title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&month=2014-11
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Transcriptome analyses of Anguillicola crassus from native and novel hosts
link: https://peerj.com/articles/684
last-modified: 2014-11-27
description: Anguillicola crassus is a swim bladder nematode of eels. The parasite is native to the Asian eel Anguilla japonica, but was introduced to Europe and the European eel Anguilla anguilla in the early 1980s. A Taiwanese source has been proposed for this introduction. In the new host in the recipient area, the parasite appears to be more pathogenic. As a reason for these differences, genetically fixed differences in infectivity and development between Taiwanese and European A.crassus have been described and disentangled from plasticity induced by different host environments. To explore whether transcriptional regulation is involved in these lifecycle differences, we have analysed a “common garden”, cross infection experiment, using deep-sequencing transcriptomics. Surprisingly, in the face of clear phenotypic differences in life history traits, we identified no significant differences in gene expression between parasite populations or between experimental host species. From 120,000 SNPs identified in the transcriptome data we found that European A. crassus were not a genetic subset of the Taiwanese nematodes sampled. The loci that have the major contribution to the European-Taiwanese population differentiation show an enrichment of synonymous and non-coding polymorphism. This argues against positive selection in population differentiation. However, genes involved in protein processing in the endoplasmatic reticulum membrane and genes bearing secretion signal sequences were enriched in the set of genes most differentiated between European and Taiwanese A. crassus. These genes could be a source for the phenotypically visible genetically fixed differences between European and Taiwanese A. crassus.
creator: Emanuel Heitlinger
creator: Horst Taraschewski
creator: Urszula Weclawski
creator: Karim Gharbi
creator: Mark Blaxter
uri: https://doi.org/10.7717/peerj.684
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Heitlinger et al.

title: Removal of corallivorous snails as a proactive tool for the conservation of acroporid corals
link: https://peerj.com/articles/680
last-modified: 2014-11-27
description: Corallivorous snail feeding is a common source of tissue loss for the threatened coral, Acropora palmata, accounting for roughly one-quarter of tissue loss in monitored study plots over seven years. In contrast with larger threats such as bleaching, disease, or storms, corallivory by Coralliophila abbreviata is one of the few direct sources of partial mortality that may be locally managed. We conducted a field experiment to explore the effectiveness and feasibility of snail removal. Long-term monitoring plots on six reefs in the upper Florida Keys were assigned to one of three removal treatments: (1) removal from A. palmata only, (2) removal from all host coral species, or (3) no-removal controls. During the initial removal in June 2011, 436 snails were removed from twelve 150 m2 plots. Snails were removed three additional times during a seven month “removal phase”, then counted at five surveys over the next 19 months to track recolonization. At the conclusion, snails were collected, measured and sexed. Before-After-Control-Impact analysis revealed that both snail abundance and feeding scar prevalence were reduced in removal treatments compared to the control, but there was no difference between removal treatments. Recolonization by snails to baseline abundance is estimated to be 3.7 years and did not differ between removal treatments. Recolonization rate was significantly correlated with baseline snail abundance. Maximum snail size decreased from 47.0 mm to 34.6 mm in the removal treatments. The effort required to remove snails from A. palmata was 30 diver minutes per 150 m2 plot, compared with 51 min to remove snails from all host corals. Since there was no additional benefit observed with removing snails from all host species, removals can be more efficiently focused on only A. palmata colonies and in areas where C. abbreviata abundance is high, to effectively conserve A. palmata in targeted areas.
creator: Dana E. Williams
creator: Margaret W. Miller
creator: Allan J. Bright
creator: Caitlin M. Cameron
uri: https://doi.org/10.7717/peerj.680
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Williams et al.

title: Visual analytics in healthcare education: exploring novel ways to analyze and represent big data in undergraduate medical education
link: https://peerj.com/articles/683
last-modified: 2014-11-25
description: Introduction. The big data present in the medical curriculum that informs undergraduate medical education is beyond human abilities to perceive and analyze. The medical curriculum is the main tool used by teachers and directors to plan, design, and deliver teaching and assessment activities and student evaluations in medical education in a continuous effort to improve it. Big data remains largely unexploited for medical education improvement purposes. The emerging research field of visual analytics has the advantage of combining data analysis and manipulation techniques, information and knowledge representation, and human cognitive strength to perceive and recognize visual patterns. Nevertheless, there is a lack of research on the use and benefits of visual analytics in medical education.Methods. The present study is based on analyzing the data in the medical curriculum of an undergraduate medical program as it concerns teaching activities, assessment methods and learning outcomes in order to explore visual analytics as a tool for finding ways of representing big data from undergraduate medical education for improvement purposes. Cytoscape software was employed to build networks of the identified aspects and visualize them.Results. After the analysis of the curriculum data, eleven aspects were identified. Further analysis and visualization of the identified aspects with Cytoscape resulted in building an abstract model of the examined data that presented three different approaches; (i) learning outcomes and teaching methods, (ii) examination and learning outcomes, and (iii) teaching methods, learning outcomes, examination results, and gap analysis.Discussion. This study identified aspects of medical curriculum that play an important role in how medical education is conducted. The implementation of visual analytics revealed three novel ways of representing big data in the undergraduate medical education context. It appears to be a useful tool to explore such data with possible future implications on healthcare education. It also opens a new direction in medical education informatics research.
creator: Christos Vaitsis
creator: Gunnar Nilsson
creator: Nabil Zary
uri: https://doi.org/10.7717/peerj.683
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Vaitsis et al.

title: Spawning aggregation behavior and reproductive ecology of the giant bumphead parrotfish, Bolbometopon muricatum, in a remote marine reserve
link: https://peerj.com/articles/681
last-modified: 2014-11-25
description: The giant bumphead parrotfish (Bolbometopon muricatum) has experienced precipitous population declines throughout its range due to its importance as a highly-prized fishery target and cultural resource. Because of its diet, Bolbometopon may serve as a keystone species on Indo-Pacific coral reefs, yet comprehensive descriptions of its reproductive ecology do not exist. We used a variety of underwater visual census (UVC) methods to study an intact population of Bolbometopon at Wake Atoll, a remote and protected coral atoll in the west Pacific. Key observations include spawning activities in the morning around the full and last quarter moon, with possible spawning extending to the new moon. We observed peaks in aggregation size just prior to and following the full and last quarter moon, respectively, and observed a distinct break in spawning at the site that persisted for four days; individuals returned to the aggregation site one day prior to the last quarter moon and resumed spawning the following day. The mating system was lek-based, characterized by early male arrival at the spawning site followed by vigorous defense (including head-butting between large males) of small territories. These territories were apparently used to attract females that arrived later in large schools, causing substantial changes in the sex ratio on the aggregation site at any given time during the morning spawning period. Aggression between males and courtship of females led to pair spawning within the upper water column. Mating interference was not witnessed but we noted instances suggesting that sperm competition might occur. Densities of Bolbometopon on the aggregation site averaged 10.07(±3.24 SE) fish per hectare (ha) with maximum densities of 51.5 fish per ha. By comparing our observations to the results of biennial surveys conducted by the National Oceanic and Atmospheric Administration (NOAA) Coral Reef Ecosystem Division (CRED), we confirmed spatial consistency of the aggregation across years as well as a temporal break in spawning activity and aggregation that occurred during the lunar phase. We estimated the area encompassed by the spawning aggregation to be 0.72 ha, suggesting that spawning site closures and temporal closures centered around the full to the new moon might form one component of a management and conservation plan for this species. Our study of the mating system and spawning aggregation behavior of Bolbometopon from the protected, relatively pristine population at Wake Atoll provides crucial baselines of population density, sex ratio composition, and productivity of a spawning aggregation site from an oceanic atoll. Such information is key for conservation efforts and provides a basic platform for the design of marine protected areas for this threatened iconic coral reef fish, as well as for species with similar ecological and life history characteristics.
creator: Roldan C. Muñoz
creator: Brian J. Zgliczynski
creator: Bradford Z. Teer
creator: Joseph L. Laughlin
uri: https://doi.org/10.7717/peerj.681
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: © 2014 Muñoz et al.

