title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1946 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Demographic rates of northern royal albatross at Taiaroa Head, New Zealand link: https://peerj.com/articles/906 last-modified: 2015-04-28 description: Demographic rates, such as annual survival rate, are generally difficult to estimate for long-lived seabirds, because of the length of time required for this kind of study and the remoteness of colonies. However, a small colony of northern royal albatross (Diomedea sanfordi) established itself on the mainland of New Zealand at Taiaroa Head, making possible regular banding and monitoring of its individuals since the first chick fledged, in 1938. Data on the presence/absence of birds, as well as on breeding outcomes, were available for the period from 1989–90 to 2011–12, and included 2128 annual resightings of 355 banded individuals of known age. The main goal of the present study was to estimate the annual survival rate of juveniles, pre-breeders, and adults at Taiaroa Head. These rates were estimated simultaneously in a single Bayesian multi-state capture-recapture model. Several models were fitted to the data, with different levels of complexity. From the most parsimonious model, the overall annual adult survival rate was estimated as 0.950 (95% CI [0.941–0.959]). In this model, adult survival declined with age, from 0.976 (95% CI [0.963–0.988]) at 6 years, the minimum age at first breeding, to 0.915 (95% CI [0.879–0.946]) at 40 years. Mean annual survival of pre-breeders was 0.966 (95% CI [0.950–0.980]), and 0.933 (95% CI [0.908–0.966]) for juveniles. There was no discernible difference in survival between males and females, and there was no apparent trend in survival over time. Estimates of other demographic rates were also obtained during the estimation process. The mean age at first return of juveniles to the colony was estimated as 4.8 years (95% CI [4.6–5.1]), and the mean age at first breeding as 8.9 years (95% CI [8.5–9.3]). Because all the birds of the colony were banded, it was possible to estimate the total population size. The number of northern royal albatross present annually at the Taiaroa Head colony has doubled since 1989–90, and the current total population size was estimated to be over 200 individuals. The ratio of the total population size to the number of annual breeding pairs varied from 5 to 12 among years, with an overall mean of 7.65 (95% CI [7.56–7.78]), and this high variability highlights the need for a sufficient number of surveys of seabird breeding populations before reliable conclusions on population trends can be made. Although long-term data allowed estimates of demographic rates of northern royal albatross at Taiaroa Head, the location of the colony and the ongoing management by staff mean that the population dynamics may differ from those of the main population on the Chatham Islands. creator: Yvan Richard creator: Lyndon Perriman creator: Chris Lalas creator: Edward R. Abraham uri: https://doi.org/10.7717/peerj.906 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Richard et al. title: Tunable translational control using site-specific unnatural amino acid incorporation in Escherichia coli link: https://peerj.com/articles/904 last-modified: 2015-04-28 description: Translation of target gene transcripts in Escherichia coli harboring UAG amber stop codons can be switched on by the amber-codon-specific incorporation of an exogenously supplied unnatural amino acid, 3-iodo-L-tyrosine. Here, we report that this translational switch can control the translational efficiency at any intermediate magnitude by adjustment of the 3-iodo-L-tyrosine concentration in the medium, as a tunable translational controller. The translational efficiency of a target gene reached maximum levels with 10−5 M 3-iodo-L-tyrosine, and intermediate levels were observed with suboptimal concentrations (approximately spanning a 2-log10 concentration range, 10−7–10−5 M). Such intermediate-level expression was also confirmed in individual bacteria. creator: Yusuke Kato uri: https://doi.org/10.7717/peerj.904 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kato title: Organization and distribution of glomeruli in the bowhead whale olfactory bulb link: https://peerj.com/articles/897 last-modified: 2015-04-28 description: Although modern baleen whales (Mysticeti) retain a functional olfactory system that includes olfactory bulbs, cranial nerve I and olfactory receptor genes, their olfactory capabilities have been reduced to a great degree. This reduction likely occurred as a selective response to their fully aquatic lifestyle. The glomeruli that occur in the olfactory bulb can be divided into two non-overlapping domains, a dorsal domain and a ventral domain. Recent molecular studies revealed that all modern whales have lost olfactory receptor genes and marker genes that are specific to the dorsal domain. Here we show that olfactory bulbs of bowhead whales (Balaena mysticetus) lack glomeruli on the dorsal side, consistent with the molecular data. In addition, we estimate that there are more than 4,000 glomeruli elsewhere in the bowhead whale olfactory bulb, which is surprising given that bowhead whales possess only 80 intact olfactory receptor genes. Olfactory sensory neurons that express the same olfactory receptors in rodents generally project to two specific glomeruli in an olfactory bulb, implying an approximate 1:2 ratio of the number of olfactory receptors to the number of glomeruli. Here we show that this ratio does not apply to bowhead whales, reiterating the conceptual limits of using rodents as model organisms for understanding the initial