title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-05
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Genetic approaches to the conservation of migratory bats: a study of the eastern red bat (Lasiurus borealis)
link: https://peerj.com/articles/983
last-modified: 2015-05-28
description: Documented fatalities of bats at wind turbines have raised serious concerns about the future impacts of increased wind power development on populations of migratory bat species. However, for most bat species we have no knowledge of the size of populations and their demographic trends, the degree of structuring into discrete subpopulations, and whether different subpopulations use spatially segregated migratory routes. Here, we utilize genetic data from eastern red bats (Lasiurus borealis), one of the species most highly affected by wind power development in North America, to (1) evaluate patterns of population structure across the landscape, (2) estimate effective population size (Ne), and (3) assess signals of growth or decline in population size. Using data on both nuclear and mitochondrial DNA variation, we demonstrate that this species forms a single, panmictic population across their range with no evidence for the historical use of divergent migratory pathways by any portion of the population. Further, using coalescent estimates we estimate that the effective size of this population is in the hundreds of thousands to millions of individuals. The high levels of gene flow and connectivity across the population of eastern red bats indicate that monitoring and management of eastern red bats must integrate information across the range of this species.
creator: Maarten J. Vonhof
creator: Amy L. Russell
uri: https://doi.org/10.7717/peerj.983
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Vonhof and Russell

title: VirSorter: mining viral signal from microbial genomic data
link: https://peerj.com/articles/985
last-modified: 2015-05-28
description: Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.
creator: Simon Roux
creator: Francois Enault
creator: Bonnie L. Hurwitz
creator: Matthew B. Sullivan
uri: https://doi.org/10.7717/peerj.985
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Roux et al.

title: ACE and UCP2 gene polymorphisms and their association with baseline and exercise-related changes in the functional performance of older adults
link: https://peerj.com/articles/980
last-modified: 2015-05-28
description: Maintaining high levels of physical function is an important aspect of successful ageing. While muscle mass and strength contribute to functional performance in older adults, little is known about the possible genetic basis for the heterogeneity of physical function in older adults and in how older adults respond to exercise. Two genes that have possible roles in determining levels of muscle mass, strength and function in young and older adults are angiotensin-converting enzyme (ACE) and mitochondrial uncoupling protein 2 (UCP2). This study examined whether polymorphisms in these two individual genes were associated with baseline functional performance levels and/or the training-related changes following exercise in previously untrained older adults. Five-eight Caucasian older adults (mean age 69.8 years) with no recent history of resistance training enrolled in a 12 week program of resistance, balance and cardiovascular exercises aimed at improving functional performance. Performance in 6 functional tasks was recorded at baseline and after 12 weeks. Genomic DNA was assayed for the ACE intron 16 insertion/deletion (I/D) and the UCP2 G-866A polymorphism. Baseline differences among genotype groups were tested using analysis of variance. Genotype differences in absolute and relative changes in physical function among the exercisers were tested using a general linear model, adjusting for age and gender. The genotype frequencies for each of the studied polymorphisms conformed to the Hardy-Weinberg equilibrium. The ACE I/D genotype was significantly associated with mean baseline measures of handgrip strength (II 30.9 ± 3.01 v. ID 31.7 ± 1.48 v. DD 29.3 ± 2.18 kg, p < 0.001), 8ft Up and Go time (II 6.45 ± 0.48 v. ID/DD 4.41 ± 0.19 s, p < 0.001) and 6 min walk distance (II 458 ± 28.7 v. ID/DD 546 ± 12.1m, p = 0.008). The UCP2 G-866A genotype was also associated with baseline 8ft Up and Go time (GG 5.45 ± 0.35 v. GA 4.47 ± 0.26 v. AA 3.89 ± 0.71 s, p = 0.045). After 12 weeks of training, a significant difference between UCP2 G-886A genotype groups for change in 8ft Up and Go time was detected (GG −0.68 ± 0.17 v. GA −0.10 ± 0.14 v. AA +0.05 ± 0.31 s, p = 0.023). While several interesting and possibly consistent associations with older adults’ baseline functional performance were found for the ACE and UCP2 polymorphisms, we found no strong evidence of genetic associations with exercise responses in this study. The relative equivalence of some of these training-response findings to the literature may have reflected the current study’s focus on physical function rather than just strength, the relatively high levels of baseline function for some genotype groups as well as the greater statistical power for detecting baseline differences than the training-related changes.
creator: Justin W.L. Keogh
creator: Barry R. Palmer
creator: Denise Taylor
creator: Andrew E. Kilding
uri: https://doi.org/10.7717/peerj.980
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Keogh et al.

title: Vorinostat enhances chemosensitivity to arsenic trioxide in K562 cell line
link: https://peerj.com/articles/962
last-modified: 2015-05-28
description: Objective. This study aimed to investigate the chemosensitive augmentation effect and mechanism of HDAC inhibitor Vorinostat (SAHA) in combination with arsenic trioxide (ATO) on proliferation and apoptosis of K562 cells.Methods. The CCK-8 assay was used to compare proliferation of the cells. Annexin-V and PI staining by flow cytometry and acridine orange/ethidium bromide stains were used to detect and quantify apoptosis. Western blot was used to detect expression of p21, Akt, pAkt, p210, Acetyl-Histone H3, and Acetyl-Histone H4 proteins.Results. SAHA and ATO inhibited proliferation of K562 cells in an additive and time- and dose-dependent manner. SAHA in combination with ATO showed significant apoptosis of K562 cells in comparison to the single drugs alone (p < 0.01). Both SAHA and ATO alone and in combination showed lower levels of p210 expression. SAHA and SAHA and ATO combined treatment showed increased levels of Acetyl-Histone H3 and Acetyl-Histone H4 protein expression. SAHA alone showed increased expression of p21, while ATO alone and in combination with SAHA showed no significant change. SAHA and ATO combined therapy showed lower levels of Akt and pAkt protein expression than SAHA or ATO alone.Conclusion. SAHA and ATO combined treatment inhibited proliferation, induced apoptosis, and showed a chemosensitive augmentation effect on K562 cells. The mechanism might be associated with increasing histone acetylation levels as well as regulating the Akt signaling pathway.
creator: Nainong Li
creator: Xiaoyan Guan
creator: Fang Li
creator: Xiaofan Li
creator: Yuanzhong Chen
uri: https://doi.org/10.7717/peerj.962
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Li et al.

title: Morphometric comparisons of Diaphorina citri (Hemiptera: Liviidae) populations from Iran, USA and Pakistan
link: https://peerj.com/articles/946
last-modified: 2015-05-28
description: The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), vector of citrus greening disease pathogen, Huanglongbing (HLB), is considered the most serious pest of citrus in the world. Prior molecular based studies have hypothesized a link between the D. citri in Iran and the USA (Florida). The purpose of this study was to collect morphometric data from D. citri populations from Iran (mtCOI haplotype-1), Florida (mtCOI haplotype-1), and Pakistan (mtCOI haplotype-6), to determine whether different mtCOI haplotypes have a relationship to a specific morphometric variation. 240 samples from 6 ACP populations (Iran—Jiroft, Chabahar; Florida—Ft. Pierce, Palm Beach Gardens, Port St. Lucie; and Pakistan—Punjab) were collected for comparison. Measurements of 20 morphological characters were selected, measured and analysed using ANOVA and MANOVA. The results indicate differences among the 6 ACP populations (Wilks’ lambda = 0.0376, F = 7.29, P < 0.0001). The body length (BL), circumanal ring length (CL), antenna length (AL), forewing length (WL) and Rs vein length of forewing (RL) were the most important characters separating the populations. The cluster analysis showed that the Iran and Florida populations are distinct from each other but separate from the Pakistan population. Thus, three subgroups can be morphologically discriminated within D. citri species in this study, (1) Iran, (2) USA (Florida) and (3) Pakistan population. Morphometric comparisons provided further resolution to the mtCOI haplotypes and distinguished the Florida and Iranian populations.
creator: Mohammadreza Lashkari
creator: Matthew G. Hentz
creator: Laura M. Boykin
uri: https://doi.org/10.7717/peerj.946
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Lashkari et al.