title: The PGI enzyme system and fitness response to temperature as a measure of environmental tolerance in an invasive species
link: https://peerj.com/articles/676
last-modified: 2014-11-25
description: In the field of invasion ecology, the determination of a species’ environmental tolerance, is a key parameter in the prediction of its potential distribution, particularly in the context of global warming. In poikilothermic species such as insects, temperature is often considered the most important abiotic factor that affects numerous life-history and fitness traits through its effect on metabolic rate. Therefore the response of an insect to challenging temperatures may provide key information as to its climatic and therefore spatial distribution. Variation in the phosphoglucose-6-isomerase (PGI) metabolic enzyme-system has been proposed in some insects to underlie their relative fitness, and is recognised as a key enzyme in their thermal adaptation. However, in this context it has not been considered as a potential mechanism contributing to a species invasive cability. The present study aimed to compare the thermal tolerance of an invasive scarabaeid beetle, Costelytra zealandica (White) with that of the closely related, and in part sympatrically occurring, congeneric non-invasive species C. brunneum (Broun), and to consider whether any correlation with particular PGI genotypes was apparent. Third instar larvae of each species were exposed to one of three different temperatures (10, 15 and 20 °C) over six weeks and their fitness (survival and growth rate) measured and PGI phenotyping performed via cellulose acetate electrophoresis. No consistent relationship between PGI genotypes and fitness was detected, suggesting that PGI may not be contributing to the invasion success and pest status of C. zealandica.
creator: Marie-Caroline Lefort
creator: Samuel Brown
creator: Stéphane Boyer
creator: Susan Worner
creator: Karen Armstrong
uri: https://doi.org/10.7717/peerj.676
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Lefort et al.

title: Systematics of putative euparkeriids (Diapsida: Archosauriformes) from the Triassic of China
link: https://peerj.com/articles/658
last-modified: 2014-11-25
description: The South African species Euparkeria capensis is of great importance for understanding the early radiation of archosauromorphs (including archosaurs) following the Permo–Triassic mass extinction, as most phylogenetic analyses place it as the sister taxon to crown group Archosauria within the clade Archosauriformes. Although a number of species from Lower–Middle Triassic deposits worldwide have been referred to the putative clade Euparkeriidae, the monophyly of Euparkeriidae is controversial and has yet to be demonstrated by quantitative phylogenetic analysis. Three Chinese taxa have been recently suggested to be euparkeriids: Halazhaisuchus qiaoensis, ‘Turfanosuchus shageduensis’, and Wangisuchus tzeyii, all three of which were collected from the Middle Triassic Ermaying Formation of northern China. Here, we reassess the taxonomy and systematics of these taxa. We regard Wangisuchus tzeyii as a nomen dubium, because the holotype is undiagnostic and there is no convincing evidence that the previously referred additional specimens represent the same taxon as the holotype. We also regard ‘Turfanosuchus shageduensis’ as a nomen dubium as we are unable to identify any diagnostic features. We refer the holotype to Archosauriformes, and more tentatively to Euparkeriidae. Halazhaisuchus qiaoensis and the holotype of ‘Turfanosuchus shageduensis’ are resolved as sister taxa in a phylogenetic analysis, and are in turn the sister taxon to Euparkeria capensis, forming a monophyletic Euparkeriidae that is the sister to Archosauria+Phytosauria. This is the first quantitative phylogenetic analysis to recover a non-monospecific, monophyletic Euparkeriidae, but euparkeriid monophyly is only weakly supported and will require additional examination. Given their similar sizes, stratigraphic positions and phylogenetic placement, the holotype of ‘Turfanosuchus shageduensis’ may represent a second individual of Halazhaisuchus qiaoensis, but no apomorphies or unique character combination can be identified to unambiguously unite the two. Our results have important implications for understanding the species richness and palaeobiogeographical distribution of early archosauriforms.
creator: Roland B. Sookias
creator: Corwin Sullivan
creator: Jun Liu
creator: Richard J. Butler
uri: https://doi.org/10.7717/peerj.658
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Sookias et al.

title: Bacillus anthracis pXO1 plasmid encodes a putative membrane-bound bacteriocin
link: https://peerj.com/articles/679
last-modified: 2014-11-20
description: Evolutionary advantages over cousin cells in bacterial pathogens may decide about the success of a specific cell in its environment. Bacteria use a plethora of methods to defend against other cells and many devices to attack their opponents when competing for resources. Bacteriocins are antibacterial proteins that are used to eliminate competition. We report the discovery of a putative membrane-bound bacteriocin encoded by the Bacillus anthracis pathogenic pXO1 plasmid. We analyze the genomic structure of the bacteriocin operon. The proposed mechanisms of action predestine this operon as a potent competitive advantage over cohabitants of the same niche.
creator: Agata Perlińska
creator: Marcin Grynberg
uri: https://doi.org/10.7717/peerj.679
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Perlińska and Grynberg

title: Unexpected cross-species contamination in genome sequencing projects
link: https://peerj.com/articles/675
last-modified: 2014-11-20
description: The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.
creator: Samier Merchant
creator: Derrick E. Wood
creator: Steven L. Salzberg
uri: https://doi.org/10.7717/peerj.675
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Merchant et al.

title: Bioinformatic analysis of cis-regulatory interactions between progesterone and estrogen receptors in breast cancer
link: https://peerj.com/articles/654
last-modified: 2014-11-18
description: Chromatin factors interact with each other in a cell and sequence-specific manner in order to regulate transcription and a wealth of publically available datasets exists describing the genomic locations of these interactions. Our recently published BiSA (Binding Sites Analyser) database contains transcription factor binding locations and epigenetic modifications collected from published studies and provides tools to analyse stored and imported data. Using BiSA we investigated the overlapping cis-regulatory role of estrogen receptor alpha (ERα) and progesterone receptor (PR) in the T-47D breast cancer cell line. We found that ERα binding sites overlap with a subset of PR binding sites. To investigate further, we re-analysed raw data to remove any biases introduced by the use of distinct tools in the original publications. We identified 22,152 PR and 18,560 ERα binding sites (<5% false discovery rate) with 4,358 overlapping regions among the two datasets. BiSA statistical analysis revealed a non-significant overall overlap correlation between the two factors, suggesting that ERα and PR are not partner factors and do not require each other for binding to occur. However, Monte Carlo simulation by Binary Interval Search (BITS), Relevant Distance, Absolute Distance, Jaccard and Projection tests by Genometricorr revealed a statistically significant spatial correlation of binding regions on chromosome between the two factors. Motif analysis revealed that the shared binding regions were enriched with binding motifs for ERα, PR and a number of other transcription and pioneer factors. Some of these factors are known to co-locate with ERα and PR binding. Therefore spatially close proximity of ERα binding sites with PR binding sites suggests that ERα and PR, in general function independently at the molecular level, but that their activities converge on a specific subset of transcriptional targets.
creator: Matloob Khushi
creator: Christine L. Clarke
creator: J. Dinny Graham
uri: https://doi.org/10.7717/peerj.654
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Khushi et al.

