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: Non-lethal approach identifies variability of δ15N values in the fin rays of Atlantic Goliath Grouper, Epinephelus itajara
link: https://peerj.com/articles/1010
last-modified: 2015-06-11
description: The Atlantic Goliath Grouper, Epinephelus itajara, is critically endangered throughout its range but has begun to show initial signs of recovery in Florida state waters. As the population continues to rebound, researchers face a pressing need to fill the knowledge gaps about this iconic species. Here, we examined the δ15N isotopic records in fin rays collected from Atlantic Goliath Grouper, and related changes of isotopic ratios over time to life history characteristics. Fin-ray analysis was used as a non-lethal technique to sample individuals from two locations at similar latitudes from the west and east coasts of Florida, USA. δ15N data were acquired by mechanically separating the annuli of each fin ray and then analyzing the material in an Irradiance Elemental Analyzer Mass Spectrometer. The δ15N values were consistent among individuals within populations from each coast of Florida, and mirrored the expected changes over the lives of the fish. Overall, differences were found between δ15N values at juvenile life history phases versus adult phases, but the patterns associated with these differences were unique to each coastal group. We demonstrated, for the first time, that δ15N values from fin rays can be used to assess the life histories of Atlantic Goliath Grouper. The non-lethal strategies outlined here can be used to acquire information essential to the management of species of concern, such as those that are threatened or endangered.
creator: Orian E. Tzadik
creator: Ethan A. Goddard
creator: David J. Hollander
creator: Christopher C. Koenig
creator: Christopher D. Stallings
uri: https://doi.org/10.7717/peerj.1010
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Tzadik et al.

title: Rotation survival forest for right censored data
link: https://peerj.com/articles/1009
last-modified: 2015-06-11
description: Recently, survival ensembles have found more and more applications in biological and medical research when censored time-to-event data are often confronted. In this research, we investigate the plausibility of extending a rotation forest, originally proposed for classification purpose, to survival analysis. Supported by the proper statistical analysis, we show that rotation survival forests are able to outperform the state-of-art survival ensembles on right censored data. We also provide a C-index based variable importance measure for evaluating covariates in censored survival data.
creator: Lifeng Zhou
creator: Qingsong Xu
creator: Hong Wang
uri: https://doi.org/10.7717/peerj.1009
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhou et al.

title: Uneven distribution of enamel in the tooth crown of a Plains Zebra (Equus quagga)
link: https://peerj.com/articles/1002
last-modified: 2015-06-11
description: Unworn teeth of herbivorous mammals are not immediately functional. They have to be partially worn to expose enamel ridges which can then act as shear-cutting blades to break the food down. We use the Plains Zebra (Equus quagga) as a hypsodont, herbivorous model organism to investigate how initial wear of the tooth crown is controlled by underlying structures. We find that the enamel proportion is smaller at the apical half of the tooth crown in all upper tooth positions and suggest that lower enamel content here could promote early wear. Besides this uneven enamel distribution, we note that the third molar has a higher overall enamel content than any other tooth position. The M3 is thus likely to have a slightly different functional trait in mastication, resisting highest bite forces along the tooth row and maintaining functionality when anterior teeth are already worn down.
creator: Daniela E. Winkler
creator: Thomas M. Kaiser
uri: https://doi.org/10.7717/peerj.1002
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Winkler and Kaiser

