title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1944 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases link: https://peerj.com/articles/972 last-modified: 2015-05-19 description: Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases.Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined.Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ.Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general. creator: Mads Svane Liljekvist creator: Kristoffer Andresen creator: Hans-Christian Pommergaard creator: Jacob Rosenberg uri: https://doi.org/10.7717/peerj.972 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Liljekvist et al. title: PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data link: https://peerj.com/articles/970 last-modified: 2015-05-19 description: Objective. Bringing together genomics, transcriptomics, proteomics, and other -omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate data faster than it can be interpreted.Materials and Methods. We have developed PANDA (Pathway AND Annotation) Explorer, a visualization tool that integrates gene-level annotation in the context of biological pathways to help interpret complex data from disparate sources. PANDA is a web-based application that displays data in the context of well-studied pathways like KEGG, BioCarta, and PharmGKB. PANDA represents data/annotations as icons in the graph while maintaining the other data elements (i.e., other columns for the table of annotations). Custom pathways from underrepresented diseases can be imported when existing data sources are inadequate. PANDA also allows sharing annotations among collaborators.Results. In our first use case, we show how easy it is to view supplemental data from a manuscript in the context of a user’s own data. Another use-case is provided describing how PANDA was leveraged to design a treatment strategy from the somatic variants found in the tumor of a patient with metastatic sarcomatoid renal cell carcinoma.Conclusion. PANDA facilitates the interpretation of gene-centric annotations by visually integrating this information with context of biological pathways. The application can be downloaded or used directly from our website: http://bioinformaticstools.mayo.edu/research/panda-viewer/. creator: Steven N. Hart creator: Raymond M. Moore creator: Michael T. Zimmermann creator: Gavin R. Oliver creator: Jan B. Egan creator: Alan H. Bryce creator: Jean-Pierre A. Kocher uri: https://doi.org/10.7717/peerj.970 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hart et al. title: Astym treatment vs. eccentric exercise for lateral elbow tendinopathy: a randomized controlled clinical trial link: https://peerj.com/articles/967 last-modified: 2015-05-19 description: Introduction. Patients with chronic lateral elbow (LE) tendinopathy, commonly known as tennis elbow, often experience prolonged symptoms and frequent relapses. Astym treatment, evidenced in animal studies to promote the healing and regeneration of soft tissues, is hypothesized to improve outcomes in LE tendinopathy patients. This study had two objectives: (1) to compare the efficacy of Astym treatment to an evidence-based eccentric exercise program (EE) for patients with chronic LE tendinopathy, and (2) to quantify outcomes of subjects non-responsive to EE who were subsequently treated with Astym treatment.Study Design. Prospective, two group, parallel, randomized controlled trial completed at a large orthopedic center in Indiana. Inclusion criteria: age range of 18–65 years old, with clinical indications of LE tendinopathy greater than 12 weeks, with no recent corticosteriod injection or disease altering comorbidities.Methods. Subjects with chronic LE tendinopathy (107 subjects with 113 affected elbows) were randomly assigned using computer-generated random number tables to 4 weeks of Astym treatment (57 elbows) or EE treatment (56 elbows). Data collected at baseline, 4, 8, 12 weeks, 6 and 12 months. Primary outcome measure: DASH; secondary outcome measures: pain with activity, maximum grip strength and function. The treating physicians and the rater were blinded; subjects and treating clinicians could not be blinded due to the nature of the treatments.Results. Resolution response rates were 78.3% for the Astym group and 40.9% for the EE group. Astym subjects showed greater gains in DASH scores (p = 0.047) and in maximum grip strength (p = 0.008) than EE subjects. Astym therapy also resolved 20/21 (95.7%) of the EE non-responders, who showed improvements in DASH scores (p < 0.005), pain with activity (p = 0.002), and function (p = 0.004) following Astym treatment. Gains continued at 6 and 12 months. No adverse effects were reported.Conclusion. This study suggests Astym therapy is an effective treatment option for patients with LE tendinopathy, as an initial treatment, and after an eccentric exercise program has failed.Registration/Funding. Ball Memorial Hospital provided limited funding. Trial registration was not required by FDAAA 801.Known about the Subject. Under the new paradigm of degenerative tendinopathy, eccentric exercise (EE) is emerging as a first line conservative treatment for LE tendinopathy. EE and Astym treatment are among the few treatment options aiming to improve the degenerative pathophysiology of the tendon. In this trial, Astym therapy, which has shown success in the treatment of tendinopathy, is compared to EE, which has also shown success in the treatment of tendinopathy.Clinical Relevance. There is a need for more effective, conservative treatment options. Based on the current efficacy study, Astym therapy appears to be a promising, non-invasive treatment option. creator: Thomas L. Sevier creator: Caroline W. Stegink-Jansen uri: https://doi.org/10.7717/peerj.967 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sevier and Stegink-Jansen title: A white-box model of S-shaped and double S-shaped single-species population growth link: https://peerj.com/articles/948 last-modified: 2015-05-19 description: Complex systems may be mechanistically modelled by white-box modeling with using logical deterministic individual-based cellular automata. Mathematical models of complex systems are of three types: black-box (phenomenological), white-box (mechanistic, based on the first principles) and grey-box (mixtures of phenomenological and mechanistic models). Most basic ecological models are of black-box type, including Malthusian, Verhulst, Lotka–Volterra models. In black-box models, the individual-based (mechanistic) mechanisms of population dynamics remain hidden. Here we mechanistically model the S-shaped and double S-shaped population growth of vegetatively propagated rhizomatous lawn grasses. Using purely logical deterministic individual-based cellular automata we create a white-box model. From a general physical standpoint, the vegetative propagation of plants is an analogue of excitation propagation in excitable media. Using the Monte Carlo method, we investigate a role of different initial positioning of an individual in the habitat. We have investigated mechanisms of the single-species population growth limited by habitat size, intraspecific competition, regeneration time and fecundity of individuals in two types of boundary conditions and at two types of fecundity. Besides that, we have compared the S-shaped and J-shaped population growth. We consider this white-box modeling approach as a method of artificial intelligence which works as automatic hyper-logical inference from the first principles of the studied subject. This approach is perspective for direct mechanistic insights into nature of any complex systems. creator: Lev V. Kalmykov creator: Vyacheslav L. Kalmykov uri: https://doi.org/10.7717/peerj.948 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kalmykov and Kalmykov title: Longitudinal relations among inattention, working memory, and academic achievement: testing mediation and the moderating role of gender link: https://peerj.com/articles/939 last-modified: 2015-05-19 description: Introduction. Behavioral inattention, working memory (WM), and academic achievement share significant variance, but the direction of relationships across development is unknown. The aim of the present study was to determine whether WM mediates the pathway between inattentive behaviour and subsequent academic outcomes.Methods. 204 students from grades 1–4 (49.5% female) were recruited from elementary schools. Participants received assessments of WM and achievement at baseline and one year later. WM measures included a visual-spatial storage task and auditory-verbal storage and manipulation tasks. Teachers completed the SWAN behaviour rating scale both years. Mediation analysis with PROCESS (Hayes, 2013) was used to determine mediation pathways.Results. Teacher-rated inattention indirectly influenced math addition fluency, subtraction fluency and calculation scores through its effect on visual-spatial WM, only for boys. There was a direct relationship between inattention and math outcomes one year later for girls and boys. Children who displayed better attention had higher WM scores, and children with higher WM scores had stronger scores on math outcomes. Bias-corrected bootstrap confidence intervals for the indirect effects were entirely below zero for boys, for the three math outcomes. WM did not mediate the direct relationship between inattention and reading scores.Discussion. Findings identify inattention and WM as longitudinal predictors for math addition and subtraction fluency and math calculation outcomes one year later, with visual-spatial WM as a significant mediator for boys. Results highlight the close relationship between inattention and WM and their importance in the development of math skills. creator: Sarah A. Gray creator: Maria Rogers creator: Rhonda Martinussen creator: Rosemary Tannock uri: https://doi.org/10.7717/peerj.939 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gray et al. title: Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam link: https://peerj.com/articles/915 last-modified: 2015-05-19 description: The seed oil of meadowfoam, a new crop in the Limnanthaceae family, is highly enriched in very long chain fatty acids that are desaturated at the Δ5 position. The unusual oil is desirable for cosmetics and innovative industrial applications and the seed meal remaining after oil extraction contains glucolimnanthin, a methoxylated benzylglucosinolate whose degradation products are herbicidal and anti-microbial. Here we describe EST analysis of the developing seed transcriptome that identified major genes involved in biosynthesis and assembly of the seed oil and in glucosinolate metabolic pathways. mRNAs encoding acyl-CoA Δ5 desaturase were notably abundant. The library was searched for simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). Fifty-four new SSR markers and eight candidate gene markers were developed and combined with previously developed SSRs to construct a new genetic map for Limnanthes alba. Mapped genes in the lipid biosynthetic pathway encode 3-ketoacyl-CoA synthase (KCS), Δ5 desaturase (Δ5DS), lysophosphatidylacyl-acyl transferase (LPAT), and acyl-CoA diacylglycerol acyl transferase (DGAT). Mapped genes in glucosinolate biosynthetic and degradation pathways encode CYP79A, myrosinase (TGG), and epithiospecifier modifier protein (ESM). The resources developed in this study will further the domestication and improvement of meadowfoam as an oilseed crop. creator: Mary B. Slabaugh creator: Laurel D. Cooper creator: Venkata K. Kishore creator: Steven J. Knapp creator: Jennifer G. Kling uri: https://doi.org/10.7717/peerj.915 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Slabaugh et al. title: Copepods enhance nutritional status, growth and development in Atlantic cod (Gadus morhua L.) larvae — can we identify the underlying factors? link: https://peerj.com/articles/902 last-modified: 2015-05-19 description: The current commercial production protocols for Atlantic cod depend on enriched rotifers and Artemia during first-feeding, but development and growth remain inferior to fish fed natural zooplankton. Two experiments were conducted in order to identify the underlying factors for this phenomenon. In the first experiment (Exp-1), groups of cod larvae were fed either (a) natural zooplankton, mainly copepods, increasing the size of prey as the larvae grew or (b) enriched rotifers followed by Artemia (the intensive group). In the second experiment (Exp-2), two groups of larvae were fed as in Exp-1, while a third group was fed copepod nauplii (approximately the size of rotifers) throughout the larval stage. In both experiments, growth was not significantly different between the groups during the first three weeks after hatching, but from the last part of the rotifer feeding period and onwards, the growth of the larvae fed copepods was higher than that of the intensive group. In Exp-2, the growth was similar between the two copepod groups during the expeimental period, indicating that nutrient composition, not prey size caused the better growth on copepods. Analyses of the prey showed that total fatty acid composition and the ratio of phospholipids to total lipids was slightly different in the prey organisms, and that protein, taurine, astaxanthin and zinc were lower on a dry weight basis in rotifers than in copepods. Other measured nutrients as DHA, all analysed vitamins, manganese, copper and selenium were similar or higher in the rotifers. When compared to the present knowledge on nutrient requirements, protein and taurine appeared to be the most likely limiting nutrients for growth in cod larvae fed rotifers and Artemia. Larvae fed rotifers/Artemia had a higher whole body lipid content than larvae fed copepods at the end of the experiment (stage 5) after the fish had been fed the same formulated diet for approximately 2 weeks. creator: Ørjan Karlsen creator: Terje van der Meeren creator: Ivar Rønnestad creator: Anders Mangor-Jensen creator: Trina F. Galloway creator: Elin Kjørsvik creator: Kristin Hamre uri: https://doi.org/10.7717/peerj.902 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Karlsen et al. title: Swabs to genomes: a comprehensive workflow link: https://peerj.com/articles/960 last-modified: 2015-05-14 description: The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it. creator: Madison I. Dunitz creator: Jenna M. Lang creator: Guillaume Jospin creator: Aaron E. Darling creator: Jonathan A. Eisen creator: David A. Coil uri: https://doi.org/10.7717/peerj.960 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Dunitz et al. title: Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults link: https://peerj.com/articles/964 last-modified: 2015-05-14 description: There is evidence to suggest that impulsivity is predicted by socioeconomic background, with people from more deprived backgrounds tending to be more impulsive, and by current mood, with poorer mood associated with greater impulsivity. However, impulsivity is not a unitary construct, and previous research in this area has focused on measures of ‘waiting’ impulsivity rather than behavioural disinhibition. We administered a standard measure of behavioural disinhibition, the stop-signal task, to 58 adult participants from a community sample. We had measured socioeconomic background using participant postcode at age 16, and assigned participants to receive either a neutral or a negative mood induction. We found no effects of mood on behavioural disinhibition, but we found a significant effect of socioeconomic background. Participants who had lived in more deprived postcodes at age 16 showed longer stop-signal reaction times, and hence greater behavioural disinhibition. The pattern was independent of participant age and overall reaction time. Though caution is required inferring causality from correlation, it is possible that that experiencing socioeconomic deprivation in childhood and adolescence may lead to greater behavioural disinhibition in adulthood. creator: Tünde Paál creator: Thomas Carpenter creator: Daniel Nettle uri: https://doi.org/10.7717/peerj.964 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Paál et al. title: Individual consistency in the behaviors of newly-settled reef fish link: https://peerj.com/articles/961 last-modified: 2015-05-14 description: Flexibility in behavior is advantageous for organisms that transition between stages of a complex life history. However, various constraints can set limits on plasticity, giving rise to the existence of personalities that have associated costs and benefits. Here, we document a field and laboratory experiment that examines the consistency of measures of boldness, activity, and aggressive behavior in the young of a tropical reef fish, Pomacentrus amboinensis (Pomacentridae) immediately following their transition between pelagic larval and benthic juvenile habitats. Newly-settled fish were observed in aquaria and in the field on replicated patches of natural habitat cleared of resident fishes. Seven behavioral traits representing aspects of boldness, activity and aggression were monitored directly and via video camera over short (minutes), medium (hours), and long (3 days) time scales. With the exception of aggression, these behaviors were found to be moderately or highly consistent over all time scales in both laboratory and field settings, implying that these fish show stable personalities within various settings. Our study is the first to examine the temporal constancy of behaviors in both field and laboratory settings in over various time scales at a critically important phase during the life cycle of a reef fish. creator: James R. White creator: Mark G. Meekan creator: Mark I. McCormick uri: https://doi.org/10.7717/peerj.961 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 White et al.