title: Genetic reprogramming of human amniotic cells with episomal vectors: neural rosettes as sentinels in candidate selection for validation assays
link: https://peerj.com/articles/668
last-modified: 2014-11-18
description: The promise of genetic reprogramming has prompted initiatives to develop banks of induced pluripotent stem cells (iPSCs) from diverse sources. Sentinel assays for pluripotency could maximize available resources for generating iPSCs. Neural rosettes represent a primitive neural tissue that is unique to differentiating PSCs and commonly used to identify derivative neural/stem progenitors. Here, neural rosettes were used as a sentinel assay for pluripotency in selection of candidates to advance to validation assays. Candidate iPSCs were generated from independent populations of amniotic cells with episomal vectors. Phase imaging of living back up cultures showed neural rosettes in 2 of the 5 candidate populations. Rosettes were immunopositive for the Sox1, Sox2, Pax6 and Pax7 transcription factors that govern neural development in the earliest stage of development and for the Isl1/2 and Otx2 transcription factors that are expressed in the dorsal and ventral domains, respectively, of the neural tube in vivo. Dissociation of rosettes produced cultures of differentiation competent neural/stem progenitors that generated immature neurons that were immunopositive for βIII-tubulin and glia that were immunopositive for GFAP. Subsequent validation assays of selected candidates showed induced expression of endogenous pluripotency genes, epigenetic modification of chromatin and formation of teratomas in immunodeficient mice that contained derivatives of the 3 embryonic germ layers. Validated lines were vector-free and maintained a normal karyotype for more than 60 passages. The credibility of rosette assembly as a sentinel assay for PSCs is supported by coordinate loss of nuclear-localized pluripotency factors Oct4 and Nanog in neural rosettes that emerge spontaneously in cultures of self-renewing validated lines. Taken together, these findings demonstrate value in neural rosettes as sentinels for pluripotency and selection of promising candidates for advance to validation assays.
creator: Patricia G. Wilson
creator: Tiffany Payne
uri: https://doi.org/10.7717/peerj.668
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Wilson and Payne

title: Placental vascular pathology and increased thrombin generation as mechanisms of disease in obstetrical syndromes
link: https://peerj.com/articles/653
last-modified: 2014-11-18
description: Obstetrical complications including preeclampsia, fetal growth restriction, preterm labor, preterm prelabor rupture of membranes and fetal demise are all the clinical endpoint of several underlying mechanisms (i.e., infection, inflammation, thrombosis, endocrine disorder, immunologic rejection, genetic, and environmental), therefore, they may be regarded as syndromes. Placental vascular pathology and increased thrombin generation were reported in all of these obstetrical syndromes. Moreover, elevated concentrations of thrombin-anti thrombin III complexes and changes in the coagulation as well as anticoagulation factors can be detected in the maternal circulation prior to the clinical development of the disease in some of these syndromes. In this review, we will assess the changes in the hemostatic system during normal and complicated pregnancy in maternal blood, maternal–fetal interface and amniotic fluid, and describe the contribution of thrombosis and vascular pathology to the development of the great obstetrical syndromes.
creator: Salvatore Andrea Mastrolia
creator: Moshe Mazor
creator: Giuseppe Loverro
creator: Vered Klaitman
creator: Offer Erez
uri: https://doi.org/10.7717/peerj.653
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Mastrolia et al.

title: Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites
link: https://peerj.com/articles/673
last-modified: 2014-11-13
description: Integration of transcriptome data is a crucial step for the identification of rare protein variants in mass-spectrometry (MS) data with important consequences for all branches of biotechnology research. Here, we used Splooce, a database of splicing variants recently developed by us, to search MS data derived from a variety of human tumor cell lines. More than 800 new protein variants were identified whose corresponding MS spectra were specific to protein entries from Splooce. Although the types of splicing variants (exon skipping, alternative splice sites and intron retention) were found at the same frequency as in the transcriptome, we observed a large variety of modifications at the protein level induced by alternative splicing events. Surprisingly, we found that 40% of all protein modifications induced by alternative splicing led to the use of alternative translation initiation sites. Other modifications include frameshifts in the open reading frame and inclusion or deletion of peptide sequences. To make the dataset generated here available to the community in a more effective form, the Splooce portal (http://www.bioinformatics-brazil.org/splooce) was modified to report the alternative splicing events supported by MS data.
creator: José E. Kroll
creator: Sandro J. de Souza
creator: Gustavo A. de Souza
uri: https://doi.org/10.7717/peerj.673
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Kroll et al.

title: Beyond xMOOCs in healthcare education: study of the feasibility in integrating virtual patient systems and MOOC platforms
link: https://peerj.com/articles/672
last-modified: 2014-11-13
description: Background. Massive Open Online Courses (MOOCs) are an emerging trend in online learning. However, their technology is not yet completely adjusted to the needs of healthcare education. Integration of Virtual Patients within MOOCs to increase interactivity and foster clinical reasoning skills training, has been discussed in the past, but not verified by a practical implementation.Objective. To investigate the technical feasibility of integrating MOOCs with Virtual Patients for the purpose of enabling further research into the potential pedagogical benefits of this approach.Methods. We selected OpenEdx and Open Labyrinth as representative constituents of a MOOC platform and Virtual Patient system integration. Based upon our prior experience we selected the most fundamental technical requirement to address. Grounded in the available literature we identified an e-learning standard to guide the integration. We attempted to demonstrate the feasibility of the integration by designing a “proof-of-concept” prototype. The resulting pilot implementation was subject of verification by two test cases.Results. A Single Sign-On mechanism connecting Open Labyrinth with OpenEdx and based on the IMS LTI standard was successfully implemented and verified.Conclusion. We investigated the technical perspective of integrating Virtual Patients with MOOCs. By addressing this crucial technical requirement we set a base for future research on the educational benefits of using virtual patients in MOOCs. This provides new opportunities for integrating specialized software in healthcare education at massive scale.
creator: Natalia Stathakarou
creator: Nabil Zary
creator: Andrzej A. Kononowicz
uri: https://doi.org/10.7717/peerj.672
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Stathakarou et al.