title: Musculoskeletal modelling of an ostrich (Struthio camelus) pelvic limb: influence of limb orientation on muscular capacity during locomotion
link: https://peerj.com/articles/1001
last-modified: 2015-06-11
description: We developed a three-dimensional, biomechanical computer model of the 36 major pelvic limb muscle groups in an ostrich (Struthio camelus) to investigate muscle function in this, the largest of extant birds and model organism for many studies of locomotor mechanics, body size, anatomy and evolution. Combined with experimental data, we use this model to test two main hypotheses. We first query whether ostriches use limb orientations (joint angles) that optimize the moment-generating capacities of their muscles during walking or running. Next, we test whether ostriches use limb orientations at mid-stance that keep their extensor muscles near maximal, and flexor muscles near minimal, moment arms. Our two hypotheses relate to the control priorities that a large bipedal animal might evolve under biomechanical constraints to achieve more effective static weight support. We find that ostriches do not use limb orientations to optimize the moment-generating capacities or moment arms of their muscles. We infer that dynamic properties of muscles or tendons might be better candidates for locomotor optimization. Regardless, general principles explaining why species choose particular joint orientations during locomotion are lacking, raising the question of whether such general principles exist or if clades evolve different patterns (e.g., weighting of muscle force–length or force–velocity properties in selecting postures). This leaves theoretical studies of muscle moment arms estimated for extinct animals at an impasse until studies of extant taxa answer these questions. Finally, we compare our model’s results against those of two prior studies of ostrich limb muscle moment arms, finding general agreement for many muscles. Some flexor and extensor muscles exhibit self-stabilization patterns (posture-dependent switches between flexor/extensor action) that ostriches may use to coordinate their locomotion. However, some conspicuous areas of disagreement in our results illustrate some cautionary principles. Importantly, tendon-travel empirical measurements of muscle moment arms must be carefully designed to preserve 3D muscle geometry lest their accuracy suffer relative to that of anatomically realistic models. The dearth of accurate experimental measurements of 3D moment arms of muscles in birds leaves uncertainty regarding the relative accuracy of different modelling or experimental datasets such as in ostriches. Our model, however, provides a comprehensive set of 3D estimates of muscle actions in ostriches for the first time, emphasizing that avian limb mechanics are highly three-dimensional and complex, and how no muscles act purely in the sagittal plane. A comparative synthesis of experiments and models such as ours could provide powerful synthesis into how anatomy, mechanics and control interact during locomotion and how these interactions evolve. Such a framework could remove obstacles impeding the analysis of muscle function in extinct taxa.
creator: John R. Hutchinson
creator: Jeffery W. Rankin
creator: Jonas Rubenson
creator: Kate H. Rosenbluth
creator: Robert A. Siston
creator: Scott L. Delp
uri: https://doi.org/10.7717/peerj.1001
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hutchinson et al.

title: Can endocranial volume be estimated accurately from external skull measurements in great-tailed grackles (Quiscalus mexicanus)?
link: https://peerj.com/articles/1000
last-modified: 2015-06-11
description: There is an increasing need to validate and collect data approximating brain size on individuals in the field to understand what evolutionary factors drive brain size variation within and across species. We investigated whether we could accurately estimate endocranial volume (a proxy for brain size), as measured by computerized tomography (CT) scans, using external skull measurements and/or by filling skulls with beads and pouring them out into a graduated cylinder for male and female great-tailed grackles. We found that while females had higher correlations than males, estimations of endocranial volume from external skull measurements or beads did not tightly correlate with CT volumes. We found no accuracy in the ability of external skull measures to predict CT volumes because the prediction intervals for most data points overlapped extensively. We conclude that we are unable to detect individual differences in endocranial volume using external skull measurements. These results emphasize the importance of validating and explicitly quantifying the predictive accuracy of brain size proxies for each species and each sex.
creator: Corina J. Logan
creator: Christin R. Palmstrom
uri: https://doi.org/10.7717/peerj.1000
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Logan et al.

