title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1808 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests link: https://peerj.com/articles/2193 last-modified: 2016-08-10 description: Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter “conspicuous behaviour”), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs. creator: Marie-Andrée Giroux creator: Myriam Trottier-Paquet creator: Joël Bêty creator: Vincent Lamarre creator: Nicolas Lecomte uri: https://doi.org/10.7717/peerj.2193 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Giroux et al. title: A horizon scan of future threats and opportunities for pollinators and pollination link: https://peerj.com/articles/2249 last-modified: 2016-08-09 description: Background. Pollinators, which provide the agriculturally and ecologically essential service of pollination, are under threat at a global scale. Habitat loss and homogenisation, pesticides, parasites and pathogens, invasive species, and climate change have been identified as past and current threats to pollinators. Actions to mitigate these threats, e.g., agri-environment schemes and pesticide-use moratoriums, exist, but have largely been applied post-hoc. However, future sustainability of pollinators and the service they provide requires anticipation of potential threats and opportunities before they occur, enabling timely implementation of policy and practice to prevent, rather than mitigate, further pollinator declines.Methods.Using a horizon scanning approach we identified issues that are likely to impact pollinators, either positively or negatively, over the coming three decades.Results.Our analysis highlights six high priority, and nine secondary issues. High priorities are: (1) corporate control of global agriculture, (2) novel systemic pesticides, (3) novel RNA viruses, (4) the development of new managed pollinators, (5) more frequent heatwaves and drought under climate change, and (6) the potential positive impact of reduced chemical use on pollinators in non-agricultural settings.Discussion. While current pollinator management approaches are largely driven by mitigating past impacts, we present opportunities for pre-emptive practice, legislation, and policy to sustainably manage pollinators for future generations. creator: Mark J.F. Brown creator: Lynn V. Dicks creator: Robert J. Paxton creator: Katherine C.R. Baldock creator: Andrew B. Barron creator: Marie-Pierre Chauzat creator: Breno M. Freitas creator: Dave Goulson creator: Sarina Jepsen creator: Claire Kremen creator: Jilian Li creator: Peter Neumann creator: David E. Pattemore creator: Simon G. Potts creator: Oliver Schweiger creator: Colleen L. Seymour creator: Jane C. Stout uri: https://doi.org/10.7717/peerj.2249 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Brown et al. title: A study of institutional spending on open access publication fees in Germany link: https://peerj.com/articles/2323 last-modified: 2016-08-09 description: Publication fees as a revenue source for open access publishing hold a prominent place on the agendas of researchers, policy makers, and academic publishers. This study contributes to the evolving empirical basis for funding these charges and examines how much German universities and research organisations spent on open access publication fees. Using self-reported cost data from the Open APC initiative, the analysis focused on the amount that was being spent on publication fees, and compared these expenditure with data from related Austrian (FWF) and UK (Wellcome Trust, Jisc) initiatives, in terms of both size and the proportion of articles being published in fully and hybrid open access journals. We also investigated how thoroughly self-reported articles were indexed in Crossref, a DOI minting agency for scholarly literature, and analysed how the institutional spending was distributed across publishers and journal titles. According to self-reported data from 30 German universities and research organisations between 2005 and 2015, expenditures on open access publication fees increased over the years in Germany and amounted to € 9,627,537 for 7,417 open access journal articles. The average payment was € 1,298, and the median was € 1,231. A total of 94% of the total article volume included in the study was supported in accordance with the price cap of € 2,000, a limit imposed by the Deutsche Forschungsgemeinschaft (DFG) as part of its funding activities for open access funding at German universities. Expenditures varied considerably at the institutional level. There were also differences in how much the institutions spent per journal and publisher. These differences reflect, at least in part, the varying pricing schemes in place including discounted publication fees. With an indexing coverage of 99%, Crossref thoroughly indexed the open access journals articles included in the study. A comparison with the related openly available cost data from Austria and the UK revealed that German universities and research organisations primarily funded articles in fully open access journals. By contrast, articles in hybrid journal accounted for the largest share of spending according to the Austrian and UK data. Fees paid for hybrid journals were on average more expensive than those paid for fully open access journals. creator: Najko Jahn creator: Marco Tullney uri: https://doi.org/10.7717/peerj.2323 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jahn et al. title: Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking link: https://peerj.com/articles/2322 last-modified: 2016-08-09 description: Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models afforded R2, ${Q}_{\mathrm{CV }}^{2}$QCV2 and ${Q}_{\mathrm{Ext}}^{2}$QExt2 values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R2, ${Q}_{\mathrm{CV }}^{2}$QCV2 and ${Q}_{\mathrm{Ext}}^{2}$QExt2 values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds 13, 5 and 28 exhibited the lowest binding energies of −12.2, −12.0 and −12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding, π–π stacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors. creator: Saw Simeon creator: Nuttapat Anuwongcharoen creator: Watshara Shoombuatong creator: Aijaz Ahmad Malik creator: Virapong Prachayasittikul creator: Jarl E.S. Wikberg creator: Chanin Nantasenamat uri: https://doi.org/10.7717/peerj.2322 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Simeon et al. title: Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development link: https://peerj.com/articles/2318 last-modified: 2016-08-09 description: To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org). creator: Kyle J. Beauchemin creator: Julie M. Wells creator: Alvin T. Kho creator: Vivek M. Philip creator: Daniela Kamir creator: Isaac S. Kohane creator: Joel H. Graber creator: Carol J. Bult uri: https://doi.org/10.7717/peerj.2318 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Beauchemin et al. title: An optimized approach to germ-free rearing in the jewel wasp Nasonia link: https://peerj.com/articles/2316 last-modified: 2016-08-09 description: Development of a Nasonia in