title: Effect of Euphorbia hirta plant leaf extract on immunostimulant response of Aeromonas hydrophila infected Cyprinus carpio
link: https://peerj.com/articles/671
last-modified: 2014-11-13
description: The main objective of the present study is to improve the immune power of Cyprinus carpio by using Euphorbia hirta plant leaf extract as immunostimulants. The haematological, immunological and enzymatic studies were conducted on the medicated fish infected with Aeromonas hydrophila pathogen. The results obtained from the haematological studies show that the RBC count, WBC count and haemoglobin content were increased in the infected fish at higher concentration of leaf extract. The feeds with leaf extract of Euphorbia hirta were able to stimulate the specific immune response by increasing the titre value of antibody. It was able to stimulate the antibody production only up to the 5th day, when fed with higher concentrations of (25 g and 50 g) plant leaf extract. The plant extract showed non-specific immune responses such as lysozyme activity, phagocytic ratio, NBT assay, etc. at higher concentration (50 g) and in the same concentration (50 g), the leaf extract of Euphorbia hirta significantly eliminated the pathogen in blood and kidney. It was observed that fish have survival percentage significantly at higher concentration (50 g) of Euphorbia hirta, when compared with the control. The obtained results are statistically significant at P < 0.05 and P < 0.01 levels. This research work suggests that the plant Euphorbia hirta has immunostimulant activity by stimulating both specific and non-specific immunity at higher concentrations.
creator: Vijayakumari Pratheepa
creator: NatarajaPillai Sukumaran
uri: https://doi.org/10.7717/peerj.671
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Pratheepa and Sukumaran

title: The cranial anatomy of the neornithischian dinosaur Thescelosaurus neglectus
link: https://peerj.com/articles/669
last-modified: 2014-11-13
description: Though the dinosaur Thescelosaurus neglectus was first described in 1913 and is known from the relatively fossiliferous Lance and Hell Creek formations in the Western Interior Basin of North America, the cranial anatomy of this species remains poorly understood. The only cranial material confidently referred to this species are three fragmentary bones preserved with the paratype, hindering attempts to understand the systematic relationships of this taxon within Neornithischia. Here the cranial anatomy of T. neglectus is fully described for the first time based on two specimens that include well-preserved cranial material (NCSM 15728 and TLAM.BA.2014.027.0001). Visual inspection of exposed cranial elements of these specimens is supplemented by detailed CT data from NCSM 15728 that enabled the examination of otherwise unexposed surfaces, facilitating a complete description of the cranial anatomy of this species. The skull of T. neglectus displays a unique combination of plesiomorphic and apomorphic traits. The premaxillary and ‘cheek’ tooth morphologies are relatively derived, though less so than the condition seen in basal iguanodontians, suggesting that the high tooth count present in the premaxillae, maxillae, and dentaries may be related to the extreme elongation of the skull of this species rather than a retention of the plesiomorphic condition. The morphology of the braincase most closely resembles the iguanodontians Dryosaurus and Dysalotosaurus, especially with regard to the morphology of the prootic. One autapomorphic feature is recognized for the first time, along with several additional cranial features that differentiate this species from the closely related and contemporaneous Thescelosaurus assiniboiensis. Published phylogenetic hypotheses of neornithischian dinosaur relationships often differ in the placement of the North American taxon Parksosaurus, with some recovering a close relationship with Thescelosaurus and others with the South American taxon Gasparinisaura, but never both at the same time. The new morphological observations presented herein, combined with re-examination of the holotype of Parksosaurus, suggest that Parksosaurus shares a closer relationship with Thescelosaurus than with Gasparinisaura, and that many of the features previously cited to support a relationship with the latter taxon are either also present in Thescelosaurus, are artifacts of preservation, or are the result of incomplete preparation and inaccurate interpretation of specimens. Additionally, the overall morphology of the skull and lower jaws of both Thescelosaurus and Parksosaurus also closely resemble the Asian taxa Changchunsaurus and Haya, though the interrelationships of these taxa have yet to be tested in a phylogenetic analysis that includes these new morphological data for T. neglectus.
creator: Clint A. Boyd
uri: https://doi.org/10.7717/peerj.669
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Boyd

title: Cocaine affects foraging behaviour and biogenic amine modulated behavioural reflexes in honey bees
link: https://peerj.com/articles/662
last-modified: 2014-11-13
description: In humans and other mammals, drugs of abuse alter the function of biogenic amine pathways in the brain leading to the subjective experience of reward and euphoria. Biogenic amine pathways are involved in reward processing across diverse animal phyla, however whether cocaine acts on these neurochemical pathways to cause similar rewarding behavioural effects in animal phyla other than mammals is unclear. Previously, it has been shown that bees are more likely to dance (a signal of perceived reward) when returning from a sucrose feeder after cocaine treatment. Here we examined more broadly whether cocaine altered reward-related behaviour, and biogenic amine modulated behavioural responses in bees. Bees developed a preference for locations at which they received cocaine, and when foraging at low quality sucrose feeders increase their foraging rate in response to cocaine treatment. Cocaine also increased reflexive proboscis extension to sucrose, and sting extension to electric shock. Both of these simple reflexes are modulated by biogenic amines. This shows that systemic cocaine treatment alters behavioural responses that are modulated by biogenic amines in insects. Since insect reward responses involve both octopamine and dopamine signalling, we conclude that cocaine treatment altered diverse reward-related aspects of behaviour in bees. We discuss the implications of these results for understanding the ecology of cocaine as a plant defence compound. Our findings further validate the honey bee as a model system for understanding the behavioural impacts of cocaine, and potentially other drugs of abuse.
creator: Eirik Søvik
creator: Naïla Even
creator: Catherine W. Radford
creator: Andrew B. Barron
uri: https://doi.org/10.7717/peerj.662
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Søvik et al.

title: Error correction and diversity analysis of population mixtures determined by NGS
link: https://peerj.com/articles/645
last-modified: 2014-11-13
description: The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. The error correction method is statistically based and works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated confidence intervals to be calculated. The methods are illustrated using honeybee viral samples. Software in both Excel and Matlab and a guide are available at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/, the Warwick University Systems Biology Centre software download site.
creator: Graham R. Wood
creator: Nigel J. Burroughs
creator: David J. Evans
creator: Eugene V. Ryabov
uri: https://doi.org/10.7717/peerj.645
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Wood et al.

title: Three-dimensional reconstruction and the phylogeny of extinct chelicerate orders
link: https://peerj.com/articles/641
last-modified: 2014-11-13
description: Arachnids are an important group of arthropods. They are: diverse and abundant; a major constituent of many terrestrial ecosystems; and possess a deep and extensive fossil record. In recent years a number of exceptionally preserved arachnid fossils have been investigated using tomography and associated techniques, providing valuable insights into their morphology. Here we use X-ray microtomography to reconstruct members of two extinct arachnid orders. In the Haptopoda, we demonstrate the presence of ‘clasp-knife’ chelicerae, and our novel redescription of a member of the Phalangiotarbida highlights leg details, but fails to resolve chelicerae in the group due to their small size. As a result of these reconstructions, tomographic studies of three-dimensionally preserved fossils now exist for three of the four extinct orders, and for fossil representatives of several extant ones. Such studies constitute a valuable source of high fidelity data for constructing phylogenies. To illustrate this, here we present a cladistic analysis of the chelicerates to accompany these reconstructions. This is based on a previously published matrix, expanded to include fossil taxa and relevant characters, and allows us to: cladistically place the extinct arachnid orders; explicitly test some earlier hypotheses from the literature; and demonstrate that the addition of fossils to phylogenetic analyses can have broad implications. Phylogenies based on chelicerate morphology—in contrast to molecular studies—have achieved elements of consensus in recent years. Our work suggests that these results are not robust to the addition of novel characters or fossil taxa. Hypotheses surrounding chelicerate phylogeny remain in a state of flux.
creator: Russell J. Garwood
creator: Jason Dunlop
uri: https://doi.org/10.7717/peerj.641
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Garwood and Dunlop