title: Development of a cognitive bias methodology for measuring low mood in chimpanzees
link: https://peerj.com/articles/998
last-modified: 2015-06-11
description: There is an ethical and scientific need for objective, well-validated measures of low mood in captive chimpanzees. We describe the development of a novel cognitive task designed to measure ‘pessimistic’ bias in judgments of expectation of reward, a cognitive marker of low mood previously validated in a wide range of species, and report training and test data from three common chimpanzees (Pan troglodytes). The chimpanzees were trained on an arbitrary visual discrimination in which lifting a pale grey paper cone was associated with reinforcement with a peanut, whereas lifting a dark grey cone was associated with no reward. The discrimination was trained by sequentially presenting the two cone types until significant differences in latency to touch the cone types emerged, and was confirmed by simultaneously presenting both cone types in choice trials. Subjects were subsequently tested on their latency to touch unrewarded cones of three intermediate shades of grey not previously seen. Pessimism was indicated by the similarity between the latency to touch intermediate cones and the latency to touch the trained, unreinforced, dark grey cones. Three subjects completed training and testing, two adult males and one adult female. All subjects learnt the discrimination (107–240 trials), and retained it during five sessions of testing. There was no evidence that latencies to lift intermediate cones increased over testing, as would have occurred if subjects learnt that these were never rewarded, suggesting that the task could be used for repeated testing of individual animals. There was a significant difference between subjects in their relative latencies to touch intermediate cones (pessimism index) that emerged following the second test session, and was not changed by the addition of further data. The most dominant male subject was least pessimistic, and the female most pessimistic. We argue that the task has the potential to be used to assess longitudinal changes in sub-clinical levels of low mood in chimpanzees, however further work with a larger sample of animals is required to validate this claim.
creator: Melissa Bateson
creator: Daniel Nettle
uri: https://doi.org/10.7717/peerj.998
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bateson and Nettle

title: A rapid assessment of post-disclosure experiences of urban HIV-positive and HIV-negative school-aged children in Kenya
link: https://peerj.com/articles/956
last-modified: 2015-06-11
description: There has been limited involvement of HIV-negative children in HIV disclosure studies; most studies conducted on the effects of disclosure on children have been with HIV-positive children and HIV-positive mother-child dyads. Seven HIV-positive and five HIV-negative children participated in a larger study conducted to understand the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. In this study, the experiences of these 12 children after receiving disclosure of their own and their parents’ illnesses respectively are presented. Each child underwent an in-depth qualitative semi-structured digitally recorded interview. The recorded interviews were transcribed and loaded into NVivo8 for phenomenological data analysis. Five themes emerged from the data, indicating that HIV-positive and negative children appear to have differing post-disclosure experiences revolving around acceptance of illness, stigma and discrimination, medication consumption, sexual awareness, and use of coping mechanisms. Following disclosure, HIV-negative children accepted their parents’ illnesses within a few hours to a few weeks; HIV-positive children took weeks to months to accept their own illnesses. HIV-negative children knew of high levels of stigma and discrimination within the community; HIV-positive children reported experiencing indirect incidences of stigma and discrimination. HIV-negative children wanted their parents to take their medications, stay healthy, and pay their school fees so they could have a better life in the future; HIV-positive children viewed medication consumption as an ordeal necessary to keep them healthy. HIV-negative children wanted their parents to speak to them about sexual-related matters; HIV-positive children had lingering questions about relationships, use of condoms, marriage, and childbearing options. All but one preadolescent HIV-positive child had self-identified a person to speak with for social support. When feeling overwhelmed by their circumstances, the children self-withdrew and performed positive activities (e.g., praying, watching TV, listening to the radio, singing, dancing) to help themselves feel better. Many HIV-affected families have a combination of HIV-positive and negative siblings within the household. Pending further studies conducted with larger sample sizes, the results of this study should assist healthcare professionals to better facilitate disclosure between HIV-positive parents and their children of mixed HIV statuses.
creator: Grace Gachanja
uri: https://doi.org/10.7717/peerj.956
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gachanja

title: Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora
link: https://peerj.com/articles/890
last-modified: 2015-06-11
description: Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study.
creator: Zhao-Ming Gao
creator: Yong Wang
creator: Ren-Mao Tian
creator: On On Lee
creator: Yue Him Wong
creator: Zenon B. Batang
creator: Abdulaziz Al-Suwailem
creator: Feras F. Lafi
creator: Vladimir B. Bajic
creator: Pei-Yuan Qian
uri: https://doi.org/10.7717/peerj.890
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gao et al.