coding of odor information among mammals. creator: Takushi Kishida creator: JGM Thewissen creator: Sharon Usip creator: Robert S. Suydam creator: John C. George uri: https://doi.org/10.7717/peerj.897 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kishida et al. title: Tiludronate concentrations and cytologic findings in synovial fluid after intravenous regional limb perfusion with tiludronate in horses link: https://peerj.com/articles/889 last-modified: 2015-04-28 description: Anecdotal accounts of tiludronate administration via intravenous regional limb perfusion (IVRLP) exist despite a lack of information regarding safety for synovial structures in the perfused area. The objective of this study was to determine whether tiludronate concentrations in synovial structures after IVRLP with low dose (0.5 mg, LDT) or high dose (50 mg, HDT) tiludronate remain below a value demonstrated in vitro to be safe for articular cartilage (<19,000 ng/ml), and to determine effects of tiludronate on synovial fluid cytology variables compared to saline perfused control limbs. Using a randomized controlled experimental study design, horses received IVRLP with LDT (n = 6) or HDT (n = 6) in one forelimb and IVRLP with saline in the contralateral limb. Synovial fluid cytology variables and tiludronate concentrations were evaluated in navicular bursae (NB), and distal interphalangeal (DIP) and metacarpophalangeal (MCP) joints one week before and 30–45 min after IVRLP, and in DIP and MCP joints 24 h after IVRLP. Data were analyzed with 2-way rmANOVA (p < 0.05). Highest measured synovial fluid tiludronate concentrations occurred 30–45 min post-perfusion. Mean tiludronate concentrations were lower in LDT limbs (MCP = 39.6 ± 14.3 ng/ml, DIP = 118.1 ± 66.6 ng/ml, NB = 82.1 ± 30.2 ng/ml) than in HDT limbs (MCP = 3,745.1 ± 1,536.6 ng/ml, DIP = 16,274.0 ± 5,460.2 ng/ml, NB = 6,049.3 ± 1,931.7 ng/ml). Tiludronate concentration was >19,000 ng/ml in DIP joints of two HDT limbs. Tiludronate was measurable only in synovial fluid from HDT limbs 24 h post-perfusion. There were no differences in synovial fluid cytology variables between control and treated limbs.Conclusions. In some horses, IVRLP with HDT may result in synovial fluid concentrations of tiludronate that may have adverse effects on articular cartilage, based on in vitro data. IVRLP with LDT is unlikely to promote articular cartilage degradation. Further studies to determine a safe and effective dose for IVRLP with tiludronate are needed. creator: Barbara G. Hunter creator: Katja F. Duesterdieck-Zellmer creator: Maureen K. Larson uri: https://doi.org/10.7717/peerj.889 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hunter et al. title: DCEMRI.jl: a fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis link: https://peerj.com/articles/909 last-modified: 2015-04-23 description: We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10–20× speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 × 192 breast image, we achieved run times of <1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N1.9), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise. creator: David S. Smith creator: Xia Li creator: Lori R. Arlinghaus creator: Thomas E. Yankeelov creator: E. Brian Welch uri: https://doi.org/10.7717/peerj.909 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Smith et al. title: Bayesian estimation of predator diet composition from fatty acids and stable isotopes link: https://peerj.com/articles/920 last-modified: 2015-04-23 description: Quantitative analysis of stable isotopes (SI) and, more recently, fatty acid profiles (FAP) are useful and complementary tools for estimating the relative contribution of different prey items in the diet of a predator. The combination of these two approaches, however, has thus far been limited and qualitative. We propose a mixing model for FAP that follows the Bayesian machinery employed in state-of-the-art mixing models for SI. This framework provides both point estimates and probability distributions for individual and population level diet proportions. Where fat content and conversion coefficients are available, they can be used to improve diet estimates. This model can be explicitly integrated with analogous models for SI to increase resolution and clarify predator–prey relationships. We apply our model to simulated data and an experimental dataset that allows us to illustrate modeling strategies and demonstrate model performance. Our methods are provided as an open source software package for the statistical computing environment R. creator: Philipp Neubauer creator: Olaf P. Jensen uri: https://doi.org/10.7717/peerj.920 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Neubauer and Jensen title: Test re-test reliability and construct validity of the star-track test of manual dexterity link: https://peerj.com/articles/917 last-modified: 2015-04-23 description: Objectives. We wished to determine test re-test reliability and construct validity of the star-track test of manual dexterity.Design. Test re-test reliability was examined in a controlled study. Construct validity was tested in a blinded randomized crossover study.Setting. The study was performed at a university hospital in Denmark.Participants. A total of 11 subjects for test re-test and 20 subjects for the construct validity study were included. All subjects were healthy volunteers.Intervention. The test re-test trial had two measurements with 2 days pause in between. The interventions in the construct validity study included baseline measurement, intervention 1: fatigue, intervention 2: stress, and intervention 3: fatigue and stress. There was a 2 day pause between each