title: Quality of life of Syrian refugees living in camps in the Kurdistan Region of Iraq
link: https://peerj.com/articles/670
last-modified: 2014-11-11
description: The current study explores the perceived quality of life of Syrian refugees who have entered the Kurdistan Region of Iraq. Two hundred and seventy participants residing in refugee camps in the Erbil region in Kurdistan completed the WHOQOL-BREF, which measures Quality of Life (QOL) within four domains; physical, psychological, social relationships and environment. Syrian refugees in Kurdistan scored significantly lower for general population norms on physical health, psychological and environment QOL, and score significantly lower for physical health and psychological QOL for refugees in the Gaza strip. However, respondents in the current sample scored significantly higher on environment QOL compared to refugees in the Gaza strip, and significantly higher on all the QOL domains than those reported for refugees in West Africa. Finally, Syrian refugees in Kurdistan scored significantly higher than general population norms for social relationships QOL. The current findings provide the first report of QOL domain scores among Syrian refugees in the Kurdistan camps and suggest that social relationships and environmental QOL circumstances are relatively satisfactory, and that further investigation might be focused on physical and psychological QOL.
creator: Izaddin A. Aziz
creator: Claire V. Hutchinson
creator: John Maltby
uri: https://doi.org/10.7717/peerj.670
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Aziz et al.

title: Recent self-harm and psychological measures in the emergency department
link: https://peerj.com/articles/667
last-modified: 2014-11-11
description: The assessment of self-harm risk is a common, difficult, and perplexing task for many physicians, especially those working in emergency departments (ED). Attempts have been made to determine objective methods for assessing patients with suicidal ideation or self-harm though there is still a lack of knowledge about objective assessments of these patients. A study was conducted where 181 suicidal patients were enrolled in two EDs within the city of Edmonton, Canada. Initial interviews were conducted in the ED which collected basic demographics and medical history as well as psychometric measures including the Beck Hopelessness Scale, Barratt Impulsiveness Scale, Brief Symptom Inventory, Drug Abuse Screening Test 10, and CAGE questionnaire. The results of these measures were compared between those who presented to the ED with self-harm and those who presented only with ideation. Those with recent self-harm scored lower on many of the scales and subscales of distress and impulsivity measured compared to those with no recent self-harm. Possible explanations for this difference include differences in psychological traits between the two groups and possible cathartic effects of self-harm. The lower scores obtained by those that present with self-harm may complicate attempts to use psychometric tools to determine future self-harm risk.
creator: Jason R. Randall
creator: Brian H. Rowe
creator: Kathryn A. Dong
creator: Ian Colman
uri: https://doi.org/10.7717/peerj.667
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Randall et al.

title: The awareness of novelty for strangely familiar words: a laboratory analogue of the déjà vu experience
link: https://peerj.com/articles/666
last-modified: 2014-11-11
description: Déjà vu is a nebulous memory experience defined by a clash between evaluations of familiarity and novelty for the same stimulus. We sought to generate it in the laboratory by pairing a DRM recognition task, which generates erroneous familiarity for critical words, with a monitoring task by which participants realise that some of these erroneously familiar words are in fact novel. We tested 30 participants in an experiment in which we varied both participant awareness of stimulus novelty and erroneous familiarity strength. We found that déjà vu reports were most frequent for high novelty critical words (∼25%), with low novelty critical words yielding only baseline levels of déjà vu report frequency (∼10%). There was no significant variation in déjà vu report frequency according to familiarity strength. Discursive accounts of the experimentally-generated déjà vu experience suggest that aspects of the naturalistic déjà vu experience were captured by this analogue, but that the analogue was also limited in its focus and prone to influence by demand characteristics. We discuss theoretical and methodological considerations relevant to further development of this procedure and propose that verifiable novelty is an important component of both naturalistic and experimental analogues of déjà vu.
creator: Josephine A. Urquhart
creator: Akira R. O’Connor
uri: https://doi.org/10.7717/peerj.666
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Urquhart and O’Connor

title: Approaches to describing inter-rater reliability of the overall clinical appearance of febrile infants and toddlers in the emergency department
link: https://peerj.com/articles/651
last-modified: 2014-11-11
description: Objectives. To measure inter-rater agreement of overall clinical appearance of febrile children aged less than 24 months and to compare methods for doing so.Study Design and Setting. We performed an observational study of inter-rater reliability of the assessment of febrile children in a county hospital emergency department serving a mixed urban and rural population. Two emergency medicine healthcare providers independently evaluated the overall clinical appearance of children less than 24 months of age who had presented for fever. They recorded the initial ‘gestalt’ assessment of whether or not the child was ill appearing or if they were unsure. They then repeated this assessment after examining the child. Each rater was blinded to the other’s assessment. Our primary analysis was graphical. We also calculated Cohen’s κ, Gwet’s agreement coefficient and other measures of agreement and weighted variants of these. We examined the effect of time between exams and patient and provider characteristics on inter-rater agreement.Results. We analyzed 159 of the 173 patients enrolled. Median age was 9.5 months (lower and upper quartiles 4.9–14.6), 99/159 (62%) were boys and 22/159 (14%) were admitted. Overall 118/159 (74%) and 119/159 (75%) were classified as well appearing on initial ‘gestalt’ impression by both examiners. Summary statistics varied from 0.223 for weighted κ to 0.635 for Gwet’s AC2. Inter rater agreement was affected by the time interval between the evaluations and the age of the child but not by the experience levels of the rater pairs. Classifications of ‘not ill appearing’ were more reliable than others.Conclusion. The inter-rater reliability of emergency providers’ assessment of overall clinical appearance was adequate when described graphically and by Gwet’s AC. Different summary statistics yield different results for the same dataset.
creator: Paul Walsh
creator: Justin Thornton
creator: Julie Asato
creator: Nicholas Walker
creator: Gary McCoy
creator: Joe Baal
creator: Jed Baal
creator: Nanse Mendoza
creator: Faried Banimahd
uri: https://doi.org/10.7717/peerj.651
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Walsh et al.