vitrogerm-free rearing system in 2012 enabled investigation of Nasonia-microbiota interactions and real-time visualization of parasitoid metamorphosis. However, the use of antibiotics, bleach, and fetal bovine serum introduced artifacts relative to conventional rearing of Nasonia. Here, we optimize the germ-free rearing procedure by using filter sterilization in lieu of antibiotics and by removing residual bleach and fetal bovine serum. Comparison of these methods reveals no influence on larval survival or growth, and a 52% improvement in adult production. Additionally, adult males produced in the new germ-free system are similar in size to conventionally reared males. Experimental implications of these changes are discussed. creator: J. Dylan Shropshire creator: Edward J. van Opstal creator: Seth R. Bordenstein uri: https://doi.org/10.7717/peerj.2316 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shropshire et al. title: An investigation into the bilateral functional differences of the lower limb muscles in standing and walking link: https://peerj.com/articles/2315 last-modified: 2016-08-09 description: To date, most studies use surface electromyographic (sEMG) signals as the control source on active rehabilitation robots, and unilateral data are collected based on the gait symmetry hypothesis, which has caused much controversy. The purpose of this study is to quantitatively evaluate the sEMG activity asymmetry of bilateral muscles in lower extremities during functional tasks. Nine participants were instructed to perform static and dynamic steady state tests. sEMG signals from the tibialis anterior, soleus, medial gastrocnemius and lateral gastrocnemius muscles of bilateral lower extremities were recorded in the experiments. Muscle activities are quantified in terms of sEMG amplitude. We investigated whether characteristics of left limb and the one of the right limb have the same statistical characteristics during functional tasks using The Wilcoxon rank-sum test, and studied dynamic signal irregularity degree for sEMG activities via sample entropy. The total of muscle activities showed significant differences between left limb and right limb during the static steady state (p = 0.000). For dynamic steady states, there were significant differences for most muscle activities between left limb and right limb at different speeds (p = 0.000). Nevertheless, there was no difference between the lateral gastrocnemius for bilateral limb at 2.0 kilometers per hour (p = 0.060). For medial gastrocnemius, differences were not found between left limb and right limb at 1.0 and 3.0 kilometers per hours (p = 0.390 and p = 0.085, respectively). Similarly, there was no difference for soleus at 3.0 kilometers per hour (p = 0.115). The importance of the differences in muscle activities between left limb and right limb were found. These results can potentially be used for evaluating lower limb extremity function of special populations (elderly people or stroke patients) in an objective and simple method. creator: Shengyun Liang creator: Jiali Xu creator: Lei wang creator: Guoru Zhao uri: https://doi.org/10.7717/peerj.2315 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liang et al. title: The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons link: https://peerj.com/articles/2297 last-modified: 2016-08-09 description: The brain’s biological clock, the suprachiasmatic nucleus (SCN), exhibits endogenous 24-hour rhythms in gene expression and spontaneous firing rate; however, the functional relationship between these neuronal rhythms is not fully understood. Here, we used a Per1::GFP transgenic mouse line that allows for the simultaneous quantification of molecular clock state and firing rate in SCN neurons to examine the relationship between these key components of the circadian clock. We find that there is a stable, phased relationship between E-box-driven clock gene expression and spontaneous firing rate in SCN neurons and that these relationships are independent of light input onto the system or of GABAA receptor-mediated synaptic activity. Importantly, the concordant phasing of gene and neural rhythms is disrupted in the absence of the homologous clock gene Per1, but persists in the absence of the core clock gene Per2. These results suggest that Per1 plays a unique, non-redundant role in phasing gene expression and firing rate rhythms in SCN neurons to increase the robustness of cellular timekeeping. creator: Jeff R. Jones creator: Douglas G. McMahon uri: https://doi.org/10.7717/peerj.2297 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jones and McMahon title: A comparison of blood gases, biochemistry, and hematology to ecomorphology in a health assessment of pinfish (Lagodon rhomboides) link: https://peerj.com/articles/2262 last-modified: 2016-08-09 description: Despite the promise of hematological parameters and blood chemistry in monitoring the health of marine fishes, baseline data is often lacking for small fishes that comprise central roles in marine food webs. This study establishes blood chemistry and hematological baseline parameters for the pinfish Lagodon rhomboides, a small marine teleost that is among the most dominant members of near-shore estuarine communities of the Atlantic Ocean and Gulf of Mexico. Given their prominence, pinfishes are an ideal candidate species to use as a model for monitoring changes across a wide range of near-shore marine communities. However, pinfishes exhibit substantial morphological differences associated with a preference for feeding in primarily sea-grass or sand dominated habitats, suggesting that differences in the foraging ecology of individuals could confound health assessments. Here we collect baseline data on the blood physiology of pinfish while assessing the relationship between blood parameters and measured aspects of feeding morphology using data collected from 37 individual fish. Our findings provide new baseline health data for this important near shore fish species and find no evidence for a strong linkage between blood physiology and either sex or measured aspects of feeding morphology. Comparing our hematological and biochemical data to published results from other marine teleost species suggests that analyses of trends in blood value variation correlated with major evolutionary transitions in ecology will shed new light on the physiological changes that underlie the successful diversification of fishes. creator: Sara Collins creator: Alex Dornburg creator: Joseph M. Flores creator: Daniel S. Dombrowski creator: Gregory A. Lewbart uri: https://doi.org/10.7717/peerj.2262 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Collins et al. title: Systematic relationships of five newly sequenced cervid species link: https://peerj.com/articles/2307 last-modified: 2016-08-04 description: Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging. creator: Nicola S. Heckeberg creator: Dirk Erpenbeck creator: Gert Wörheide creator: Gertrud E. Rössner uri: https://doi.org/10.7717/peerj.2307 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Heckeberg et al.