title: Using 3D printed eggs to examine the egg-rejection behaviour of wild birds
link: https://peerj.com/articles/965
last-modified: 2015-05-26
description: The coevolutionary relationships between brood parasites and their hosts are often studied by examining the egg rejection behaviour of host species using artificial eggs. However, the traditional methods for producing artificial eggs out of plasticine, plastic, wood, or plaster-of-Paris are laborious, imprecise, and prone to human error. As an alternative, 3D printing may reduce human error, enable more precise manipulation of egg size and shape, and provide a more accurate and replicable protocol for generating artificial stimuli than traditional methods. However, the usefulness of 3D printing technology for egg rejection research remains to be tested. Here, we applied 3D printing technology to the extensively studied egg rejection behaviour of American robins, Turdus migratorius. Eggs of the robin’s brood parasites, brown-headed cowbirds, Molothrus ater, vary greatly in size and shape, but it is unknown whether host egg rejection decisions differ across this gradient of natural variation. We printed artificial eggs that encompass the natural range of shapes and sizes of cowbird eggs, painted them to resemble either robin or cowbird egg colour, and used them to artificially parasitize nests of breeding wild robins. In line with previous studies, we show that robins accept mimetically coloured and reject non-mimetically coloured artificial eggs. Although we found no evidence that subtle differences in parasitic egg size or shape affect robins’ rejection decisions, 3D printing will provide an opportunity for more extensive experimentation on the potential biological or evolutionary significance of size and shape variation of foreign eggs in rejection decisions. We provide a detailed protocol for generating 3D printed eggs using either personal 3D printers or commercial printing services, and highlight additional potential future applications for this technology in the study of egg rejection.
creator: Branislav Igic
creator: Valerie Nunez
creator: Henning U. Voss
creator: Rebecca Croston
creator: Zachary Aidala
creator: Analía V. López
creator: Aimee Van Tatenhove
creator: Mandë E. Holford
creator: Matthew D. Shawkey
creator: Mark E. Hauber
uri: https://doi.org/10.7717/peerj.965
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Igic et al.

title: Have the “mega-journals” reached the limits to growth?
link: https://peerj.com/articles/981
last-modified: 2015-05-26
description: A “mega-journal” is a new type of scientific journal that publishes freely accessible articles, which have been peer reviewed for scientific trustworthiness, but leaves it to the readers to decide which articles are of interest and importance to them. In the wake of the phenomenal success of PLOS ONE, several other publishers have recently started mega-journals. This article presents the evolution of mega-journals since 2010 in terms of article publication rates. The fastest growth seems to have ebbed out at around 35,000 annual articles for the 14 journals combined. Acceptance rates are in the range of 50–70%, and speed of publication is around 3–5 months. Common features in mega-journals are alternative impact metrics, easy reusability of figures and data, post-publication discussions and portable reviews from other journals.
creator: Bo-Christer Björk
uri: https://doi.org/10.7717/peerj.981
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Björk

title: Earthworm assemblages in different intensity of agricultural uses and their relation to edaphic variables
link: https://peerj.com/articles/979
last-modified: 2015-05-26
description: The objective of this study was to relate earthworm assemblage structure with three different soil use intensities, and to indentify the physical, chemical, and microbiological soil variables that are associated to the observed differences. Three soil uses were evaluated: 1-Fifty year old naturalized grasslands, low use intensity; 2-Recent agricultural fields, intermediate use intensity, and 3-Fifty year old intensive agricultural fields, high use intensity. Three different sites for each soil use were evaluated from winter 2008 through summer 2011. Nine earthworm species were identified across all sampling sites. The sites shared five species: the native Microscolex dubius, and the introduced Aporrectodea caliginosa, A. rosea, Octalasion cyaneum, and O. lacteum, but they differed in relative abundance by soil use. The results show that the earthworm community structure is linked to and modulated by soil properties. Both species abundance and diversity showed significant differences depending on soil use intensity. A principal component analysis showed that species composition is closely related to the environmental variability. The ratio of native to exotic species was significantly lower in the intensive agricultural system when compared to the other two, lower disturbance systems. Microscolex dubius abundance was related to naturalized grasslands along with soil Ca, pH, mechanical resistance, and microbial respiration. Aporrectodea caliginosa abundance was related to high K levels, low enzymatic activity, slightly low pH, low Ca, and appeared related to the highly disturbed environment. Eukerria stagnalis and Aporrectodea rosea, commonly found in the recent agricultural system, were related to high soil moisture condition, low pH, low Ca and low enzymatic activity. These results show that earthworm assemblages can be good indicators of soil use intensities. In particular, Microscolex dubius, Aporrectodea caliginosa, and Aporrectodea rosea, showed different temporal patterns and species associations, due to the changes in soil properties attributable to soil use intensity, defined as the amount and type of agricultural operations.
creator: LB Falco
creator: R Sandler
creator: F Momo
creator: C Di Ciocco
creator: L Saravia
creator: C Coviella
uri: https://doi.org/10.7717/peerj.979
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Falco et al.

title: Evolution of heritable behavioural differences in a model of social division of labour
link: https://peerj.com/articles/977
last-modified: 2015-05-26
description: The spectacular diversity of personality and behaviour of animals and humans has evoked many hypotheses intended to explain its developmental and evolutionary background. Although the list of the possible contributing mechanisms seems long, we propose that an underemphasised explanation is the division of labour creating negative frequency dependent selection. We use analytical and numerical models of social division of labour to show how selection can create consistent and heritable behavioural differences in a population, where randomly sampled individuals solve a collective task together. We assume that the collective task needs collaboration of individuals performing one of the two possible subtasks. The total benefit of the group is highest when the ratio of different subtasks is closest to 1. The probability of choosing one of the two costly subtasks and the costs assigned to them are under selection. By using adaptive dynamics we show that if a trade-off between the costs of the subtasks is strong enough, then evolution leads to coexistence of specialized individuals performing one of the subtasks with high probability and low cost. Our analytical results were verified and extended by numerical simulations.
creator: Zsóka Vásárhelyi
creator: Géza Meszéna
creator: István Scheuring
uri: https://doi.org/10.7717/peerj.977
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Vásárhelyi et al.

title: Caveolar disruption causes contraction of rat femoral arteries via reduced basal NO release and subsequent closure of BKCa channels
link: https://peerj.com/articles/966
last-modified: 2015-05-26
description: Background and Purpose. Caveolae act as signalling hubs in endothelial and smooth muscle cells. Caveolar disruption by the membrane cholesterol depleting agent methyl-β-cyclodextrin (M-β-CD) has various functional effects on arteries including (i) impairment of endothelium-dependent relaxation, and (ii) alteration of smooth muscle cell (SMC) contraction independently of the endothelium. The aim of this study was to explore the effects of M-β-CD on rat femoral arteries.Methods. Isometric force was measured in rat femoral arteries stimulated to contract with a solution containing 20 mM K+ and 200 nM Bay K 8644 (20 K/Bay K) or with one containing 80 mM K+(80 K).Results. Incubation of arteries with M-β-CD (5 mM, 60 min) increased force in response to 20 K/Bay K but not that induced by 80 K. Application of cholesterol saturated M-β-CD (Ch-MCD, 5 mM, 50 min) reversed the effects of M-β-CD. After mechanical removal of endothelial cells M-β-CD caused only a small enhancement of contractions to 20 K/Bay K. This result suggests M-β-CD acts via altering release of an endothelial-derived vasodilator or vasoconstrictor. When nitric oxide synthase was blocked by pre-incubation of arteries with L-NAME (250 µM) the contraction of arteries to 20 K/Bay K was enhanced, and this effect was abolished by pre-treatment with M-β-CD. This suggests M-β-CD is inhibiting endothelial NO release. Inhibition of large conductance voltage- and Ca2+-activated (BKCa) channels with 2 mM TEA+ or 100 nM Iberiotoxin (IbTX) enhanced 20 K/Bay K contractions. L-NAME attenuated the contractile effect of IbTX, as did endothelial removal.Conclusions. Our results suggest caveolar disruption results in decreased release of endothelial-derived nitric oxide in rat femoral artery, resulting in a reduced contribution of BKCa channels to the smooth muscle cell membrane potential, causing depolarisation and contraction.
creator: AY Al-Brakati
creator: T Kamishima
creator: C Dart
creator: JM Quayle
uri: https://doi.org/10.7717/peerj.966
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Al-Brakati et al.