title: Naïve prey exhibit reduced antipredator behavior and survivorship
link: https://peerj.com/articles/665
last-modified: 2014-11-06
description: Prey naiveté has been hypothesized to be one of the major driving forces behind population declines following the introduction of novel predators or release of inexperienced prey into predator rich environments. In these cases, naïve prey may lack sufficient antipredator behavior and, as a result, suffer increased mortality. Despite this, some evidence suggests that many prey utilize a generalized response to predators. Here, the naiveté hypothesis is tested using a predator–prey pair sharing an evolutionary history: the red swamp crayfish (Procambarus clarkii Girard, 1852) and largemouth bass (Micropterus salmoides Lacépède, 1802). Using farm-reared, naïve crayfish and wild-caught, experienced individuals, laboratory experiments demonstrated that naïve, farmed crayfish lack behavioral responses to chemical cues from bass, both in terms of movement and use of structural refuge. In contrast, experienced crayfish responded strongly to the same cues. In a subsequent field tethering experiment, these naïve individuals suffered a three-fold increase in predation rate. Based on these results, recognition of predators may not be innate in all prey, and previous experience and learning likely play a key role in the development of antipredator behavior.
creator: Charles W. Martin
uri: https://doi.org/10.7717/peerj.665
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Martin

title: Structural models for the design of novel antiviral agents against Greek Goat Encephalitis
link: https://peerj.com/articles/664
last-modified: 2014-11-06
description: The Greek Goat Encephalitis virus (GGE) belongs to the Flaviviridae family of the genus Flavivirus. The GGE virus constitutes an important pathogen of livestock that infects the goat’s central nervous system. The viral enzymes of GGE, helicase and RNA-dependent RNA polymerase (RdRP), are ideal targets for inhibitor design, since those enzymes are crucial for the virus’ survival, proliferation and transmission. In an effort to understand the molecular structure underlying the functions of those viral enzymes, the three dimensional structures of GGE NS3 helicase and NS5 RdRP have been modelled. The models were constructed in silico using conventional homology modelling techniques and the known 3D crystal structures of solved proteins from closely related species as templates. The established structural models of the GGE NS3 helicase and NS5 RdRP have been evaluated for their viability using a repertoire of in silico tools. The goal of this study is to present the 3D conformations of the GGE viral enzymes as reliable structural models that could provide the platform for the design of novel anti-GGE agents.
creator: Louis Papageorgiou
creator: Styliani Loukatou
creator: Vassiliki Lila Koumandou
creator: Wojciech Makałowski
creator: Vasileios Megalooikonomou
creator: Dimitrios Vlachakis
creator: Sophia Kossida
uri: https://doi.org/10.7717/peerj.664
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Papageorgiou et al.

title: Microsatellite frequencies vary with body mass and body temperature in mammals, suggesting correlated variation in mutation rate
link: https://peerj.com/articles/663
last-modified: 2014-11-06
description: Substitution rate is often found to correlate with life history traits such as body mass, a predictor of population size and longevity, and body temperature. The underlying mechanism is unclear but most models invoke either natural selection or factors such as generation length that change the number of mutation opportunities per unit time. Here we use published genome sequences from 69 mammals to ask whether life history traits impact another form of genetic mutation, the high rates of predominantly neutral slippage in microsatellites. We find that the length-frequency distributions of three common dinucleotide motifs differ greatly between even closely related species. These frequency differences correlate with body mass and body temperature and can be used to predict the phenotype of an unknown species. Importantly, different length microsatellites show complicated patterns of excess and deficit that cannot be explained by a simple model where species with short generation lengths have experienced more mutations. Instead, the patterns probably require changes in mutation rate that impact alleles of different length to different extents. Body temperature plausibly influences mutation rate by modulating the propensity for slippage. Existing hypotheses struggle to account for a link between body mass and mutation rate. However, body mass correlates inversely with population size, which in turn predicts heterozygosity. We suggest that heterozygote instability, HI, the idea that heterozygous sites show increased mutability, could provide a plausible link between body mass and mutation rate.
creator: William Amos
creator: Laura N.S. Filipe
uri: https://doi.org/10.7717/peerj.663
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Amos and Filipe

title: Quantitative measurement of odor detection thresholds using an air dilution olfactometer, and association with genetic variants in a sample of diverse ancestry
link: https://peerj.com/articles/643
last-modified: 2014-11-06
description: Genetic association studies require a quantitative and reliable method for odor threshold assessment in order to examine the contribution of genetic variants to complex olfactory phenotypes. Our main goal was to assess the feasibility of a portable Scentroid air dilution olfactometer for use in such studies. Using the Scentroid SM110C and the SK5 n-butanol Sensitivity Kit (IDES Canada Inc.), n-butanol odor thresholds were determined for 182 individuals of diverse ancestry (mean age: 20.4 ± 2.5 years; n = 128 female; n = 54 male). Threshold scores from repeat participants were used to calculate a test–retest reliability coefficient, which was statistically significant (r = 0.754, p < 0.001, n = 29), indicating that the Scentroid provides reliable estimates of odor thresholds. In addition, we performed a preliminary genetic analysis evaluating the potential association of n-butanol odor thresholds to six single-nucleotide polymorphisms (SNPs) putatively involved in general olfactory sensitivity (GOS). The results of multiple linear regression analysis revealed no significant association between the SNPs tested and threshold scores. However, our sample size was relatively small, and our study was only powered to identify genetic markers with strong effects on olfactory sensitivity. Overall, we find that the Scentroid provides reliable quantitative measures of odor detection threshold and is well suited for genetic studies of olfactory sensitivity.
creator: Gillian R. Cook
creator: S Krithika
creator: Melissa Edwards
creator: Paula Kavanagh
creator: Esteban J. Parra
uri: https://doi.org/10.7717/peerj.643
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Cook et al.

title: Jumping performance in the highly aquatic frog, Xenopus tropicalis: sex-specific relationships between morphology and performance
link: https://peerj.com/articles/661
last-modified: 2014-11-04
description: Frogs are characterized by a morphology that has been suggested to be related to their unique jumping specialization. Yet, the functional demands associated with jumping and swimming may not be that different as suggested by studies with semi-aquatic frogs. Here, we explore whether features previously identified as indicative of good burst swimming performance also predict jumping performance in a highly aquatic frog, Xenopus tropicalis. Moreover, we test whether the morphological determinants of jumping performance are similar in the two sexes and whether jumping performance differs in the two sexes. Finally we test whether jumping capacity is positively associated with burst swimming and terrestrial endurance capacity in both sexes. Our results show sex-specific differences in jumping performance when correcting for differences in body size. Moreover, the features determining jumping performance are different in the two sexes. Finally, the relationships between different performance traits are sex-dependent as well with females, but not males, showing a trade-off between peak jumping force and the time jumped to exhaustion. This suggests that different selective pressures operate on the two sexes, with females being subjected to constraints on locomotion due to their greater body mass and investment in reproductive capacity. In contrast, males appear to invest more in locomotor capacity giving them higher performance for a given body size compared to females.
creator: Anthony Herrel
creator: Menelia Vasilopoulou-Kampitsi
creator: Camille Bonneaud
uri: https://doi.org/10.7717/peerj.661
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Herrel et al.

title: Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array
link: https://peerj.com/articles/660
last-modified: 2014-11-04
description: Genetic admixture has been utilized as a tool for identifying loci associated with complex traits and diseases in recently admixed populations such as African Americans. In particular, admixture mapping is an efficient approach to identifying genetic basis for those complex diseases with substantial racial or ethnic disparities. Though current advances in admixture mapping algorithms may utilize the entire panel of SNPs, providing ancestry-informative markers (AIMs) that can differentiate parental populations and estimate ancestry proportions in an admixed population may particularly benefit admixture mapping in studies of limited samples, help identify unsuitable individuals (e.g., through genotyping the most informative ancestry markers) before starting large genome-wide association studies (GWAS), or guide larger scale targeted deep re-sequencing for determining specific disease-causing variants. Defining panels of AIMs based on commercial, high-throughput genotyping platforms will facilitate the utilization of these platforms for simultaneous admixture mapping of complex traits and diseases, in addition to conventional GWAS. Here, we describe AIMs detected based on the Shannon Information Content (SIC) or Fst for African Americans with genome-wide coverage that were selected from ∼2.3 million single nucleotide polymorphisms (SNPs) covered by the Affymetrix Axiom Pan-African array, a newly developed genotyping platform optimized for individuals of African ancestry.
creator: Xu Zhang
creator: Wenbo Mu
creator: Cong Liu
creator: Wei Zhang
uri: https://doi.org/10.7717/peerj.660
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Zhang et al.

title: Prior mating success can affect allocation towards future sexual signaling in crickets
link: https://peerj.com/articles/657
last-modified: 2014-11-04
description: Fitness is often correlated with the expression level of a sexually selected trait. However, sexually selected traits are costly to express such that investment in their expression should be optimised to maximize their overall fitness gains. Social interactions, in the form of successful and unsuccessful matings, may offer males one type of feedback allowing them to gauge how to allocate their resources towards sexual signaling. Here we tested whether adult male black field crickets (Teleogryllus commodus) modify the extent of their calling effort (the sexually selected trait) in response to successful and unsuccessful matings with females. To examine the effect that mating interactions with females have on investment into sexual signaling, we monitored male calling effort after maturation and then provided males with a female at two points within their life, manipulating whether or not males were able to successfully mate each time. Our results demonstrate that males alter their investment towards sexual signaling in response to successful matings, but only if the experience occurs early in their life. Males that mated early decreased their calling effort sooner than males that were denied a mating. Our results demonstrate that social feedback in the form of successful and unsuccessful matings has the potential to alter the effort a male places towards sexual signaling.
creator: Rachel Chiswell
creator: Madeline Girard
creator: Claudia Fricke
creator: Michael M. Kasumovic
uri: https://doi.org/10.7717/peerj.657
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Chiswell et al.

title: Training understanding of reversible sentences: a study comparing language-impaired children with age-matched and grammar-matched controls
link: https://peerj.com/articles/656
last-modified: 2014-11-04
description: Introduction. Many children with specific language impairment (SLI) have problems with language comprehension, and little is known about how to remediate these. We focused here on errors in interpreting sentences such as “the ball is above the cup”, where the spatial configuration depends on word order. We asked whether comprehension of such short reversible sentences could be improved by computerized training, and whether learning by children with SLI resembled that of younger, typically-developing children.Methods. We trained 28 children with SLI aged 6–11 years, 28 typically-developing children aged from 4 to 7 years who were matched to the SLI group for raw scores on a test of receptive grammar, and 20 typically-developing children who were matched to the SLI group on chronological age. A further 20 children with SLI were given pre- and post-test assessments, but did not undergo training. Those in the trained groups were given training on four days using a computer game adopting an errorless learning procedure, during which they had to select pictures to correspond to spoken sentences such as “the cup is above the drum” or “the bird is below the hat”. Half the trained children heard sentences using above/below and the other half heard sentences using before/after (with a spatial interpretation). A total of 96 sentences was presented over four sessions. Half the sentences were unique, whereas the remainder consisted of 12 repetitions of each of four sentences that became increasingly familiar as training proceeded.Results. Age-matched control children performed near ceiling (≥ 90% correct) in the first session and were excluded from the analysis. Around half the trained SLI children also performed this well. Training effects were examined in 15 SLI and 16 grammar-matched children who scored less than 90% correct on the initial training session. Overall, children’s scores improved with training. Memory span was a significant predictor of improvement, even after taking into account performance on training session 1. Unlike the grammar-matched controls, children with SLI showed greater accuracy with repeated sentences compared with unique sentences. Training did not improve children’s performance on a standardized test of receptive grammar.Discussion. Overall, these results indicate that a subset of children with SLI perform well below ceiling on reversible sentences with three key words and simple syntactic structure. For these children, weak verbal short-term memory appears to impair comprehension of spoken sentences. In contrast to the general finding that rule-learning benefits from variable input, these children seem to do best if given repeated exposure to the same nouns used with a given sentence frame. Generalisation to other sentences using the same syntactic frame may be more effective if preceded by such item-specific learning.
creator: Hsinjen Julie Hsu
creator: Dorothy V.M. Bishop
uri: https://doi.org/10.7717/peerj.656
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Hsu and Bishop

title: Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
link: https://peerj.com/articles/644
last-modified: 2014-11-04
description: The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines “Variant Calling with SAMtools”, “Tuxedo Pipeline for RNA-seq Data Analysis” and “Cistrome Pipeline for ChIP-seq Data Analysis” integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.
creator: Olga Golosova
creator: Ross Henderson
creator: Yuriy Vaskin
creator: Andrei Gabrielian
creator: German Grekhov
creator: Vijayaraj Nagarajan
creator: Andrew J. Oler
creator: Mariam Quiñones
creator: Darrell Hurt
creator: Mikhail Fursov
creator: Yentram Huyen
uri: https://doi.org/10.7717/peerj.644
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Golosova et al.

title: Fish market prices drive overfishing of the ‘big ones’
link: https://peerj.com/articles/638
last-modified: 2014-11-04
description: The relationship between fish market price and body size has not been explored much in fisheries science. Here, the mean market prices and fish body size were collected in order to examine the hypothesis that large fish, both among- and within-species, are being selectively targeted by fisheries because they may yield greater profit. Trophic levels, vulnerability to fishing and global landings were also collected because these variables may also be related to the market fish price. These relationships were examined using generalized additive models (GAM), which showed that, among species, fish market price was positively dependent on maximum total length (P = 0.0024) and negatively on landings (P = 0.0006), whereas it was independent of trophic level (P > 0.05) and vulnerability to fishing (P > 0.05). When the fish price vs. size relationship was tested within-species, large individuals were consistently attaining higher market prices compared to their medium and small-sized counterparts. We conclude that the selective removal of the larger fish, which is driven by their market price and to a lesser extent by their availability, may contribute to their overfishing.
creator: Athanassios C. Tsikliras
creator: Konstantinos Polymeros
uri: https://doi.org/10.7717/peerj.638
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Tsikliras and Polymeros

title: Evolving California genotypes of Avena barbata are derived from multiple introductions but still maintain substantial population structure
link: https://peerj.com/articles/633
last-modified: 2014-11-04
description: Multiple introductions are thought to enhance the chance of successful colonization, in part because recombination may generate adaptive variation to a new environment. Avena barbata (slender wild oat) is a successful colonist in California, historically noted for striking genetic divergence into two multilocus genotypes, but is still undergoing adaptive change. We sought to understand whether multiple introductions might be contributing to this change. We used cpDNA phylogeography of A. barbata within its home range and in its invaded range in California to determine the minimum number of separate introductions, and the spatial distribution of these introduced lineages. We collected from sites throughout the state of California, where it is an invasive species. Accessions from a representative portion of A. barbata’s full native range were obtained from germplasm repositories. We sequenced seven intergenic chloroplast DNA loci for A. barbata individuals both in California (novel geographic range) and its ancestral range. 204 individuals were assayed for chloroplast haplotype within California using single strand conformational polymorphism SSCPs. Genome size was determined by flow cytometry. Californian accessions are tetraploid as expected, but their genome sizes were smaller than the Old World accessions. There were three haplotypes present in California that were identical to haplotypes in the native range. Within California, the presence of multiple haplotypes at a site was observed primarily in Northern and Central populations. Between populations there was still substantial structure with FST ∼ 0.33, due to a shallow latitudinal cline caused by a preponderance of xeric haplotypes in Southern California. There was a minimum of three seed introductions to California. Recombination is thus likely to occur, and contribute to adaptation in new range in this highly-selfing, invader.
creator: Kate Crosby
creator: Taylor O. Stokes
creator: Robert G. Latta
uri: https://doi.org/10.7717/peerj.633
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Crosby et al.

