title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2013-08 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB link: https://peerj.com/articles/145 last-modified: 2013-08-29 description: Our previously presented method for high throughput computational screening of mutant activity (Hediger et al., 2012) is benchmarked against experimentally measured amidase activity for 22 mutants of Candida antarctica lipase B (CalB). Using an appropriate cutoff criterion for the computed barriers, the qualitative activity of 15 out of 22 mutants is correctly predicted. The method identifies four of the six most active mutants with ≥3-fold wild type activity and seven out of the eight least active mutants with ≤0.5-fold wild type activity. The method is further used to screen all sterically possible (386) double-, triple- and quadruple-mutants constructed from the most active single mutants. Based on the benchmark test at least 20 new promising mutants are identified. creator: Martin R. Hediger creator: Luca De Vico creator: Julie B. Rannes creator: Christian Jäckel creator: Werner Besenmatter creator: Allan Svendsen creator: Jan H. Jensen uri: https://doi.org/10.7717/peerj.145 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Hediger et al. title: The homeodomain factor Gbx1 is required for locomotion and cell specification in the dorsal spinal cord link: https://peerj.com/articles/142 last-modified: 2013-08-29 description: Dorsal horn neurons in the spinal cord integrate and relay sensory information to higher brain centers. These neurons are organized in specific laminae and different transcription factors are involved in their specification. The murine homeodomain Gbx1 protein is expressed in the mantle zone of the spinal cord at E12.5-13.5, correlating with the appearance of a discernable dorsal horn around E14 and eventually defining a narrow layer in the dorsal horn around perinatal stages. At postnatal stages, Gbx1 identifies a specific subpopulation of GABAergic neurons in the dorsal spinal cord. We have generated a loss of function mutation for Gbx1 and analyzed its consequences during spinal cord development. Gbx1−/− mice are viable and can reproduce as homozygous null mutants. However, the adult mutant mice display an altered gait during forward movement that specifically affects the hindlimbs. This abnormal gait was evaluated by a series of behavioral tests, indicating that locomotion is impaired, but not muscle strength or motor coordination. Molecular analysis showed that the development of the dorsal horn is not profoundly affected in Gbx1−/− mutant mice. However, analysis of terminal neuronal differentiation revealed that the proportion of GABAergic inhibitory interneurons in the superficial dorsal horn is diminished. Our study unveiled a role for Gbx1 in specifying a subset of GABAergic neurons in the dorsal horn of the spinal cord involved in the control of posterior limb movement. creator: Hamid Meziane creator: Valérie Fraulob creator: Fabrice Riet creator: Wojciech Krezel creator: Mohammed Selloum creator: Michaela Geffarth creator: Dario Acampora creator: Yann Hérault creator: Antonio Simeone creator: Michael Brand creator: Pascal Dollé creator: Muriel Rhinn uri: https://doi.org/10.7717/peerj.142 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Meziane et al. title: Determinants of phosphatidylinositol-4-phosphate 5-kinase type Iγ90 uropod location in T-lymphocytes and its role in uropod formation link: https://peerj.com/articles/131 last-modified: 2013-08-29 description: We have previously identified phosphatidylinositol-4-phosphate 5-kinase type I (PIPKI)γ90 as a T cell uropod component. However, the molecular determinants and functional consequences of its localization remain unknown. In this report, we seek to better understand the mechanisms involved in PIPKIγ90 uropod targeting and the role that PIPKIγ90 plays in T cell uropod formation. During T cell activation, PIPKIγ90 cocaps with the membrane microdomain-associated proteins flotillin-1 and -2 and accumulates in the uropod. We report that the C-terminal 26 amino acid extension of PIPKIγ90 is required for its localization to the uropod. We further use T cells from PIPKIγ90−/− mice and human T cells expressing a kinase-dead PIPKIγ90 mutant to examine the role of PIPKIγ90 in a T cell uropod formation. We find that PIPKIγ90 deficient T cells have elongated uropods on ICAM-1. Moreover, in human T cells overexpression of PIPKIγ87, a naturally occurring isoform lacking the last 26 amino acids, suppresses uropod formation and impairs capping of uropod proteins such as flotillins. Transfection of human T cells with a dominant-negative mutant of flotillin-2 in turn attenuates capping of PIPKIγ90. Our data contribute to the understanding of the molecular mechanisms that regulate T cell uropod formation. creator: Lucia Mathis creator: Sarah Wernimont creator: Sarah Affentranger creator: Anna Huttenlocher creator: Verena Niggli uri: https://doi.org/10.7717/peerj.131 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Mathis et al. title: A Markovian analysis of bacterial genome sequence constraints link: https://peerj.com/articles/127 last-modified: 2013-08-29 description: The arrangement of nucleotides within a bacterial chromosome is influenced by numerous factors. The degeneracy of the third codon within each reading frame allows some flexibility of nucleotide selection; however, the third nucleotide in the triplet of each codon is at least partly determined by the preceding two. This is most evident in organisms with a strong G + C bias, as the degenerate codon must contribute disproportionately to maintaining that bias. Therefore, a correlation exists between the first two nucleotides and the third in all open reading frames. If the arrangement of nucleotides in a bacterial chromosome is represented as a Markov process, we would expect that the correlation would be completely captured by a second-order Markov model and an increase in the order of the model (e.g., third-, fourth-…order) would not capture any additional uncertainty in the process. In this manuscript, we present the results of a comprehensive study of the Markov property that exists in the DNA sequences of 906 bacterial chromosomes. All of the 906 bacterial chromosomes studied exhibit a statistically significant Markov property that extends beyond second-order, and therefore cannot be fully explained by codon usage. An unrooted tree containing all 906 bacterial chromosomes based on their transition probability matrices of third-order shares ∼25% similarity to a tree based on sequence homologies of 16S rRNA sequences. This congruence to the 16S rRNA tree is greater than for trees based on lower-order models (e.g., second-order), and higher-order models result in diminishing improvements in congruence. A nucleotide correlation most likely exists within every bacterial chromosome that extends past three nucleotides. This correlation places significant limits on the number of nucleotide sequences that can represent probable bacterial chromosomes. Transition matrix usage is largely conserved by taxa, indicating that this property is likely inherited, however some important exceptions exist that may indicate the convergent evolution of some bacteria. creator: Aaron D. Skewes creator: Roy D. Welch uri: https://doi.org/10.7717/peerj.127 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Skewes and Welch title: Hepatic bile acids and bile acid-related gene expression in pregnant and lactating rats link: https://peerj.com/articles/143 last-modified: 2013-08-27 description: Background. Significant physiological changes occur during pregnancy and lactation. Intrahepatic cholestasis of pregnancy (ICP) is a liver disease closely related to disruption of bile acid homeostasis. The objective of this study was to examine the regulation of bile acid synthesis and transport in normal pregnant and lactating rats.Materials and Methods. Livers from timed pregnant SD rats were collected on gestational days (GD) 10, 14 and 19, and postnatal days (PND) 1, 7, 14 and 21. Total bile acids were determined by the enzymatic method, total RNA was isolated and subjected to real time RT-PCR analysis. Liver protein was extracted for western-blot analysis.Results. Under physiological conditions hepatic bile acids were not elevated during pregnancy but increased during lactation in rats. Bile acid synthesis rate-limiting enzyme Cyp7a1 was unchanged on gestational days, but increased on PND14 and 21 at mRNA and protein levels. Expression of Cyp8b1, Cyp27a1 and Cyp7b1 was also higher during lactation. The mRNA levels of small heterodimer partner (SHP) and protein levels of farnesoid X receptor (FXR) were increased during pregnancy and lactation. Bile acid transporters Ntcp, Bsep, Mrp3 and Mrp4 were lower at gestation, but increased during lactation. Hepatic Oatp transporters were decreased during pregnancy and lactation.Conclusion. Hepatic bile acid homeostasis is maintained during normal pregnancy in rats, probably through the FXR-SHP regulation. The expression of bile acid synthesis genes and liver bile acid accumulation were increased during lactation, together with increased expression of bile acid efflux transporter Bsep, Mrp3 and Mrp4. creator: Qiong N. Zhu creator: Hong M. Xie creator: Dan Zhang creator: Jie Liu creator: Yuan F. Lu uri: https://doi.org/10.7717/peerj.143 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Zhu et al. title: Quantitative ultrasound applied to metacarpal bone in infants link: https://peerj.com/articles/141 last-modified: 2013-08-27 description: Aim. To provide bone status assessment in infancy using quantitative ultrasound (QUS) applied to second metacarpus.Methods. 103 healthy term infants and 3 patients with rickets, aged ≤ 12 months, underwent metacarpal QUS evaluation using QUS DBM Sonic Aurora IGEA (MO, Italy), which measures speed of sound (mcSOS) and bone transmission time (mcBTT).Results. In the total sample, median (interquartile range) of mcSOS was 1640.00 (26.0) m/s and mcBTT 0.82 (0.21) µs. Moreover, reference values for age were obtained based on estimation of the lower and upper percentiles. We observed a statistical significant difference between groups of age for mcSOS (p = 0.016). In a multiple linear regression model, we found a relation between age at enrolment and mcSOS (β = −0.608; p = 0.000) and mcBTT (β = −0.819; p = 0.001). A positive correlation between mcSOS and mcBTT has been observed (r = 0.631; p = 0.000). All the patients with rickets showed values of mcSOS and mcBTT lower than the 10th percentile.Conclusion. Our findings show that this new simple technique appears to be a promising tool for monitoring bone mineral status in pediatric clinical practice and in early life. Furthermore, it could be considered a useful method to investigate and to monitor the role of different factors on programming of bone health and it should be tested as a new method for monitoring subjects with rickets during therapy. creator: Francesco Savino creator: Serena Viola creator: Stefania Benetti creator: Simone Ceratto creator: Valentina Tarasco creator: Maria Maddalena Lupica creator: Luca Cordero di Montezemolo uri: https://doi.org/10.7717/peerj.141 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Savino et al. title: Poeciliid male mate preference is influenced by female size but not by fecundity link: https://peerj.com/articles/140 last-modified: 2013-08-27 description: While female mate preference is very well studied, male preference has only recently begun to receive significant attention. Its existence is found in numerous taxa, but empirical research has mostly been limited to a descriptive level and does not fully address the factors influencing its evolution. We attempted to address this issue using preference functions by comparing the strength of male preference for females of different sizes in nine populations of four poeciliid species. Due to environmental constraints (water toxicity and surface versus cave habitat), females from these populations vary in the degree to which their size is correlated to their fecundity. Hence, they vary in how their size signals their quality as mates. Since female size is strongly correlated with fecundity in this subfamily, males were sequentially presented with conspecific females of three different size categories and the strength of their preference for each was measured. Males preferred larger females in all populations, as predicted. However, the degree to which males preferred each size category, as measured by association time, was not correlated with its fecundity. In addition, cave males discriminated against smaller females more than surface males. Assuming that male preference is correlated with female fitness, these results suggest that factors other than fecundity have a strong influence on female fitness in these species. creator: Luis R. Arriaga creator: Ingo Schlupp uri: https://doi.org/10.7717/peerj.140 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Arriaga and Schlupp title: Vertical heterogeneity in predation pressure in a temperate forest canopy link: https://peerj.com/articles/138 last-modified: 2013-08-22 description: The forest canopy offers a vertical gradient across which variation in predation pressure implies variation in refuge quality for arthropods. Direct and indirect experimental approaches were combined to assess whether canopy strata differ in ability to offer refuge to various arthropod groups. Vertical heterogeneity in impact of avian predators was quantified using exclosure cages in the understory, lower, mid, and upper canopy of a north-temperate deciduous forest near Montreal, Quebec. Bait trials were completed in the same strata to investigate the effects of invertebrate predators. Exclusion of birds yielded higher arthropod densities across all strata, although treatment effects were small for some taxa. Observed gradients in predation pressure were similar for both birds and invertebrate predators; the highest predation pressure was observed in the understory and decreased with height. Our findings support a view of the forest canopy that is heterogeneous with respect to arthropod refuge from natural enemies. creator: Kathleen R. Aikens creator: Laura L. Timms creator: Christopher M. Buddle uri: https://doi.org/10.7717/peerj.138 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Aikens et al. title: Resource