title: Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species
link: https://peerj.com/articles/976
last-modified: 2015-05-21
description: Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host’s apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balancing selection maintaining the variation. Using Bayesian and likelihood methods positive and negative selection is evident at sites in the conserved part of the genes and, to a larger extent, in the active part which also shows episodic diversifying selection, further supporting the argument for balancing selection.
creator: Katrín Halldórsdóttir
creator: Einar Árnason
uri: https://doi.org/10.7717/peerj.976
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Halldórsdóttir and Árnason

title: Causes of mortality across different immigrant groups in Northeastern Italy
link: https://peerj.com/articles/975
last-modified: 2015-05-21
description: Background. Despite massive immigration towards Southern Europe in the last two decades, data on mortality by cause among immigrants in Italy are scarce. The aim of this study was to investigate mortality from all and from specific causes of death among immigrants residing in the Veneto Region (Northeastern Italy).Methods. Mortality records for the period 2008–2013 were extracted from the regional archive of causes of death, whereas population data were obtained from the 2011 Italian census. Immigrants were grouped by area of provenience based on the information on country of citizenship available both in mortality and census data. Standardized Mortality Ratios (SMR) with 95% Confidence Intervals (CI) were computed for the period 2008–2013 in subjects aged 20–59 years, with rates of Italian citizens as a reference.Results. Overall mortality was reduced both in male (SMR 0.86, CI [0.80–0.92]) and female immigrants (SMR 0.72, CI [0.65–0.78]), although an increased risk was observed for subjects from Sub-Saharan Africa. Significantly raised SMR for circulatory diseases were found among Sub-Saharan Africans and Southern Asians in both genders. Sub-Saharan Africans experienced a higher risk of death, especially from cerebrovascular diseases: SMR 4.78 (CI [2.67–7.89]) and SMR 6.09 (CI [1.96–14.2]) in males and females, respectively. Among Southern Asians, the increase in mortality from ischemic heart diseases reached statistical significance in males (SMR 2.53, CI [1.42–4.18]). In spite of a lower risk of death for all neoplasms combined, mortality from cancer of cervix uteri was increased among immigrants (SMR 2.61, CI [1.35–4.56]), as well as for other cancer sites in selected immigrant groups. A raised mortality was found for infectious diseases in Sub-Saharan Africans (both genders), and for transport accidents among females from Eastern Europe.Conclusion. Our study showed great variations in mortality by cause and area of provenience among immigrants resident in the Veneto Region and highlighted specific health issues that should be addressed through tailored efforts in chronic diseases prevention.
creator: Ugo Fedeli
creator: Eliana Ferroni
creator: Mara Pigato
creator: Francesco Avossa
creator: Mario Saugo
uri: https://doi.org/10.7717/peerj.975
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Fedeli et al.

title: Sex differences in human gregariousness
link: https://peerj.com/articles/974
last-modified: 2015-05-21
description: Research on human sociality rarely includes kinship, social structure, sex, and familiarity, even though these variables influence sociality in non-human primates. However, cross-cultural ethnographic and observational studies with humans indicate that, beginning after age 5 years, males and females form differing social structures with unrelated individuals in a community. Specifically, compared with females, human males exhibit greater tolerance for and form larger, interconnected groups of peers which we term “gregariousness.” To examine sex differences in gregariousness early in life when children first interact with peers without adult supervision, 3- to 6-year-old children were given the choice to enter one of three play areas: an empty one, one with an adult, or one with a familiar, same-sex peer. More males than females initially chose the play area with the same-sex peer, especially after age 5 years. Sex differences in gregariousness with same-sex peers likely constitute one facet of human sociality.
creator: Joyce F. Benenson
creator: Sandra Stella
creator: Anthony Ferranti
uri: https://doi.org/10.7717/peerj.974
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Benenson et al.

title: Identification of miR-194-5p as a potential biomarker for postmenopausal osteoporosis
link: https://peerj.com/articles/971
last-modified: 2015-05-21
description: The incidence of osteoporosis is high in postmenopausal women due to altered estrogen levels and continuous calcium loss that occurs with aging. Recent studies have shown that microRNAs (miRNAs) are involved in the development of osteoporosis. These miRNAs may be used as potential biomarkers to identify women at a high risk for developing the disease. In this study, whole blood samples were collected from 48 postmenopausal Chinese women with osteopenia or osteoporosis and pooled into six groups according to individual T-scores. A miRNA microarray analysis was performed on pooled blood samples to identify potential miRNA biomarkers for postmenopausal osteoporosis. Five miRNAs (miR-130b-3p, -151a-3p, -151b, -194-5p, and -590-5p) were identified in the microarray analysis. These dysregulated miRNAs were subjected to a pathway analysis investigating whether they were involved in regulating osteoporosis-related pathways. Among them, only miR-194-5p was enriched in multiple osteoporosis-related pathways. Enhanced miR-194-5p expression in women with osteoporosis was confirmed by quantitative reverse transcription–polymerase chain reaction analysis. For external validation, a significant correlation between the expression of miR-194-5p and T-scores was found in an independent patient collection comprised of 24 postmenopausal women with normal bone mineral density, 30 postmenopausal women with osteopenia, and 32 postmenopausal women with osteoporosis (p < 0.05). Taken together, the present findings suggest that miR-194-5p may be a viable miRNA biomarker for postmenopausal osteoporosis.
creator: Jia Meng
creator: Dapeng Zhang
creator: Nanan Pan
creator: Ning Sun
creator: Qiujun Wang
creator: Jingxue Fan
creator: Ping Zhou
creator: Wenliang Zhu
creator: Lihong Jiang
uri: https://doi.org/10.7717/peerj.971
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Meng et al.

title: Rapid cessation of acute diarrhea using a novel solution of bioactive polyphenols: a randomized trial in Nicaraguan children
link: https://peerj.com/articles/969
last-modified: 2015-05-21
description: Goal. We assessed the effectiveness of bioactive polyphenols contained in solution (LX) to restore normal bowel function in pediatric patients with acute diarrhea.Background. While providing oral rehydration solution (ORS) is standard treatment for diarrhea in developing countries, plant-derived products have been shown to positively affect intestinal function. If a supplement to ORS resolves diarrhea more rapidly than ORS alone, it is an improvement to current care.Study. In a randomized, double-blind, placebo-controlled cross-over study, 61 pediatric patients with uncontrolled diarrhea were randomized to receive either ORS + LX on day 1 and then ORS + water on day 2 (study arm) or ORS + water on day 1 and then ORS + LX on day 2 (control arm). Time to resolution and number of bowel movements were recorded.Results. On day 1, the mean time to diarrhea resolution was 3.1 h (study arm) versus 9.2 h (control arm) (p = 0.002). In the study arm, 60% of patients had normal stool at their first bowel movement after consumption of the phenolic redoxigen solution (LX). On day 2, patients in the study arm continued to have normal stool while patients in the control arm achieved normal stool within 24 h after consuming the test solution. Patients in the control arm experienced a reduction in the mean number of bowel movements from day 1 to day 2 after consuming the test solution (p = 0.0001). No adverse events were observed.Conclusions. Significant decreases in bowel movement frequency and rapid normalization of stool consistency were observed with consumption of this novel solution.
creator: Arthur Dover
creator: Neema Patel
creator: KT Park
uri: https://doi.org/10.7717/peerj.969
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Dover et al.

title: Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus
link: https://peerj.com/articles/968
last-modified: 2015-05-21
description: An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 16S rRNA sequence recovered from a lyophilised co-culture of the organism. Here, we sequenced the genome of V. chlorellavorus directly from 36 year-old lyophilised material that could not be resuscitated confirming its identity as a member of the Melainabacteria. We identified attributes in the genome that likely allow V. chlorellavorus to function as an obligate predator of the microalga Chlorella vulgaris, and predict that it is the first described predator to use an Agrobacterium tumefaciens-like conjugative type IV secretion system to invade its host. V. chlorellavorus is the first cyanobacterium recognised to have a predatory lifestyle and further supports the assertion that Melainabacteria are non-photosynthetic.
creator: Rochelle M. Soo
creator: Ben J. Woodcroft
creator: Donovan H. Parks
creator: Gene W. Tyson
creator: Philip Hugenholtz
uri: https://doi.org/10.7717/peerj.968
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Soo et al.