intervention.Main outcome measure. An integrated measure of completion time and number of errors was used.Results. All participants completed the study (test re-test n = 11; construct validity n = 20). The test re-testshowed a strong Pearson product-moment correlation (r = 0.90, n = 11, P < 0.01) with no sign of learning effect. The 20 subjects in the construct validity trial were randomized to the order of the four interventions, so that all subjects completed each intervention once. A repeated measures ANOVA determined that mean integrated measure differed between interventions (p = 0.002). Post hoc tests using Bonferroni correction revealed that compared with baseline all interventions had significantly higher integrated scores ranging from 47–59% difference in mean.Conclusion. The star track test of manual dexterity had a strong test re-test reliability, and was able to discriminate between a subject’s normal manual dexterity and dexterity after exposure to fatigue and/or stress. creator: Niels Kildebro creator: Ilda Amirian creator: Ismail Gögenur creator: Jacob Rosenberg uri: https://doi.org/10.7717/peerj.917 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kildebro et al. title: Diabetes screening: a pending issue in hypertense/obese patients link: https://peerj.com/articles/914 last-modified: 2015-04-23 description: The literature about possible cardiovascular consequences of diagnostic inertia in diabetes is scarce. We examined the influence of undetected high fasting blood glucose (FBG) levels on the cardiovascular risk and poor control of cardiovascular risk factors in hypertensive or obese patients, with no previous diagnosis of diabetes mellitus (i.e., diagnostic inertia). A cross-sectional study during a preventive program in a Spanish region was performed in 2003–2004. The participants were aged ≥40 years and did not have diabetes but were hypertensive (n = 5, 347) or obese (n = 7, 833). The outcomes were high cardiovascular risk (SCORE ≥5%), poor control of the blood pressure (≥140/90 mmHg) and class II obesity. The relationship was examined between FBG and the main parameters, calculating the adjusted odd ratios with multivariate models. Higher values of FBG were associated with all the outcomes. A more proactive attitude towards the diagnosis of diabetes mellitus in the hypertensive and obese population should be adopted. creator: Armina Sepehri creator: Antonio Palazón-Bru creator: Vicente Francisco Gil-Guillén creator: Dolores Ramírez-Prado creator: Felipe Navarro-Cremades creator: Ernesto Cortés creator: María Mercedes Rizo-Baeza uri: https://doi.org/10.7717/peerj.914 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sepehri et al. title: An experimental search strategy retrieves more precise results than PubMed and Google for questions about medical interventions link: https://peerj.com/articles/913 last-modified: 2015-04-23 description: Objective. We compared the precision of a search strategy designed specifically to retrieve randomized controlled trials (RCTs) and systematic reviews of RCTs with search strategies designed for broader purposes.Methods. We designed an experimental search strategy that automatically revised searches up to five times by using increasingly restrictive queries as long at least 50 citations were retrieved. We compared the ability of the experimental and alternative strategies to retrieve studies relevant to 312 test questions. The primary outcome, search precision, was defined for each strategy as the proportion of relevant, high quality citations among the first 50 citations retrieved.Results. The experimental strategy had the highest median precision (5.5%; interquartile range [IQR]: 0%–12%) followed by the narrow strategy of the PubMed Clinical Queries (4.0%; IQR: 0%–10%). The experimental strategy found the most high quality citations (median 2; IQR: 0–6) and was the strategy most likely to find at least one high quality citation (73% of searches; 95% confidence interval 68%–78%). All comparisons were statistically significant.Conclusions. The experimental strategy performed the best in all outcomes although all strategies had low precision. creator: Robert G. Badgett creator: Daniel P. Dylla creator: Susan D. Megison creator: E Glynn Harmon uri: https://doi.org/10.7717/peerj.913 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Badgett et al. title: Too packed to change: side-chain packing and site-specific substitution rates in protein evolution link: https://peerj.com/articles/911 last-modified: 2015-04-23 description: In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates are solvent accessibility and packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between a site’s Cα and the Cα of the other sites. According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein’s active conformation. While WCN is a measure of Cα packing, mutations replace side chains. Here, we consider whether a site’s evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain contact density. We tested this prediction on a data set of structurally and functionally diverse monomeric enzymes. We compared side-chain contact density with main-chain contact density measures and with relative solvent accessibility (RSA). We found that side-chain contact density is the best predictor of rate variation among sites (it explains 39.2% of the variation). Moreover, the independent contribution of main-chain contact density measures and RSA are negligible. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing. creator: María Laura Marcos creator: Julian Echave uri: https://doi.org/10.7717/peerj.911 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Marcos and Echave