competition and coexistence in heterogeneous metacommunities: many-species coexistence is unlikely to be facilitated by spatial variation in resources link: https://peerj.com/articles/136 last-modified: 2013-08-22 description: There is little debate about the potential of environmental heterogeneity to facilitate species diversity. However, attempts to show the relationship between spatial heterogeneity and diversity empirically have given mixed results. One reason for this may be the failure to consider how species respond to the factor in the environment that varies. Most models of the heterogeneity-diversity relationship assume heterogeneity in non-resource environmental factors. These models show the potential for spatial heterogeneity to promote many-species coexistence via mainly the spatial storage effect. Here, I present a model of species competition under spatial heterogeneity and resource factors. This model allows for the stable coexistence of only two species. Partitioning the model to quantify the contributions of variation-dependent coexistence mechanisms shows contributions from only one mechanism, growth-density covariance. More notably, it shows the lack of potential for any contribution from the spatial storage effect, the only mechanism that can facilitate stable many-species coexistence. This happens because the spatial storage effect measures the contribution of different species to specializing on different parts of the gradient of the heterogeneous factor. Under simple models of resource competition, in which all species grow best at high resource levels, such specialization is impossible. This analysis suggests that, in the absence of additional mechanisms, spatial heterogeneity in a single resource is unlikely to facilitate many-species coexistence and, more generally, that when evaluating the relationship between heterogeneity and diversity, a distinction should be made between resource and non-resource factors. creator: Donald R. Schoolmaster uri: https://doi.org/10.7717/peerj.136 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Schoolmaster Jr title: Characterization of resting state activity in MCI individuals link: https://peerj.com/articles/135 last-modified: 2013-08-20 description: Objectives. Aging is the major risk factor for Alzheimer Disease (AD) and Mild Cognitive Impairment (MCI). The aim of this study was to identify novel modifications of brain functional connectivity in MCI patients. MCI individuals were compared to healthy elderly subjects.Methods. We enrolled 37 subjects (age range 60–80 y.o.). Of these, 13 subjects were affected by MCI and 24 were age-matched healthy elderly control (HC). Subjects were evaluated with Mini Mental State Examination (MMSE), Frontal Assessment Battery (FAB), and prose memory (Babcock story) tests. In addition, with functional Magnetic Resonance Imaging (fMRI), we investigated resting state network (RSN) activities. Resting state (Rs) fMRI data were analyzed by means of Independent Component Analysis (ICA). Subjects were followed-up with neuropsychological evaluations for three years.Results. Rs-fMRI of MCI subjects showed increased intrinsic connectivity in the Default Mode Network (DMN) and in the Somatomotor Network (SMN). Analysis of the DMN showed statistically significant increased activation in the posterior cingulate cortex (PCC) and left inferior parietal lobule (lIPL). During the three years follow-up, 4 MCI subjects converted to AD. The subset of MCI AD-converted patients showed increased connectivity in the right Inferior Parietal Lobule (rIPL). As for SMN activity, MCI and MCI-AD converted groups showed increased level of connectivity in correspondence of the right Supramarginal Gyrus (rSG).Conclusions. Our findings indicate alterations of DMN and SMN activity in MCI subjects, thereby providing potential imaging-based markers that can be helpful for the early diagnosis and monitoring of these patients. creator: Roberto Esposito creator: Alessandra Mosca creator: Valentina Pieramico creator: Filippo Cieri creator: Nicoletta Cera creator: Stefano L. Sensi uri: https://doi.org/10.7717/peerj.135 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Esposito et al. title: The emerin-binding transcription factor Lmo7 is regulated by association with p130Cas at focal adhesions link: https://peerj.com/articles/134 last-modified: 2013-08-20 description: Loss of function mutations in the nuclear inner membrane protein, emerin, cause X-linked Emery-Dreifuss muscular dystrophy (X-EDMD). X-EDMD is characterized by contractures of major tendons, skeletal muscle weakening and wasting, and cardiac conduction system defects. The transcription factor Lmo7 regulates muscle- and heart-relevant genes and is inhibited by binding to emerin, suggesting Lmo7 misregulation contributes to EDMD disease. Lmo7 associates with cell adhesions and shuttles between the plasma membrane and nucleus, but the regulation and biological consequences of this dual localization were unknown. We report endogenous Lmo7 also associates with focal adhesions in cells, and both co-localizes and co-immunoprecipitates with p130Cas, a key signaling component of focal adhesions. Lmo7 nuclear localization and transcriptional activity increased significantly in p130Cas-null MEFs, suggesting Lmo7 is negatively regulated by p130Cas-dependent association with focal adhesions. These results support EDMD models in which Lmo7 is a downstream mediator of integrin-dependent signaling that allows tendon cells and muscles to adapt to and withstand mechanical stress. creator: Michele A. Wozniak creator: Brendon M. Baker creator: Christopher S. Chen creator: Katherine L. Wilson uri: https://doi.org/10.7717/peerj.134 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Wozniak et al. title: The direct response of the gonads to cues of stress in a temperate songbird species is season-dependent link: https://peerj.com/articles/139 last-modified: 2013-08-15 description: The gonadotropin releasing hormone (GnRH) system in the hypothalamus is often considered the final point in integration of environmental cues as they pertain to the reproductive axis. However, cues such as stress and food availability are detectable in the plasma (as glucocorticoid and metabolic fuel fluctuations). Vertebrate gonads express glucocorticoid receptor, therefore we hypothesized that the gonads can detect and respond directly to cues of stress. We provide evidence here that, in addition to regulation by the brain, the gonads of European starlings (Sturnus vulgaris) respond directly to fluctuations in corticosterone and metabolic fuels by modulating sex steroid secretion. Using a 4-h gonad culture, we show that physiologically-relevant concentrations of corticosterone and metabolic stress (via use of the glucose utilization inhibitor 2-deoxy-D-glucose and the fatty acid oxidation inhibitor ethyl 2-mercaptoacetate (2DG/MA)) can directly decrease testosterone and estradiol secretion from luteinizing hormone and follicle-stimulating hormone (LH/FSH)-stimulated testes and ovaries. This effect is regulated seasonally. Prior to the breeding season, testes and ovaries respond to corticosterone and 2DG/MA by significantly decreasing gonadal steroid release. Within the breeding season, the testes do not respond to these cues of stress, while the ovaries respond only to corticosterone. This seasonal difference in response may be due in part to the influence of these cues of stress on gonadal neuropeptide expression: corticosterone upregulates GnIH expression in the testes while metabolic stress upregulates GnIH in the ovaries. Thus the gonads can directly respond to fluctuations in corticosterone and metabolic fuels during a time of critical importance to the onset of breeding. creator: Nicolette L. McGuire creator: Annie Koh creator: George E. Bentley uri: https://doi.org/10.7717/peerj.139 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 McGuire et al. title: Augmenting transcriptome assembly by combining de novo and genome-guided tools link: https://peerj.com/articles/133 last-modified: 2013-08-15 description: Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available de novo and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of the performance of various assemblers. Additionally, we present an approach to combinatorially augment transciptome assembly by using both de novo and genome-guided tools. In our study, we obtained the best recovery and most full-length transcripts with Trinity and TopHat1-Cufflinks, respectively. The sensitivity of the assembly and isoform recovery was superior, without compromising much on the specificity, when transcripts from Trinity were augmented with those from TopHat1-Cufflinks. creator: Prachi Jain creator: Neeraja M. Krishnan creator: Binay Panda uri: https://doi.org/10.7717/peerj.133 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Jain et al. title: Polyphyly and hidden species among Hawaiʻi’s dominant mesophotic coral genera, Leptoseris and Pavona (Scleractinia: Agariciidae) link: https://peerj.com/articles/132 last-modified: 2013-08-13 description: Widespread polyphyly in stony corals (order Scleractinia) has prompted efforts to revise their systematics through approaches that integrate molecular and micromorphological evidence. To date, these approaches have not been comprehensively applied to the dominant genera in mesophotic coral ecosystems (MCEs) because several species in these genera occur primarily at depths that are poorly explored and from which sample collections are limited. This study is the first integrated morphological and molecular systematic analysis of