title: Accuracy of the interferon-gamma release assay for the diagnosis of tuberculous pleurisy: an updated meta-analysis
link: https://peerj.com/articles/951
last-modified: 2015-05-21
description: Background and Objectives. The best method for diagnosing tuberculous pleurisy (TP) remains controversial. Since a growing number of publications focus on the interferon-gamma release assay (IGRA), we meta-analyzed the available evidence on the overall diagnostic performance of IGRA applied to pleural fluid and peripheral blood.Materials and Methods. PubMed and Embase were searched for relevant English papers up to October 31, 2014. Statistical analyses were performed using Stata and Meta-DiSc. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), positive predictive value (PPV), negative predictive value (NPV) and diagnostic odds ratio (DOR) were count. Summary receiver operating characteristic curves and area under the curve (AUC) were used to summarize the overall diagnostic performance.Results. Fifteen publications met our inclusion criteria and were included in the meta analysis. The following pooled estimates for diagnostic parameters of pleural IGRA were obtained: sensitivity, 0.82 (95% CI [0.79–0.85]); specificity, 0.87 (95% CI [0.84–0.90]); PLR, 4.94 (95% CI [2.60–9.39]); NLR, 0.22 (95% CI [0.13–0.38]); PPV, 0.91 (95% CI [0.85–0.96]); NPV, 0.79 (95% CI [0.71–0.85]); DOR, 28.37 (95% CI [10.53–76.40]); and AUC, 0.91. The corresponding estimates for blood IGRA were as follows: sensitivity, 0.80 (95% CI [0.76–0.83]); specificity, 0.70 (95% CI [0.65–0.75]); PLR, 2.48 (95% CI [1.95–3.17]); NLR, 0.30 (95% CI [0.24–0.37]); PPV, 0.79 (95% CI [0.60–0.87]); NPV, 0.75 (95% CI [0.62–0.83]); DOR, 9.96 (95% CI [6.02–16.48]); and AUC, 0.89.Conclusions. This meta analysis suggested that pleural IGRA has potential for serving as a complementary method for diagnosing TP; however, its cost, high turn around time, and sub-optimal performance make it unsuitable as a stand-alone diagnostic tool. Better tests for the diagnosis of TP are required.
creator: Cai-Shuang Pang
creator: Yong-Chun Shen
creator: Pan-Wen Tian
creator: Jing Zhu
creator: Mei Feng
creator: Chun Wan
creator: Fu-Qiang Wen
uri: https://doi.org/10.7717/peerj.951
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Pang et al.

title: Can parasites halt the invader? Mermithid nematodes parasitizing the yellow-legged Asian hornet in France
link: https://peerj.com/articles/947
last-modified: 2015-05-21
description: Since its introduction in France 10 years ago, the yellow-legged Asian bee-hawking hornet Vespa velutina has rapidly spread to neighboring countries (Spain, Portugal, Belgium, Italy, and Germany), becoming a new threat to beekeeping activities. While introduced species often leave behind natural enemies from their original home, which benefits them in their new environment, they can also suffer local recruitment of natural enemies. Three mermithid parasitic subadults were obtained from V. velutina adults in 2012, from two French localities. However, these were the only parasitic nematodes reported up to now in Europe, in spite of the huge numbers of nests destroyed each year and the recent examination of 33,000 adult hornets. This suggests that the infection of V. velutina by these nematodes is exceptional. Morphological criteria assigned the specimens to the genus Pheromermis and molecular data (18S sequences) to the Mermithidae, due to the lack of Pheromermis spp. sequences in GenBank. The species is probably Pheromermis vesparum, a parasite of social wasps in Europe. This nematode is the second native enemy of Vespa velutina recorded in France, after a conopid fly whose larvae develop as internal parasitoids of adult wasps and bumblebees. In this paper, we provide arguments for the local origin of the nematode parasite and its limited impact on hornet colony survival. We also clarify why these parasites (mermithids and conopids) most likely could not hamper the hornet invasion nor be used in biological control programs against this invasive species.
creator: Claire Villemant
creator: Dario Zuccon
creator: Quentin Rome
creator: Franck Muller
creator: George O. Poinar Jr
creator: Jean-Lou Justine
uri: https://doi.org/10.7717/peerj.947
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Villemant et al.

title: Bird biodiversity assessments in temperate forest: the value of point count versus acoustic monitoring protocols
link: https://peerj.com/articles/973
last-modified: 2015-05-19
description: Effective monitoring programs for biodiversity are needed to assess trends in biodiversity and evaluate the consequences of management. This is particularly true for birds and faunas that occupy interior forest and other areas of low human population density, as these are frequently under-sampled compared to other habitats. For birds, Autonomous Recording Units (ARUs) have been proposed as a supplement or alternative to point counts made by human observers to enhance monitoring efforts. We employed two strategies (i.e., simultaneous-collection and same-season) to compare point count and ARU methods for quantifying species richness and composition of birds in temperate interior forests. The simultaneous-collection strategy compares surveys by ARUs and point counts, with methods matched in time, location, and survey duration such that the person and machine simultaneously collect data. The same-season strategy compares surveys from ARUs and point counts conducted at the same locations throughout the breeding season, but methods differ in the number, duration, and frequency of surveys. This second strategy more closely follows the ways in which monitoring programs are likely to be implemented. Site-specific estimates of richness (but not species composition) differed between methods; however, the nature of the relationship was dependent on the assessment strategy. Estimates of richness from point counts were greater than estimates from ARUs in the simultaneous-collection strategy. Woodpeckers in particular, were less frequently identified from ARUs than point counts with this strategy. Conversely, estimates of richness were lower from point counts than ARUs in the same-season strategy. Moreover, in the same-season strategy, ARUs detected the occurrence of passerines at a higher frequency than did point counts. Differences between ARU and point count methods were only detected in site-level comparisons. Importantly, both methods provide similar estimates of species richness and composition for the region. Consequently, if single visits to sites or short-term monitoring are the goal, point counts will likely perform better than ARUs, especially if species are rare or vocalize infrequently. However, if seasonal or annual monitoring of sites is the goal, ARUs offer a viable alternative to standard point-count methods, especially in the context of large-scale or long-term monitoring of temperate forest birds.
creator: Brian T. Klingbeil
creator: Michael R. Willig
uri: https://doi.org/10.7717/peerj.973
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Klingbeil and Willig

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.

title: Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest
link: https://peerj.com/articles/952
last-modified: 2015-05-14
description: Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could be used in conservation assessments and long-term monitoring at Harvard Forest and other northeastern USA forests.
creator: Ahmed A. Siddig
creator: Aaron M. Ellison
creator: Scott Jackson
uri: https://doi.org/10.7717/peerj.952
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Siddig et al.