title: Can sea urchins beat the heat? Sea urchins, thermal tolerance and climate change
link: https://peerj.com/articles/1006
last-modified: 2015-06-09
description: The massive die-off of the long-spined sea urchin, Diadema antillarum, a significant reef grazer, in the mid 1980s was followed by phase shifts from coral dominated to macroalgae dominated reefs in the Caribbean. While Diadema populations have recovered in some reefs with concomitant increases in coral cover, the additional threat of increasing temperatures due to global climate change has not been investigated in adult sea urchins. In this study, I measured acute thermal tolerance of D. antillarum and that of a sympatric sea urchin not associated with coral cover, Echinometra lucunter, over winter, spring, and summer, thus exposing them to substantial natural thermal variation. Animals were taken from the wild and placed in laboratory tanks in room temperature water (∼22 °C) that was then heated at 0.16–0.3 °C min−1 and the righting behavior of individual sea urchins was recorded. I measured both the temperature at which the animal could no longer right itself (TLoR) and the righting time at temperatures below the TLoR. In all seasons, D. antillarum exhibited a higher mean TLoR than E. lucunter. The mean TLoR of each species increased with increasing environmental temperature revealing that both species acclimatize to seasonal changes in temperatures. The righting times of D. antillarum were much shorter than those of E. lucunter. The longer relative spine length of Diadema compared to that of Echinometra may contribute to their shorter righting times, but does not explain their higher TLoR. The thermal safety margin (the difference between the mean collection temperature and the mean TLoR) was between 3.07–3.66 °C for Echinometra and 3.79–5.67 °C for Diadema. While these thermal safety margins exceed present day temperatures, they are modest compared to those of temperate marine invertebrates. If sea temperatures increase more rapidly than can be accommodated by the sea urchins (either by genetic adaptation, phenotypic plasticity, or both), this will have important consequences for the structure of coral reefs.
creator: Elizabeth Sherman
uri: https://doi.org/10.7717/peerj.1006
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sherman

title: A mathematical model for predicting glucose levels in critically-ill patients: the PIGnOLI model
link: https://peerj.com/articles/1005
last-modified: 2015-06-09
description: Background and Objectives. Glycemic control is of paramount importance in the intensive care unit. Presently, several BG control algorithms have been developed for clinical trials, but they are mostly based on experts’ opinion and consensus. There are no validated models predicting how glucose levels will change after initiating of insulin infusion in critically ill patients. The study aimed to develop an equation for initial insulin dose setting.Methods. A large critical care database was employed for the study. Linear regression model fitting was employed. Retested blood glucose was used as the independent variable. Insulin rate was forced into the model. Multivariable fractional polynomials and interaction terms were used to explore the complex relationships among covariates. The overall fit of the model was examined by using residuals and adjusted R-squared values. Regression diagnostics were used to explore the influence of outliers on the model.Main Results. A total of 6,487 ICU admissions requiring insulin pump therapy were identified. The dataset was randomly split into two subsets at 7 to 3 ratio. The initial model comprised fractional polynomials and interactions terms. However, this model was not stable by excluding several outliers. I fitted a simple linear model without interaction. The selected prediction model (Predicting Glucose Levels in ICU, PIGnOLI) included variables of initial blood glucose, insulin rate, PO volume, total parental nutrition, body mass index (BMI), lactate, congestive heart failure, renal failure, liver disease, time interval of BS recheck, dextrose rate. Insulin rate was significantly associated with blood glucose reduction (coefficient: −0.52, 95% CI [−1.03, −0.01]). The parsimonious model was well validated with the validation subset, with an adjusted R-squared value of 0.8259.Conclusion. The study developed the PIGnOLI model for the initial insulin dose setting. Furthermore, experimental study is mandatory to examine whether adjustment of the insulin infusion rate based on PIGnOLI will benefit patients’ outcomes.
creator: Zhongheng Zhang
uri: https://doi.org/10.7717/peerj.1005
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhang