medical students link: https://peerj.com/articles/164 last-modified: 2013-09-17 description: Valid, direct observation of medical student competency in clinical settings remains challenging and limits the opportunity to promote performance-based student advancement. The rationale for direct observation is to ascertain that students have acquired the core clinical competencies needed to care for patients. Too often student observation results in highly variable evaluations which are skewed by factors other than the student’s actual performance. Among the barriers to effective direct observation and assessment include the lack of effective tools and strategies for assuring that transparent standards are used for judging clinical competency in authentic clinical settings. We developed a web-based content management system under the name, Just in Time Medicine (JIT), to address many of these issues. The goals of JIT were fourfold: First, to create a self-service interface allowing faculty with average computing skills to author customizable content and criterion-based assessment tools displayable on internet enabled devices, including mobile devices; second, to create an assessment and feedback tool capable of capturing learner progress related to hundreds of clinical skills; third, to enable easy access and utilization of these tools by faculty for learner assessment in authentic clinical settings as a means of just in time faculty development; fourth, to create a permanent record of the trainees’ observed skills useful for both learner and program evaluation. From July 2010 through October 2012, we implemented a JIT enabled clinical evaluation exercise (CEX) among 367 third year internal medicine students. Observers (attending physicians and residents) performed CEX assessments using JIT to guide and document their observations, record their time observing and providing feedback to the students, and their overall satisfaction. Inter-rater reliability and validity were assessed with 17 observers who viewed six videotaped student-patient encounters and by measuring the correlation between student CEX scores and their scores on subsequent standardized-patient OSCE exams. A total of 3567 CEXs were completed by 516 observers. The average number of evaluations per student was 9.7 (±1.8 SD) and the average number of CEXs completed per observer was 6.9 (±15.8 SD). Observers spent less than 10 min on 43–50% of the CEXs and 68.6% on feedback sessions. A majority of observers (92%) reported satisfaction with the CEX. Inter-rater reliability was measured at 0.69 among all observers viewing the videotapes and these ratings adequately discriminated competent from non-competent performance. The measured CEX grades correlated with subsequent student performance on an end-of-year OSCE. We conclude that the use of JIT is feasible in capturing discrete clinical performance data with a high degree of user satisfaction. Our embedded checklists had adequate inter-rater reliability and concurrent and predictive validity. creator: Gary S. Ferenchick creator: David Solomon uri: https://doi.org/10.7717/peerj.164 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Ferenchick and Solomon title: Microgeographic maladaptive performance and deme depression in response to roads and runoff link: https://peerj.com/articles/163 last-modified: 2013-09-17 description: Despite theoretical understanding and empirical detection of local adaptation in natural environments, our knowledge of such divergence in fragmented habitats remains limited, especially in the context of microgeographic spatial scales and contemporary time scales. I used a combination of reciprocal transplant and common garden exposure experiments to evaluate potential microgeographic divergence in a pool-breeding amphibian occupying a landscape fragmented by roads. As indicated by reduced rates of survival and increased rates of malformation, I found evidence for maladaptation in road adjacent populations. This response is in direct counterpoint to recently described local adaption by a cohabiting species of amphibian. These results suggest that while divergence might commonly follow habitat modification, the direction of its outcome cannot be generalized even in identical habitats. Further, maladaptive responses can be associated with a more generalized depression effect that transcends the local environment. Alongside recent reports, these results suggest that maladaptive responses may be an emerging consequence of human-induced environmental change. Thus future studies should carefully consider the population unit as a key level for inference. creator: Steven P. Brady uri: https://doi.org/10.7717/peerj.163 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Brady title: Periodontal status among adolescents in Georgia. A pathfinder study link: https://peerj.com/articles/137 last-modified: 2013-09-17 description: Objectives. The aim of the present pathfinder study was to screen and map the periodontal status of Georgian population in accordance with the guidelines of the World Health Organization for population based surveys.Methods. During 2012, a pathfinder study was conducted to collect this data. For the periodontal portion of the study, 15-year-old school children were examined in the capital city of Tbilisi as well as in two other large cities and 4 smaller villages. All participants were examined by a trained dental team in a classroom using a dental mirror and a periodontal probe. Periodontal examination included plaque scores, calculus scores, probing depth measurements and bleeding on probing. These measurements were recorded for the Ramfjord index teeth.Results. A total of 397 15-year-old participants were examined in this pathfinder study. There were 240 females (60.45%) and 157 males (39.55%). Of the total participants 196 (49.37%) were urban adolescents while 201 (50.63%) were from rural communities. Mean probing depth was 3.34 ± 0.57 mm with a range of 1 to 10 mm; a relatively high proportion (34.26%) of these subjects presented with at least one site with pockets of 5 mm or deeper. Males presented with greater plaque, calculus and probing depths than females. When urban and rural populations were compared, urban participants presented with more plaque, probing depths and bleeding on probing. Greater pocket depths were found to be related to the presence of plaque calculus and bleeding on probing.Conclusions. Overall, rather high incidences of periodontal pockets ≥ 5 mm were detected in this population. This data should serve to prepare further more detailed epidemiological studies that will serve to plan and implement prevent and treat strategies for periodontal diseases in Georgia and also help make manpower decisions. creator: Liran Levin creator: Vladimer Margvelashvili creator: Leon Bilder creator: Manana Kalandadze creator: Nino Tsintsadze creator: Eli E. Machtei uri: https://doi.org/10.7717/peerj.137 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Levin et al. title: Masticatory biomechanics of the Laotian rock rat, Laonastes aenigmamus, and the function of the zygomaticomandibularis muscle link: https://peerj.com/articles/160 last-modified: 2013-09-12 description: The Laotian rock rat, Laonastes aenigmamus, is one of the most recently discovered species of rodent, and displays a cranial morphology that is highly specialised. The rostrum of L. aenigmamus is exceptionally elongate and bears a large attachment site for the infraorbital portion of the zygomaticomandibularis muscle (IOZM), which is particularly well-developed in this species. In this study, we used finite element analysis to investigate the biomechanical performance of the Laotian rock rat cranium and to elucidate the function of the IOZM. A finite element model of the skull of L. aenigmamus was constructed and solved for biting on each of the teeth (incisors, premolar and molars). Further load cases were created and solved in which the origin of the IOZM had been moved anteriorly and posteriorly along the rostrum. Finally, a set of load cases were produced in which the IOZM was removed entirely, and its force was redistributed between the remaining masticatory muscles. The analysis showed that, during biting, the most stressed areas of the skull were the zygomatic and orbital regions. Compared to other rodents, L. aenigmamus is highly efficient at incisor gnawing, but less efficient at molar chewing. However, a relatively constant bite force across the molar tooth row may be an adaptation to folivory. Movement of the origin of the IOZM had little on the patterns of von Mises stresses, or the overall stress experienced by the cranium. However, removal of the IOZM had a substantial effect on the total deformation experienced by the skull. In addition, the positioning and presence of the IOZM had large impact on bite force. Moving the IOZM origin to the anterior tip of the rostrum led to a substantially reduced bite force at all teeth. This was hypothesised to be a result of the increasing horizontal component to the pull of this muscle as it is moved anteriorly along the rostrum. Removal of the IOZM also resulted in reduced bite force, even when the total input muscle force was maintained at the same level. It was thus concluded that the function of the IOZM in L. aenigmamus is to increase bite force whilst reducing cranial deformation. If the IOZM can be shown to have this function in other rodent groups, this may help explain the evolution of this muscle, and may also provide an understanding of why it has evolved independently several times within rodents. creator: Philip G. Cox creator: Joanna Kirkham creator: Anthony Herrel uri: https://doi.org/10.7717/peerj.160 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Cox et al. title: BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways link: https://peerj.com/articles/159 last-modified: 2013-09-12 description: BD-Func (BiDirectional FUNCtional enrichment) is an algorithm that calculates functional enrichment by comparing lists of pre-defined genes that are known to be activated versus inhibited in a pathway or by a regulatory molecule. This paper shows that BD-Func can correctly predict cell line alternations and patient characteristics with accuracy comparable to popular algorithms, with a significantly faster run-time. BD-Func can compare scores for individual samples across multiple groups as well as provide predictive statistics and receiver operating characteristic (ROC) plots to quantify the accuracy of the signature associated with a binary phenotypic variable. BD-Func facilitates collaboration and reproducibility by encouraging users to share novel molecular signatures in the BD-Func discussion group, which is where the novel progesterone receptor and LBH589 signatures from this paper can be found. The novel LBH589 signature presented in this paper also serves as a case study showing how a custom signature using cell line data can accurately predict activity in vivo. This software is available to download at https://sourceforge.net/projects/bdfunc/. creator: Charles D. Warden creator: Noriko Kanaya creator: Shiuan Chen creator: Yate-Ching Yuan uri: https://doi.org/10.7717/peerj.159 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Warden et al. title: Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth link: https://peerj.com/articles/157 last-modified: 2013-09-12 description: In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson’s index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPDθ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult. creator: Connor O. McCoy creator: Frederick A. Matsen uri: https://doi.org/10.7717/peerj.157 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 McCoy et al. title: Cannabidiol changes P-gp and BCRP expression in trophoblast cell lines link: https://peerj.com/articles/153 last-modified: 2013-09-12 description: Objectives. Marijuana is the most commonly used illicit drug during pregnancy. Due to high lipophilicity, cannabinoids can easily penetrate physiological barriers like the human placenta and jeopardize the developing fetus. We evaluated the impact of cannabidiol (CBD), a major non-psychoactive cannabinoid, on P-glycoprotein (P-gp) and Breast Cancer Resistance Protein (BCRP) expression, and P-gp function in a placental model, BeWo and Jar choriocarcinoma cell lines (using P-gp induced MCF7 cells (MCF7/P-gp) for comparison).Study design. Following the establishment of the basal expression of these transporters in the membrane fraction of all three cell lines, P-gp and BCRP protein and mRNA levels were determined following chronic (24–72 h) exposure to CBD, by Western Blot and qPCR. CBD impact on P-gp efflux function was examined by uptake of specific P-gp fluorescent substrates (calcein-AM, DiOC2(3) and rhodamine123(rh123)). Cyclosporine A (CsA) served as a positive control.Results. Chronic exposure to CBD resulted in significant changes in the protein and mRNA levels of both transporters. While P-gp was down-regulated, BCRP levels were up-regulated in the choriocarcinoma cell lines. CBD had a remarkably different influence on P-gp and BCRP expression in MCF7/P-gp cells, demonstrating that these are cell type specific effects. P-gp dependent efflux (of calcein, DiOC2(3) and rh123) was inhibited upon short-term exposure to CBD.Conclusions. Our study shows that CBD might alter P-gp and BCRP expression in the human placenta, and inhibit P-gp efflux function. We conclude that marijuana use during pregnancy may reduce placental protective functions and change its morphological and physiological characteristics. creator: Valeria Feinshtein creator: Offer Erez creator: Zvi Ben-Zvi creator: Noam Erez creator: Tamar Eshkoli creator: Boaz Sheizaf creator: Eyal Sheiner creator: Mahmud Huleihel creator: Gershon Holcberg uri: https://doi.org/10.7717/peerj.153 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Feinshtein et al. title: Estradiol differentially affects auditory recognition and learning according to photoperiodic state in the adult male songbird, European starling (Sturnus vulgaris) link: https://peerj.com/articles/150 last-modified: 2013-09-12 description: Changes in hormones can affect many types of learning in vertebrates. Adults experience fluctuations in a multitude of hormones over a temporal scale, from local, rapid action to more long-term, seasonal changes. Endocrine changes during development can