title: Self-generated morphology in lagoon reefs
link: https://peerj.com/articles/935
last-modified: 2015-05-12
description: The three-dimensional form of a coral reef develops through interactions and feedbacks between its constituent organisms and their environment. Reef morphology therefore contains a potential wealth of ecological information, accessible if the relationships between morphology and ecology can be decoded. Traditionally, reef morphology has been attributed to external controls such as substrate topography or hydrodynamic influences. Little is known about inherent reef morphology in the absence of external control. Here we use reef growth simulations, based on observations in the cellular reefs of Western Australia’s Houtman Abrolhos Islands, to show that reef morphology is fundamentally determined by the mechanical behaviour of the reef-building organisms themselves—specifically their tendency to either remain in place or to collapse. Reef-building organisms that tend to remain in place, such as massive and encrusting corals or coralline algae, produce nodular reefs, whereas those that tend to collapse, such as branching Acropora, produce cellular reefs. The purest reef growth forms arise in sheltered lagoons dominated by a single type of reef builder, as in the branching Acropora-dominated lagoons of the Abrolhos. In these situations reef morphology can be considered a phenotype of the predominant reef building organism. The capacity to infer coral type from reef morphology can potentially be used to identify and map specific coral habitat in remotely sensed images. More generally, identifying ecological mechanisms underlying other examples of self-generated reef morphology can potentially improve our understanding of present-day reef ecology, because any ecological process capable of shaping a reef will almost invariably be an important process in real time on the living reef.
creator: David Blakeway
creator: Michael G. Hamblin
uri: https://doi.org/10.7717/peerj.935
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Blakeway and Hamblin

title: Impacts of sea level rise and climate change on coastal plant species in the central California coast
link: https://peerj.com/articles/958
last-modified: 2015-05-12
description: Local increases in sea level caused by global climate change pose a significant threat to the persistence of many coastal plant species through exacerbating inundation, flooding, and erosion. In addition to sea level rise (SLR), climate changes in the form of air temperature and precipitation regimes will also alter habitats of coastal plant species. Although numerous studies have analyzed the effect of climate change on future habitats through species distribution models (SDMs), none have incorporated the threat of exposure to SLR. We developed a model that quantified the effect of both SLR and climate change on habitat for 88 rare coastal plant species in San Luis Obispo, Santa Barbara, and Ventura Counties, California, USA (an area of 23,948 km2). Our SLR model projects that by the year 2100, 60 of the 88 species will be threatened by SLR. We found that the probability of being threatened by SLR strongly correlates with a species’ area, elevation, and distance from the coast, and that 10 species could lose their entire current habitat in the study region. We modeled the habitat suitability of these 10 species under future climate using a species distribution model (SDM). Our SDM projects that 4 of the 10 species will lose all suitable current habitats in the region as a result of climate change. While SLR accounts for up to 9.2 km2 loss in habitat, climate change accounts for habitat suitability changes ranging from a loss of 1,439 km2 for one species to a gain of 9,795 km2 for another species. For three species, SLR is projected to reduce future suitable area by as much as 28% of total area. This suggests that while SLR poses a higher risk, climate changes in precipitation and air temperature represents a lesser known but potentially larger risk and a small cumulative effect from both.
creator: Kendra L. Garner
creator: Michelle Y. Chang
creator: Matthew T. Fulda
creator: Jonathan A. Berlin
creator: Rachel E. Freed
creator: Melissa M. Soo-Hoo
creator: Dave L. Revell
creator: Makihiko Ikegami
creator: Lorraine E. Flint
creator: Alan L. Flint
creator: Bruce E. Kendall
uri: https://doi.org/10.7717/peerj.958
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Garner et al.

title: Tactile roughness perception in the presence of olfactory and trigeminal stimulants
link: https://peerj.com/articles/955
last-modified: 2015-05-12
description: Previous research has shown that odorants consistently evoke associations with textures and their tactile properties like smoothness and roughness. Also, it has been observed that olfaction can modulate tactile perception. We therefore hypothesized that tactile roughness perception may be biased towards the somatosensory connotation of an ambient odorant. We performed two experiments to test this hypothesis. In the first experiment, we investigated the influence of ambient chemosensory stimuli with different roughness connotations on tactile roughness perception. In addition to a pleasant odor with a connotation of softness (PEA), we also included a trigeminal stimulant with a rough, sharp or prickly connotation (Ethanol). We expected that—compared to a No-odorant control condition—tactile texture perception would be biased towards smoothness in the presence of PEA and towards roughness in the presence of Ethanol. However, our results show no significant interaction between chemosensory stimulation and perceived tactile surface roughness. It could be argued that ambient odors may be less effective in stimulating crossmodal associations, since they are by definition extraneous to the tactile stimuli. In an attempt to optimize the conditions for sensory integration, we therefore performed a second experiment in which the olfactory and tactile stimuli were presented in synchrony and in close spatial proximity. In addition, we included pleasant (Lemon) and unpleasant (Indole) odorants that are known to have the ability to affect tactile perception. We expected that tactile stimuli would be perceived as less rough when simultaneously presented with Lemon or PEA (both associated with softness) than when presented with Ethanol or Indole (odors that can be associated with roughness). Again, we found no significant main effect of chemosensory condition on perceived tactile roughness. We discuss the limitations of this study and we present suggestions for future research.
creator: Lara A. Koijck
creator: Alexander Toet
creator: Jan B.F. Van Erp
uri: https://doi.org/10.7717/peerj.955
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Koijck et al.

title: Comparison of methods used to estimate coral cover in the Hawaiian Islands
link: https://peerj.com/articles/954
last-modified: 2015-05-12
description: Nine coral survey methods were compared at ten sites in various reef habitats with different levels of coral cover in Kāne‘ohe Bay, O’ahu, Hawaiʻi. Mean estimated coverage at the different sites ranged from less than 10% cover to greater than 90% cover. The methods evaluated include line transects, various visual and photographic belt transects, video transects and visual estimates. At each site 25 m transect lines were laid out and secured. Observers skilled in each method measured coral cover at each site. The time required to run each transect, time required to process data and time to record the results were documented. Cost of hardware and software for each method was also tabulated. Results of this investigation indicate that all of the methods used provide a good first estimate of coral cover on a reef. However, there were differences between the methods in detecting the number of coral species. For example, the classic “quadrat” method allows close examination of small and cryptic coral species that are not detected by other methods such as the “towboard” surveys. The time, effort and cost involved with each method varied widely, and the suitability of each method for answering particular research questions in various environments was evaluated. Results of this study support the finding of three other comparison method studies conducted at various geographic locations throughout the world. Thus, coral cover measured by different methods can be legitimately combined or compared in many situations. The success of a recent modeling effort based on coral cover data consisting of observations taken in Hawai‘i using the different methods supports this conclusion.
creator: Paul L. Jokiel
creator: Kuʻulei S. Rodgers
creator: Eric K. Brown
creator: Jean C. Kenyon
creator: Greta Aeby
creator: William R. Smith
creator: Fred Farrell
uri: https://doi.org/10.7717/peerj.954
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Jokiel et al.

title: The unnatural history of Kāne‘ohe Bay: coral reef resilience in the face of centuries of anthropogenic impacts
link: https://peerj.com/articles/950
last-modified: 2015-05-12
description: Kāneʻohe Bay, which is located on the on the NE coast of Oʻahu, Hawaiʻi, represents one of the most intensively studied estuarine coral reef ecosystems in the world. Despite a long history of anthropogenic disturbance, from early settlement to post European contact, the coral reef ecosystem of Kāneʻohe Bay appears to be in better condition in comparison to other reefs around the world. The island of Moku o Loʻe (Coconut Island) in the southern region of the bay became home to the Hawaiʻi Institute of Marine Biology in 1947, where researchers have since documented the various aspects of the unique physical, chemical, and biological features of this coral reef ecosystem. The first human contact by voyaging Polynesians occurred at least 700 years ago. By A.D. 1250 Polynesians voyagers had settled inhabitable islands in the region which led to development of an intensive agricultural, fish pond and ocean resource system that supported a large human population. Anthropogenic disturbance initially involved clearing of land for agriculture, intentional or accidental introduction of alien species, modification of streams to supply water for taro culture, and construction of massive shoreline fish pond enclosures and extensive terraces in the valleys that were used for taro culture. The arrival by the first Europeans in 1778 led to further introductions of plants and animals that radically changed the landscape. Subsequent development of a plantation agricultural system led to increased human immigration, population growth and an end to traditional land and water management practices. The reefs were devastated by extensive dredge and fill operations as well as rapid growth of human population, which led to extensive urbanization of the watershed. By the 1960’s the bay was severely impacted by increased sewage discharge along with increased sedimentation due to improper grading practices and stream channelization, resulting in extensive loss of coral cover. The reefs of Kāneʻohe Bay developed under estuarine conditions and thus have been subjected to multiple natural stresses. These include storm floods, a more extreme temperature range than more oceanic reefs, high rates of sedimentation, and exposure at extreme low tides. Deposition and degradation of organic materials carried into the bay from the watershed results in low pH conditions such that according to some ocean acidification projections the rich coral reefs in the bay should not exist. Increased global temperature due to anthropogenic fossil fuel emmisions is now impacting these reefs with the first “bleaching event” in 1996 and a second more severe event in 2014. The reefs of Kāneʻohe Bay have developed and persist under rather severe natural and anthropogenic perturbations. To date, these reefs have proved to be very resilient once the stressor has been removed. A major question remains to be answered concerning the limits of Kāneʻohe Bay reef resilience in the face of global climate change.
creator: Keisha D. Bahr
creator: Paul L. Jokiel
creator: Robert J. Toonen
uri: https://doi.org/10.7717/peerj.950
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bahr et al.

title: Transgenic LRRK2R1441G rats–a model for Parkinson disease?
link: https://peerj.com/articles/945
last-modified: 2015-05-12
description: Parkinson disease (PD) is the most common movement disorder, characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra. While the cause of this disease is largely unknown, a rare autosomal dominant familial form of PD is caused by a genetic mutation in the leucine-rich repeat kinase 2 (LRRK2) gene that presumably leads to a gain-of-function of LRRK2 kinase activity. Here, we explored the potential of over expression of this human gene in a new transgenic rat model to serve as an animal model for PD. Commercially available BAC transgenic rats expressing human LRRK2 with the familial PD mutation, R1441G, and their wild-type siblings were tested for deficits in motor function, sensorimotor gating, and higher cognitive function reminiscent of PD through the ages of 3, 6, 9 and 12 months. At 12 months of age, rats were exposed to intraperitoneal injections of the environmental toxin Paraquat or saline. Our results indicate that LRRK2R1441G transgenic rats do not show signs of neurodegeneration and do not develop significant motor or cognitive deficits until the age of 16 months. In addition, LRRK2R1441G transgenic rats did not show increased vulnerability to sub-toxic doses of Paraquat. Gene expression studies indicate that despite genomic presence and initial expression of the transgene, its expression was greatly reduced in our aged rats. We conclude that the transgenic LRRK2R1441G rat is not a valid model for studying the pathology of PD and discuss this in relation to other transgenic rat models.
creator: Komal T. Shaikh
creator: Alvin Yang
creator: Ekaterina Youshin
creator: Susanne Schmid
uri: https://doi.org/10.7717/peerj.945
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Shaikh et al.

title: The diversity of membrane transporters encoded in bacterial arsenic-resistance operons
link: https://peerj.com/articles/943
last-modified: 2015-05-12
description: Transporter-facilitated arsenite extrusion is the major pathway of arsenic resistance within bacteria. So far only two types of membrane-bound transporter proteins, ArsB and ArsY (ACR3), have been well studied, although the arsenic transporters in bacteria display considerable diversity. Utilizing accumulated genome sequence data, we searched arsenic resistance (ars) operons in about 2,500 bacterial strains and located over 700 membrane-bound transporters which are encoded in these operons. Sequence analysis revealed at least five distinct transporter families, with ArsY being the most dominant, followed by ArsB, ArsP (a recently reported permease family), Major Facilitator protein Superfamily (MFS) and Major Intrinsic Protein (MIP). In addition, other types of transporters encoded in the ars operons were found, but in much lower frequencies. The diversity and evolutionary relationships of these transporters with regard to arsenic resistance will be discussed.
creator: Yiren Yang
creator: Shiyang Wu
creator: Ross McCausland Lilley
creator: Ren Zhang
uri: https://doi.org/10.7717/peerj.943
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yang et al.

title: New insights into the lifestyle of Allosaurus (Dinosauria: Theropoda) based on another specimen with multiple pathologies
link: https://peerj.com/articles/940
last-modified: 2015-05-12
description: Adult large-bodied theropods are often found with numerous pathologies. A large, almost complete, probably adult Allosaurus specimen from the Howe Stephens Quarry, Morrison Formation (Late Kimmeridgian–Early Tithonian), Wyoming, exhibits multiple pathologies. Pathologic bones include the left dentary, two cervical vertebrae, one cervical and several dorsal ribs, the left scapula, the left humerus, the right ischium, and two left pedal phalanges. These pathologies can be classified as follows: the fifth cervical vertebra, the scapula, several ribs and the ischium are probably traumatic, and a callus on the shaft of the left pedal phalanx II-2 is probably traumatic-infectious. Traumatically fractured elements exposed to frequent movement (e.g., the scapula and the ribs) show a tendency to develop pseudarthroses instead of a callus. The pathologies in the lower jaw and a reduced extensor tubercle of the left pedal phalanx II-2 are most likely traumatic or developmental in origin. The pathologies on the fourth cervical are most likely developmental in origin or idiopathic, that on the left humerus could be traumatic, developmental, infectious or idiopathic, whereas the left pedal phalanx IV-1 is classified as idiopathic. With exception of the ischium, all as traumatic/traumatic-infectious classified pathologic elements show unambiguous evidences of healing, indicating that the respective pathologies did not cause the death of this individual. Alignment of the scapula and rib pathologies from the left side suggests that all may have been caused by a single traumatic event. The ischial fracture may have been fatal. The occurrence of multiple lesions interpreted as traumatic pathologies again underlines that large-bodied theropods experienced frequent injuries during life, indicating an active predatory lifestyle, and their survival perhaps supports a gregarious behavior for Allosaurus. Alternatively, the frequent survival of traumatic events could be also related to the presence of non-endothermic metabolic rates that allow survival based on sporadic food consumption or scavenging behavior. Signs of pathologies consistent with infections are scarce and locally restricted, indicating a successful prevention of the spread of pathogens, as it is the case in extant reptiles (including birds).
creator: Christian Foth
creator: Serjoscha W. Evers
creator: Ben Pabst
creator: Octávio Mateus
creator: Alexander Flisch
creator: Mike Patthey
creator: Oliver W.M. Rauhut
uri: https://doi.org/10.7717/peerj.940
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Foth et al.

title: Thylacinus (Marsupialia: Thylacinidae) from the Mio-Pliocene boundary and the diversity of Late Neogene thylacinids in Australia
link: https://peerj.com/articles/931
last-modified: 2015-05-12
description: Thylacinus yorkellus is described as a new, moderately small-bodied species of thylacinid from the latest Miocene or, more likely, earliest Pliocene of South Australia. The new species can be diagnosed by the autapomorphic presence a strongly developed precingulid that terminates in a cuspidule on the anterobuccal face of the paraconid of the lower molars and a tiny basal anterior cuspidule on P2, P3 and the lower molars. It is found by cladistic analysis to be the sister species of the recently extinct Th. cynocephalus and distinct from the approximately coeval Th. megiriani from the Northern Territory. New dentary material is described and referred to Th. megiriani. These add character data and allow this species to be re-diagnosed based on autapomorphic character traits. Each of the three known late Miocene to early Pliocene Thylacinus species (Th. potens, Th. megiriani and Th. yorkellus) suggest that, instead of declining, there was a modest radiation of Thylacinus in the late Miocene.
creator: Adam M. Yates
uri: https://doi.org/10.7717/peerj.931
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yates

title: Male convict cichlid 11-ketotestosterone levels throughout the reproductive cycle: an exploratory profile study in laboratory and field populations
link: https://peerj.com/articles/949
last-modified: 2015-05-07
description: The convict cichlid (Amatitlania nigrofasciata) has been extensively examined in relation to many behavioral topics, such as courtship, pair-bonding, bi-parental care, and territoriality. Recently, this model species has been utilized in studies on genetics, endocrinology, and neuroanatomy, with an ultimate goal of connecting behavior with its underlying mechanisms. The goal of this study was two-fold: (1) profile the circulating levels of plasma 11KT in the male convict cichlid at multiple points during the reproductive cycle and (2) generally compare the hormonal profiles of the widely used laboratory populations and those of a free-living population in the streams of Costa Rica. The results of the field experiment showed that male convict cichlids had higher levels of circulating 11KT during courtship and lower during the parental care and non-breeding phases. The profile of the laboratory population was similar to the profile of the free-living individuals, with significantly higher levels of 11KT occurring during courtship than during parental care, though the level of 11KT during non-breeding phase was elevated in the laboratory. The high levels of 11KT during courtship and low levels of 11KT during parental care found in both the field and the laboratory is similar to what has been reported in other species of teleosts, and may suggest an important function of 11KT in the expression of courtship behavior and the subsequent onset of parental behaviors in this model species.
creator: Natalie April van Breukelen
creator: Jennifer L. Snekser
creator: Murray Itzkowitz
uri: https://doi.org/10.7717/peerj.949
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 van Breukelen et al.

title: Calcium affinity of human α-actinin 1
link: https://peerj.com/articles/944
last-modified: 2015-05-07
description: Due to alternative splicing, the human ACTN1 gene codes for three different transcripts of α-actinin; one isoform that is expressed only in the brain and two with a more general expression pattern. The sequence difference is located to the C-terminal domains and the EF-hand motifs. Therefore, any functional or structural distinction should involve this part of the protein. To investigate this further, the calcium affinities of these three isoforms of α-actinin 1 have been determined by isothermal calorimetry.
creator: Lars Backman
uri: https://doi.org/10.7717/peerj.944
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Backman

title: Patient understanding of radiation risk from medical computed tomography—A comparison of Hispanic vs. non-Hispanic emergency department populations
link: https://peerj.com/articles/937
last-modified: 2015-05-07
description: Background. Cultural differences and language barriers may adversely impact patients with respect to understanding the risks/benefits of medical testing.Objective. We hypothesized that there would be no difference in Hispanic vs. non-Hispanic patients’ knowledge of radiation risk that results from CT of the abdomen/pelvis (CTAP).Methods. We enrolled a convenience sample of adults at an inner-city emergency department (ED). Patients provided written answers to rate agreement on a 10-point scale for two correct statements comparing radiation exposure equality between: CTAP and 5 years of background radiation (question 1); CTAP and 200 chest x-rays (question 3). Patients also rated their agreement that multiple CT scans increase the lifetime cancer risk (question 2). Scores of >8 were considered good knowledge. Multivariate logistic regression analyses were performed to estimate the independent effect of the Hispanic variable.Results. 600 patients in the study group; 63% Hispanic, mean age 39.2 ± 13.9 years. Hispanics and non-Hispanics whites were similar with respect to good knowledge-level answers to question 1 (17.3 vs. 15.1%; OR = 1.2; 95% CI [0.74–2.0]), question 2 (31.2 vs. 39.3%; OR = 0.76; 95% CI [0.54–1.1]), and question 3 (15.2 vs. 16.5%; OR = 1.1; 95% CI [0.66–1.8]). Compared to patients who earned <20,000, patients with income >40,000 were more likely to answer question 2 with good knowledge (OR = 1.96; 95% CI [1.2–3.1]).Conclusion. The study group’s overall knowledge of radiation risk was poor, but we did not find significant differences between Hispanic vs. non-Hispanic patients.
creator: Afton McNierney-Moore
creator: Cynthia Smith
creator: Jose Guardiola
creator: K. Tom Xu
creator: Peter B. Richman
uri: https://doi.org/10.7717/peerj.937
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McNierney-Moore et al.

title: Analgesic effects of lappaconitine in leukemia bone pain in a mouse model
link: https://peerj.com/articles/936
last-modified: 2015-05-07
description: Bone pain is a common and severe symptom in cancer patients. The present study employed a mouse model of leukemia bone pain by injection K562 cells into tibia of mouse to evaluate the analgesic effects of lappacontine. Our results showed that the lappaconitine treatment at day 15, 17 and 19 could effectively reduce the spontaneous pain scoring values, restore reduced degree in the inclined-plate test induced by injection of K562 cells, as well as restore paw mechanical withdrawal threshold and paw withdrawal thermal latency induced by injection of K562 cells to the normal levels. Additionally, the molecular mechanisms of lappaconitine’s analgesic effects may be related to affect the expression levels of endogenous opioid system genes (POMC, PENK and MOR), as well as apoptosis-related genes (Xiap, Smac, Bim, NF-κB and p53). Our present results indicated that lappaconitine may become a new analgesic agent for leukemia bone pain management.
creator: Xiao-Cui Zhu
creator: Chen-Tao Ge
creator: Pan Wang
creator: Jia-Li Zhang
creator: Yuan-Yang Yu
creator: Cai-Yun Fu
uri: https://doi.org/10.7717/peerj.936
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhu et al.

title: Seasonal trends in the condition of nesting females of a solitary bee: wing wear, lipid content, and oocyte size
link: https://peerj.com/articles/930
last-modified: 2015-05-07
description: During the nesting season, adult females of the solitary bee Megachile rotundata (F.) face considerable physical and energy demands that could include increasing wear and tear on their bodies and decreasing lipid reserves. Consequently, their reproductive performance may be affected not only by extrinsic factors (e.g., weather and floral resource availability), but intrinsic changes in their own bodies. Because of the potential fitness effects of seasonal changes in body condition, our objectives were to determine how wing wear, lipid reserves, and oocyte sizes vary during nesting seasons, beginning when females emerge as adults. As nesting progressed, females in two populations experienced a steady increase in wing wear, which is known to reduce foraging efficiency and increase risk of mortality in other bees. Soon after emergence, females exhibited sharp declines in lipid content which remained low for the remainder of the season. Newly-emerged females ingested pollen, an activity known to be correlated with the initiation of egg maturation in this species. Additionally, the early summer drop in lipid stores was correlated with an increase in the size of the oocytes carried. However, by ∼6 weeks after emergence, oocytes began to decrease in length and volume, perhaps due to nutrient deficiencies related to loss of stored lipids. Our results suggest management of M. rotundata should include rearing bees at temperatures that maximize stored lipid reserves in adults and timing bee release so that significant pollen resources are available for both adults and offspring.
creator: Kevin M. O’Neill
creator: Casey M. Delphia
creator: Theresa L. Pitts-Singer
uri: https://doi.org/10.7717/peerj.930
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 O’Neill et al.

title: Associations between lower extremity muscle mass and metabolic parameters related to obesity in Japanese obese patients with type 2 diabetes
link: https://peerj.com/articles/942
last-modified: 2015-05-05
description: Background. Age-related loss of muscle mass (sarcopenia) increases the incidence of obesity in the elderly by reducing physical activity. This sarcopenic obesity may become self-perpetuating, increasing the risks for metabolic syndrome, disability, and mortality. We investigated the associations of two sarcopenic indices, the ratio of lower extremity muscle mass to body weight (L/W ratio) and the ratio of lower extremity muscle mass to upper extremity muscle mass (L/U ratio), with metabolic parameters related to obesity in patients with type 2 diabetes and obesity.Methods. Of 148 inpatients with type 2 diabetes treated between October 2013 and April 2014, we recruited 26 with obesity but no physical disability. Daily physical activity was measured by a triaxial accelerometer during a period of hospitalization, and which was also evaluated by our previously reported non-exercise activity thermogenesis questionnaire. We measured body composition by bioelectrical impedance and investigated the correlations of L/W and L/U ratios with body weight, body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), visceral fat area, subcutaneous fat area, serum lipid profile, and daily physical activity.Results. The L/W ratio was significantly and negatively correlated with BMI, WC, WHR, body fat mass, body fat percentage, subcutaneous fat area, and serum free fatty acid concentration, was positively correlated with daily physical activity: the locomotive non-exercise activity thermogenesis score, but was not correlated with visceral fat area. The L/U ratio was significantly and positively correlated with serum high-density lipoprotein cholesterol.Conclusions. High L/W and L/U ratios, indicative of relatively preserved lower extremity muscle mass, were predictive of improved metabolic parameters related to obesity. Preserved muscle fitness in obesity, especially of the lower extremities, may prevent sarcopenic obesity and lower associated risks for metabolic syndrome and early mortality.
creator: Hidetaka Hamasaki
creator: Yu Kawashima
creator: Hiroki Adachi
creator: Sumie Moriyama
creator: Hisayuki Katsuyama
creator: Akahito Sako
creator: Hidekatsu Yanai
uri: https://doi.org/10.7717/peerj.942
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hamasaki et al.