title: Evidence for coal forest refugia in the seasonally dry Pennsylvanian tropical lowlands of the Illinois Basin, USA
link: https://peerj.com/articles/630
last-modified: 2014-11-04
description: The Moscovian plant macroflora at Cottage Grove southeastern Illinois, USA, is a key example of Pennsylvanian (323–299 Million years ago) dryland vegetation. There is currently no palynological data from the same stratigraphic horizons as the plant macrofossils, leaves and other vegetative and reproductive structures, at this locality. Consequently, reconstructions of the standing vegetation at Cottage Grove from these sediments lack the complementary information and a more regional perspective that can be provided by sporomorphs (prepollen, pollen, megaspores and spores). In order to provide this, we have analysed the composition of fossil sporomorph assemblages in two rock samples taken from macrofossil-bearing inter-coal shale at Cottage Grove. Our palynological data differ considerably in composition and in the dominance-diversity profile from the macrofossil vegetation at this locality. Walchian conifers and pteridosperms are common elements in the macroflora, but are absent in the sporomorph assemblages. Reversely, the sporomorph assemblages at Cottage Grove comprise 17 spore taxa (∼16% and ∼63% of the total assemblages) that are known from the lycopsid orders Isoetales, Lepidodendrales and Selaginallales, while Cottage Grove’s macrofloral record fails to capture evidence of a considerable population of coal forest lycopsids. We interpret our results as evidence that the Pennsylvanian dryland glacial landscape at Cottage Grove included fragmented populations of wetland plants living in refugia.
creator: Cindy V. Looy
creator: Robert A. Stevenson
creator: Thomas B. Van Hoof
creator: Luke Mander
uri: https://doi.org/10.7717/peerj.630
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Looy et al.

title: Changes in species diversity of arboreal spiders in Mexican coffee agroecosystems: untangling the web of local and landscape influences driving diversity
link: https://peerj.com/articles/623
last-modified: 2014-11-04
description: Agricultural intensification is implicated as a major driver of global biodiversity loss. Local management and landscape scale factors both influence biodiversity in agricultural systems, but there are relatively few studies to date looking at how local and landscape scales influence biodiversity in tropical agroecosystems. Understanding what drives the diversity of groups of organisms such as spiders is important from a pragmatic point of view because of the important biocontrol services they offer to agriculture. Spiders in coffee are somewhat enigmatic because of their positive or lack of response to agricultural intensification. In this study, we provide the first analysis, to our knowledge, of the arboreal spiders in the shade trees of coffee plantations. In the Soconusco region of Chiapas, Mexico we sampled across 38 sites on 9 coffee plantations. Tree and canopy connectedness were found to positively influence overall arboreal spider richness and abundance. We found that different functional groups of spiders are responding to different local and landscape factors, but overall elevation was most important variable influencing arboreal spider diversity. Our study has practical management applications that suggest having shade grown coffee offers more suitable habitat for arboreal spiders due to a variety of the characteristics of the shade trees. Our results which show consistently more diverse arboreal spider communities in lower elevations are important in light of looming global climate change. As the range of suitable elevations for coffee cultivation shrinks promoting arboreal spider diversity will be important in sustaining the viability of coffee.
creator: Zachary Hajian-Forooshani
creator: David J. Gonthier
creator: Linda Marín
creator: Aaron L. Iverson
creator: Ivette Perfecto
uri: https://doi.org/10.7717/peerj.623
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2014 Hajian-Forooshani et al.

title: Utilization of maternal healthcare among adolescent mothers in urban India: evidence from DLHS-3
link: https://peerj.com/articles/592
last-modified: 2014-11-04
description: Background. Low use of maternal healthcare services is one of the reasons why maternal mortality is still considerably high among adolescents mothers in India. To increase the utilization of these services, it is necessary to identify factors that affect service utilization. To our knowledge, no national level study in India has yet examined the issue in the context urban adolescent mothers. The present study is an attempt to fill this gap.Data and Methods. Using information from the third wave of District Level Household Survey (2007–08), we have examined factors associated with the utilization of maternal healthcare services among urban Indian married adolescent women (aged 13–19 years) who have given live/still births during last three years preceding the survey. The three outcome variables included in the analyses are ‘full antenatal care (ANC)’, ‘safe delivery’ and ‘postnatal care within 42 days of delivery’. We have used Chi-square test to determine the difference in proportion and the binary logistic regression to understand the net effect of predictor variables on the utilization of maternity care.Results. About 22.9% of mothers have received full ANC, 65.1% of mothers have had at least one postnatal check-up within 42 days of pregnancy. The proportion of mother having a safe delivery, i.e., assisted by skilled personnel, is about 70.5%. Findings indicate that there is considerable amount of variation in use of maternity care by educational attainment, household wealth, religion, parity and region of residence. Receiving full antenatal care is significantly associated with mother’s education, religion, caste, household wealth, parity, exposure to healthcare messages and region of residence. Mother’s education, full antenatal care, parity, household wealth, religion and region of residence are also statistically significant in case of safe delivery. The use of postnatal care is associated with household wealth, woman’s education, full antenatal care, safe delivery care and region of residence.Conclusion. Several socioeconomic and demographic factors affect the utilization of maternal healthcare services among urban adolescent women in India. Promoting the use of family planning, female education and higher age at marriage, targeting vulnerable groups such as poor, illiterate, high parity women, involving media and grass root level workers and collaboration between community leaders and health care system could be some important policy level interventions to address the unmet need of maternity services among urban adolescents.
creator: Aditya Singh
creator: Abhishek Kumar
creator: Pragya Pranjali
uri: https://doi.org/10.7717/peerj.592
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2014 Singh et al.

title: Automatic identification of species with neural networks
link: https://peerj.com/articles/563
last-modified: 2014-11-04
description: A new automatic identification system using photographic images has been designed to recognize fish, plant, and butterfly species from Europe and South America. The automatic classification system integrates multiple image processing tools to extract the geometry, morphology, and texture of the images. Artificial neural networks (ANNs) were used as the pattern recognition method. We tested a data set that included 740 species and 11,198 individuals. Our results show that the system performed with high accuracy, reaching 91.65% of true positive fish identifications, 92.87% of plants and 93.25% of butterflies. Our results highlight how the neural networks are complementary to species identification.
creator: Andrés Hernández-Serna
creator: Luz Fernanda Jiménez-Segura
uri: https://doi.org/10.7717/peerj.563
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2014 Hernández-Serna and Jimenéz-Segura