affect behavioral outcomes in adulthood, but how learning is affected in adults by hormone fluctuations experienced during adulthood is less understood. Previous reports have implicated the sex steroid hormone estradiol (E2) in both male and female vertebrate cognitive functioning. Here, we examined the effects of E2 on auditory recognition and learning in male European starlings (Sturnus vulgaris). European starlings are photoperiodic, seasonally breeding songbirds that undergo different periods of reproductive activity according to annual changes in day length. We simulated these reproductive periods, specifically 1. photosensitivity, 2. photostimulation, and 3. photorefractoriness in captive birds by altering day length. During each period, we manipulated circulating E2 and examined multiple measures of learning. To manipulate circulating E2, we used subcutaneous implants containing either 17-β E2 and/or fadrozole (FAD), a highly specific aromatase inhibitor that suppresses E2 production in the body and the brain, and measured the latency for birds to learn and respond to short, male conspecific song segments (motifs). We report that photostimulated birds given E2 had higher response rates and responded with better accuracy than those given saline controls or FAD. Conversely, photosensitive, animals treated with E2 responded with less accuracy than those given FAD. These results demonstrate how circulating E2 and photoperiod can interact to shape auditory recognition and learning in adults, driving it in opposite directions in different states. creator: Rebecca M. Calisi creator: Daniel P. Knudsen creator: Jesse S. Krause creator: John C. Wingfield creator: Timothy Q. Gentner uri: https://doi.org/10.7717/peerj.150 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Calisi et al. title: A systematic review of methods for studying consumer health YouTube videos, with implications for systematic reviews link: https://peerj.com/articles/147 last-modified: 2013-09-12 description: Background. YouTube is an increasingly important medium for consumer health information – with content provided by healthcare professionals, government and non-government organizations, industry, and consumers themselves. It is a rapidly developing area of study for healthcare researchers. We examine the methods used in reviews of YouTube consumer health videos to identify trends and best practices.Methods and Materials. Published reviews of consumer-oriented health-related YouTube videos were identified through PubMed. Data extracted from these studies included type of journal, topic, characteristics of the search, methods of review including number of reviewers and method to achieve consensus between reviewers, inclusion and exclusion criteria, characteristics of the videos reported, ethical oversight, and follow-up.Results. Thirty-three studies were identified. Most were recent and published in specialty journals. Typically, these included more than 100 videos, and were examined by multiple reviewers. Most studies described characteristics of the videos, number of views, and sometime characteristics of the viewers. Accuracy of portrayal of the health issue under consideration was a common focus.Conclusion. Optimal transparency and reproducibility of studies of YouTube health-related videos can be achieved by following guidance designed for systematic review reporting, with attention to several elements specific to the video medium. Particularly when seeking to replicate consumer viewing behavior, investigators should consider the method used to select search terms, and use a snowballing rather than a sequential screening approach. Discontinuation protocols for online screening of relevance ranked search results is an area identified for further development. creator: Margaret Sampson creator: Jordi Cumber creator: Claudia Li creator: Catherine M. Pound creator: Ann Fuller creator: Denise Harrison uri: https://doi.org/10.7717/peerj.147 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Sampson et al. title: ABT-737, a small molecule Bcl-2/Bcl-xL antagonist, increases antimitotic-mediated apoptosis in human prostate cancer cells link: https://peerj.com/articles/144 last-modified: 2013-09-12 description: Castration-resistant prostate cancer (CRPC) expresses high levels of the anti-apoptotic proteins Bcl-2, Bcl-xL and Mcl-1, resulting in resistance to apoptosis and association with poor prognosis. Docetaxel, an antimitotic drug that is the first-line treatment strategy for CRPC, is known to provide a small survival benefit. However, docetaxel chemotherapy alone is not enough to counteract the high levels of Bcl-2/Bcl-xL/Mcl-1 present in CRPC. ABT-737 is a small molecule that binds to Bcl-2/Bcl-xL (but not Mcl-1) with high affinity and disrupts their interaction with pro-apoptotic Bax/Bak, thus enhancing apoptosis. Our results indicate that ABT-737 can sensitize androgen-dependent LNCaP and CRPC PC3 cells to docetaxel- and to the novel antimitotic ENMD-1198-mediated caspase-dependent apoptosis. CRPC DU145 cells, however, are more resistant to ABT-737 because they are Bax null and not because they express the highest levels of anti-apoptotic Mcl-1 (associated with ABT-737 resistance). Knockdown of Bax or Bak in LNCaP indicates that ABT-737-induced antimitotic enhancement of apoptosis is more dependent on the levels of Bax than Bak. Furthermore, we find that the ability of docetaxel to increase cyclin B1/Cdk1-mediated phosphorylation of Bcl-2/Bcl-xL and decrease Mcl-1 is required for ABT-737 to enhance apoptosis in PC3 cells, as determined by addition of Cdk1 inhibitor purvalanol A and expression of shRNA specific for cyclin B1. Overall, our data suggests that the high levels of anti-apoptotic proteins in Bax-expressing CRPC cells can be overcome by targeting Bcl-2/Bcl-xL with ABT-737 and Mcl-1 with antimitotics. creator: Ricardo Parrondo creator: Alicia de las Pozas creator: Teresita Reiner creator: Carlos Perez-Stable uri: https://doi.org/10.7717/peerj.144 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Parrondo et al. title: Matching based on biological categories in Orangutans (Pongo abelii) and a Gorilla (Gorilla gorilla gorilla) link: https://peerj.com/articles/158 last-modified: 2013-09-10 description: Following a series of experiments in which six orangutans and one gorilla discriminated photographs of different animal species in a two-choice touch screen procedure, Vonk & MacDonald (2002) and Vonk & MacDonald (2004) concluded that orangutans, but not the gorilla, seemed to learn intermediate level category discriminations, such as primates versus non-primates, more rapidly than they learned concrete level discriminations, such as orangutans versus humans. In the current experiments, four of the same orangutans and the gorilla were presented with delayed matching-to-sample tasks in which they were rewarded for matching photos of different members of the same primate species; golden lion tamarins, Japanese macaques, and proboscis monkeys, or family; gibbons, lemurs (Experiment 1), and subsequently for matching photos of different species within the following classes: birds, reptiles, insects, mammals, and fish (Experiment 2). Members of both Great Ape species were rapidly able to match the photos at levels above chance. Orangutans matched images from both category levels spontaneously whereas the gorilla showed effects of learning to match intermediate level categories. The results show that biological knowledge is not necessary to form natural categories at both concrete and intermediate levels. creator: Jennifer Vonk uri: https://doi.org/10.7717/peerj.158 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Vonk title: The affective profiles in the USA: happiness, depression, life satisfaction, and happiness-increasing strategies link: https://peerj.com/articles/156 last-modified: 2013-09-10 description: Background. The affective profiles model categorizes individuals as self-fulfilling (high positive affect, low negative affect), high affective (high positive affect, high negative affect), low affective (low positive affect, low negative affect), and self-destructive (low positive affect, high negative affect). The model has been used extensively among Swedes to discern differences between profiles regarding happiness, depression, and also life satisfaction. The aim of the present study was to investigate such differences in a sample of residents of the USA. The study also investigated differences between profiles with regard to happiness-increasing strategies.Methods. In Study I, 900 participants reported affect (Positive Affect Negative Affect Schedule; PANAS) and happiness (Happiness-Depression Scale). In Study II, 500 participants self-reported affect (PANAS), life satisfaction (Satisfaction With Life Scale), and how often they used specific strategies to increase their own happiness (Happiness-Increasing Strategies Scales).Results. The results showed that, compared to the other profiles, self-fulfilling individuals were less depressed, happier, and more satisfied with their lives. Nevertheless, self-destructive individuals were more depressed, unhappier, and less satisfied than all other profiles. The self-fulfilling individuals tended to use strategies related to agentic (e.g., instrumental goal-pursuit), communal (e.g., social affiliation), and spiritual (e.g., religion) values when pursuing happiness.Conclusion. These differences suggest that promoting positive emotions can positively influence a depressive-to-happy state as well as increasing life satisfaction. Moreover, the present study shows that pursuing happiness through strategies guided by agency, communion, and spirituality is related to a self-fulfilling experience described as high positive affect and low negative affect. creator: Erica Schütz creator: Uta Sailer creator: Ali Al Nima creator: Patricia Rosenberg creator: Ann-Christine Andersson Arntén creator: Trevor Archer creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.156 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Schtz et al. title: Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes link: https://peerj.com/articles/152 last-modified: 2013-09-10 description: Background. RNA editing is a post-transcriptional regulatory mechanism that can alter the coding sequences of certain genes in response to physiological demands. We previously identified C-to-U RNA editing (C136U, R46X) which inactivates a small fraction of succinate dehydrogenase (SDH; mitochondrial complex II) subunit B gene (SDHB) mRNAs in normal steady-state peripheral blood mononuclear cells (PBMCs). SDH is a heterotetrameric tumor suppressor complex which when mutated causes paraganglioma tumors that are characterized by constitutive activation of hypoxia inducible pathways. Here, we studied regulation, extent and cell type origin of SDHB RNA editing.Methods. We used short-term cultured PBMCs obtained from random healthy platelet donors, performed monocyte enrichment by cold aggregation, employed a novel allele-specific quantitative PCR method, flow cytometry, immunologic cell separation, gene expression microarray, database analysis and high-throughput RNA sequencing.Results. While the editing rate is low in uncultured monocyte-enriched PBMCs (average rate 2.0%, range 0.4%–6.3%, n = 42), it is markedly upregulated upon exposure to 1% oxygen tension (average rate 18.2%, range 2.8%–49.4%, n = 14) and during normoxic macrophage differentiation in the presence of serum (average rate 10.1%, range 2.7%–18.8%, n = 17). The normoxic induction of SDHB RNA editing was associated with the development of dense adherent aggregates of monocytes in culture. CD14-positive monocyte isolation increased the percentages of C136U transcripts by 1.25-fold in normoxic cultures (n = 5) and 1.68-fold in hypoxic cultures (n = 4). CD14-negative lymphocytes showed no evidence of SDHB editing. The SDHB genomic DNA remained wild-type during increased RNA editing. Microarray analysis showed expression changes in wound healing and immune response pathway genes as the editing rate increased in normoxic cultures. High-throughput sequencing of SDHB and SDHD transcripts confirmed the induction of C136U RNA editing in normoxic cultures but showed no additional verifiable coding edits. Analysis of SDHB RNA sequence data from 16 normal human tissues from the Illumina Body Map and from 45 samples representing 23 different cell types from the ENCODE projects confirmed the occurrence of site-specific C136U editing in whole blood (1.7%) and two primary CD14+ monocyte samples (1.9% and 2.6%). In contrast, the other cell types showed an average of 0.2% and 0.1% C136U editing rates in the two databases, respectively.Conclusions. These findings demonstrate that C-to-U coding RNA editing of certain genes is dynamically induced by physiologically relevant environmental factors and suggest that epigenetic downregulation of SDHB by site-specific RNA editing plays a role in hypoxia adaptation in monocytes. creator: Bora E. Baysal creator: Kitty De Jong creator: Biao Liu creator: Jianmin Wang creator: Santosh K. Patnaik creator: Paul K. Wallace creator: Robert T. Taggart uri: https://doi.org/10.7717/peerj.152 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Baysal et al. title: Do N-arachidonyl-glycine (NA-glycine) and 2-arachidonoyl glycerol (2-AG) share mode of action and the binding site on the β2 subunit of GABAA receptors? link: https://peerj.com/articles/149 last-modified: 2013-09-10 description: NA-glycine is an endogenous lipid molecule with analgesic properties, which is structurally similar to the endocannabinoids 2-AG and anandamide but does not interact with cannabinoid receptors. NA-glycine has been suggested to act at the G-protein coupled receptors GPR18 and GPR92. Recently, we have described that NA-glycine can also modulate recombinant α1β2γ2 GABAA receptors. Here we characterize in more detail this modulation and investigate the relationship of its binding site with that of the endocannabinoid 2-AG. creator: Roland Baur creator: Jürg Gertsch creator: Erwin Sigel uri: https://doi.org/10.7717/peerj.149 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Baur et al. title: On the reproducibility of science: unique identification of research resources in the biomedical literature link: https://peerj.com/articles/148 last-modified: 2013-09-05 description: Scientific reproducibility has been at the forefront of many news stories and there exist numerous initiatives to help address this problem. We posit that a contributor is simply a lack of specificity that is required to enable adequate research reproducibility. In particular, the inability to uniquely identify research resources, such as antibodies and model organisms, makes it difficult or impossible to reproduce experiments even where the science is otherwise sound. In order to better understand the magnitude of this problem, we designed an experiment to ascertain the “identifiability” of research resources in the biomedical literature. We evaluated recent journal articles in the fields of Neuroscience, Developmental Biology, Immunology, Cell and Molecular Biology and General Biology, selected randomly based on a diversity of impact factors for the journals, publishers, and experimental method reporting guidelines. We attempted to uniquely identify model organisms (mouse, rat, zebrafish, worm, fly and yeast), antibodies, knockdown reagents (morpholinos or RNAi), constructs, and cell lines. Specific criteria were developed to determine if a resource was uniquely identifiable, and included examining relevant repositories (such as model organism databases, and the Antibody Registry), as well as vendor sites. The results of this experiment show that 54% of resources are not uniquely identifiable in publications, regardless of domain, journal impact factor, or reporting requirements. For example, in many cases the organism strain in which the experiment was performed or antibody that was used could not be identified. Our results show that identifiability is a serious problem for reproducibility. Based on these results, we provide recommendations to authors, reviewers, journal editors, vendors, and publishers. Scientific efficiency and reproducibility depend upon a research-wide improvement of this substantial problem in science today. creator: Nicole A. Vasilevsky creator: Matthew H. Brush creator: Holly Paddock creator: Laura Ponting creator: Shreejoy J. Tripathy creator: Gregory M. LaRocca creator: Melissa A. Haendel uri: https://doi.org/10.7717/peerj.148 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Vasilevsky et al. title: Effect of stimulus width on simultaneous contrast link: https://peerj.com/articles/146 last-modified: 2013-09-05 description: Perceived brightness of a stimulus depends on the background against which the stimulus is set, a phenomenon known as simultaneous contrast. For instance, the same gray stimulus can look light against a black background or dark against a white background. Here we quantified the perceptual strength of simultaneous contrast as a function of stimulus width. Previous studies have reported that wider stimuli result in weaker simultaneous contrast, whereas narrower stimuli result in stronger simultaneous contrast. However, no previous research has quantified this relationship. Our results show a logarithmic relationship between stimulus width and perceived brightness. This relationship is well matched by the normalized output of a Difference-of-Gaussians (DOG) filter applied to stimuli of varied widths. creator: Veronica Shi creator: Jie Cui creator: Xoana G. Troncoso creator: Stephen L. Macknik creator: Susana Martinez-Conde uri: https://doi.org/10.7717/peerj.146 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Shi et al. title: Typhoon damage on a shallow mesophotic reef in Okinawa, Japan link: https://peerj.com/articles/151 last-modified: 2013-09-03 description: Little is known about effects of large storm systems on mesophotic reefs. This study reports on how Typhoon 17 (Jelawat) affected Ryugu Reef on Okinawa-jima, Japan in September 2012. Benthic communities were surveyed before and after the typhoon using line intercept transect method. Comparison of the benthic assemblages showed highly significant differences in coral coverage at depths of 25–32 m before and after Typhoon 17. A large deep stand of Pachyseris foliosa was apparently less resistant to the storm than the shallower high diversity area of this reef. Contradictory to common perception, this research shows that large foliose corals at deeper depths are just as susceptible to typhoon damage as shallower branching corals. However, descriptive functional group analyses resulted in only minor changes after the disturbance, suggesting the high likelihood of recovery and the high resilience capacity of this mesophotic reef. creator: Kristine N. White creator: Taku Ohara creator: Takuma Fujii creator: Iori Kawamura creator: Masaru Mizuyama creator: Javier Montenegro creator: Haruka Shikiba creator: Tohru Naruse creator: TY McClelland creator: Vianney Denis creator: James D. Reimer uri: https://doi.org/10.7717/peerj.151 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 White et al.