title: Measures of skin conductance and heart rate in alcoholic men and women during memory performance
link: https://peerj.com/articles/941
last-modified: 2015-05-05
description: We examined abnormalities in physiological responses to emotional stimuli associated with long-term chronic alcoholism. Skin conductance responses (SCR) and heart rate (HR) responses were measured in 32 abstinent alcoholic (ALC) and 30 healthy nonalcoholic (NC) men and women undergoing an emotional memory task in an MRI scanner. The task required participants to remember the identity of two emotionally-valenced faces presented at the onset of each trial during functional magnetic resonance imaging (fMRI) scanning. After viewing the faces, participants saw a distractor image (an alcoholic beverage, nonalcoholic beverage, or scrambled image) followed by a single probe face. The task was to decide whether the probe face matched one of the two encoded faces. Skin conductance measurements (before and after the encoded faces, distractor, and probe) were obtained from electrodes on the index and middle fingers on the left hand. HR measurements (beats per minute before and after the encoded faces, distractor, and probe) were obtained by a pulse oximeter placed on the little finger on the left hand. We expected that, relative to NC participants, the ALC participants would show reduced SCR and HR responses to the face stimuli, and that we would identify greater reactivity to the alcoholic beverage stimuli than to the distractor stimuli unrelated to alcohol. While the beverage type did not differentiate the groups, the ALC group did have reduced skin conductance and HR responses to elements of the task, as compared to the NC group.
creator: Kayle S. Sawyer
creator: Alan Poey
creator: Susan Mosher Ruiz
creator: Ksenija Marinkovic
creator: Marlene Oscar-Berman
uri: https://doi.org/10.7717/peerj.941
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sawyer et al.

title: Blood serum and BSA, but neither red blood cells nor hemoglobin can support vitellogenesis and egg production in the dengue vector Aedes aegypti
link: https://peerj.com/articles/938
last-modified: 2015-05-05
description: Aedes aegypti is the major vector of dengue, yellow fever and chikungunya viruses that put millions of people in endemic countries at risk. Mass rearing of this mosquito is crucial for strategies that use modified insects to reduce vector populations and transmission of pathogens, such as sterile insect technique or population replacement. A major problem for vector mosquito mass rearing is the requirement of vertebrate blood for egg production since it poses significant costs as well as potential health hazards. Also, regulations for human and animal use as blood source can pose a significant obstacle. A completely artificial diet that supports egg production in vector mosquitoes can solve this problem. In this study, we compared different blood fractions, serum and red blood cells, as dietary protein sources for mosquito egg production. We also tested artificial diets made from commercially available blood proteins (bovine serum albumin (BSA) and hemoglobin). We found that Ae. aegypti performed vitellogenesis and produced eggs when given whole bovine blood, serum, or an artificial diet containing BSA. Conversely, egg production was impaired after feeding of the red blood cell fraction or an artificial diet containing only hemoglobin. We also found that egg viability of serum-fed mosquitoes were comparable to that of whole blood and an iron supplemented BSA meal produced more viable eggs than a meal containing BSA alone. Our results indicate that serum proteins, not hemoglobin, may replace vertebrate blood in artificial diets for mass mosquito rearing.
creator: Kristina K. Gonzales
creator: Hitoshi Tsujimoto
creator: Immo A. Hansen
uri: https://doi.org/10.7717/peerj.938
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gonzales et al.

title: GFVO: the Genomic Feature and Variation Ontology
link: https://peerj.com/articles/933
last-modified: 2015-05-05
description: Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations.Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.
creator: Joachim Baran
creator: Bibi Sehnaaz Begum Durgahee
creator: Karen Eilbeck
creator: Erick Antezana
creator: Robert Hoehndorf
creator: Michel Dumontier
uri: https://doi.org/10.7717/peerj.933
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Baran et al.

title: Continued Dispensing: what medications do patients believe should be available?
link: https://peerj.com/articles/924
last-modified: 2015-05-05
description: Background. Continued Dispensing (CD) is a new medication supply method for certain medications in Australia. It aims to prevent treatment interruption as a result of patients’ inability to obtain a new valid prescription. The only currently eligible patients for this service are statin and/or oral contraceptives users who have been using these medications for 6 months or more, have not utilized the CD method during the last 12 months, and cannot obtain an immediate appointment with the prescriber in order to get a new prescription. This study aimed to investigate patients’ attitudes towards potential extension and expansion of this medication supply method.Methods. A randomly selected 301 users of these medications from all Australian States were recruited using Computer Assisted Telephone Interview (CATI).Result. The response rate was 79%. The majority of the participants (73.3%) did not agree with current restriction on CD utilization frequency. They also supported, to varying degrees, inclusion of all the proposed medications (support ranged from 44.2–78.4%). In this regard, participants who suffered from a specific disease did not differ significantly from those without the disease except in case of patients with depression (p = 0.001).Conclusions. Participants of this study strongly supported both CD extension and expansion. A future critical review of the current version of CD is highly recommended in order to enhance CD capability to achieve its goals.
creator: Salem Hasn Abukres
creator: Kreshnik Hoti
creator: Jeffery David Hughes
uri: https://doi.org/10.7717/peerj.924
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Abukres et al.

title: Synthetic neuronal datasets for benchmarking directed functional connectivity metrics
link: https://peerj.com/articles/923
last-modified: 2015-05-05
description: Background. Datasets consisting of synthetic neural data generated with quantifiable and controlled parameters are a valuable asset in the process of testing and validating directed functional connectivity metrics. Considering the recent debate in the neuroimaging community concerning the use of these metrics for fMRI data, synthetic datasets that emulate the BOLD signal dynamics have played a central role by supporting claims that argue in favor or against certain choices. Generative models often used in studies that simulate neuronal activity, with the aim of gaining insight into specific brain regions and functions, have different requirements from the generative models for benchmarking datasets. Even though the latter must be realistic, there is a tradeoff between realism and computational demand that needs to be contemplated and simulations that efficiently mimic the real behavior of single neurons or neuronal populations are preferred, instead of more cumbersome and marginally precise ones.Methods. This work explores how simple generative models are able to produce neuronal datasets, for benchmarking purposes, that reflect the simulated effective connectivity and, how these can be used to obtain synthetic recordings of EEG and fMRI BOLD signals. The generative models covered here are AR processes, neural mass models consisting of linear and nonlinear stochastic differential equations and populations with thousands of spiking units. Forward models for EEG consist in the simple three-shell head model while the fMRI BOLD signal is modeled with the Balloon-Windkessel model or by convolution with a hemodynamic response function.Results. The simulated datasets are tested for causality with the original spectral formulation for Granger causality. Modeled effective connectivity can be detected in the generated data for varying connection strengths and interaction delays.Discussion. All generative models produce synthetic neuronal data with detectable causal effects although the relation between modeled and detected causality varies and less biophysically realistic models offer more control in causal relations such as modeled strength and frequency location.
creator: João Rodrigues
creator: Alexandre Andrade
uri: https://doi.org/10.7717/peerj.923
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Rodrigues and Andrade

title: Replicability of sight word training and phonics training in poor readers: a randomised controlled trial
link: https://peerj.com/articles/922
last-modified: 2015-05-05
description: Given the importance of effective treatments for children with reading impairment, paired with growing concern about the lack of scientific replication in psychological science, the aim of this study was to replicate a quasi-randomised trial of sight word and phonics training using a randomised controlled trial (RCT) design. One group of poor readers (N = 41) did 8 weeks of phonics training (i.e., phonological decoding) and then 8 weeks of sight word training (i.e., whole-word recognition). A second group did the reverse order of training. Sight word and phonics training each had a large and significant valid treatment effect on trained irregular words and word reading fluency. In addition, combined sight word and phonics training had a moderate and significant valid treatment effect on nonword reading accuracy and fluency. These findings demonstrate the reliability of both phonics and sight word training in treating poor readers in an era where the importance of scientific reliability is under close scrutiny.
creator: G McArthur
creator: S Kohnen
creator: K Jones
creator: P Eve
creator: E Banales
creator: L Larsen
creator: A Castles
uri: https://doi.org/10.7717/peerj.922
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McArthur et al.