the genera Leptoseris and Pavona to examine material both from shallow-water reefs (<30 m) and from mid- to lower-MCEs (>60 m). Skeletal and tissue samples were collected throughout the Hawaiian Archipelago between 2–127 m. A novel mitochondrial marker (cox1-1-rRNA intron) was sequenced for 70 colonies, and the micromorphologies of 94 skeletons, plus selected type material, were analyzed. The cox1-1-rRNA intron resolved 8 clades, yet Leptoseris and Pavona were polyphyletic. Skeletal micromorphology, especially costal ornamentation, showed strong correspondence and discrete differences between mitochondrial groups. One putative new Leptoseris species was identified and the global depth range of the genus Pavona was extended to 89 m, suggesting that the diversity of mesophotic scleractinians has been underestimated. Examination of species’ depth distributions revealed a pattern of depth zonation: Species common in shallow-water were absent or rare >40 m, whereas others occurred only >60 m. These patterns emphasize the importance of integrated systematic analyses and more comprehensive sampling by depth in assessing the connectivity and diversity of MCEs. creator: Daniel G. Luck creator: Zac H. Forsman creator: Robert J. Toonen creator: Sarah J. Leicht creator: Samuel E. Kahng uri: https://doi.org/10.7717/peerj.132 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Luck et al. title: DNA barcoding unveils skate (Chondrichthyes: Rajidae) species diversity in ‘ray’ products sold across Ireland and the UK link: https://peerj.com/articles/129 last-modified: 2013-08-13 description: Skates are widely consumed across the globe, but many large species are subject to considerable concern regarding their conservation and management. Within Europe such issues have recently driven policy changes so that, for the first time, reports of skate landings now have to be made under species-specific names. Total allowable catches have also been established for many groups, which have been set to zero for a number of the most vulnerable species (e.g., Dipturus batis, Raja undulata and Rostoraja alba). Whilst accurate species identification has become an important issue for landings, the sale of skates is still usually made under a blanket term of “skate” or “ray”. The matter of identifying species of skate is further complicated by their morphologically conservative nature and the fact that they are commercially valued for their wings. Thus, before sale their bodies are usually discarded (i.e., “winged”) and often skinned, making morphological identification impossible. For the first time, DNA barcoding (of the mitochondrial COI gene) was applied to samples of skate wings from retail outlets across the British Isles, providing insight into which species are sold for consumption. A total of 98 wing samples were analysed, revealing that six species were sold; blonde ray (Raja brachyura), spotted ray (Raja montagui), thornback ray (Raja clavata), cuckoo ray (Leucoraja naevus) small-eyed ray (Raja microocellata) and shagreen ray (Leucoraja fullonica). Statistical testing demonstrated that there were significant differences in the species sold in the distinct retail groups which suggests complex drivers behind the patterns of sale in skates. The results also indicate that endangered species are not commonly being passed on to consumers. In addition, the practice of selling skate wings under ambiguous labels is highlighted as it makes it extremely difficult for consumers to exercise a right to avoid species of conservation concern. Interestingly, a single retailer chain labelled their wings as originating from three smaller-growing species (generally to be considered of lower conservation concern); of the six samples analysed from this company a third were mislabelled and originated from the thornback ray (a larger species that is currently undergoing population declines). creator: Andrew Mark Griffiths creator: Dana D. Miller creator: Aaron Egan creator: Jennifer Fox creator: Adam Greenfield creator: Stefano Mariani uri: https://doi.org/10.7717/peerj.129 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Griffiths et al. title: The effect of a conflict of interest disclosure form using closed questions on the number of positive conflicts of interest declared – a controlled study link: https://peerj.com/articles/128 last-modified: 2013-08-13 description: Objective. While declarations of conflicts of interest (COI) have become an integral part of medical articles, COIs are often not declared completely and accurately. One of several possible reasons for deficient COI declarations is the lack of standardized and comprehensive COI forms. In 2010, the International Committee of Medical Journal Editors (ICMJE) introduced a COI form using clear definitions and closed questions. Deutsches Ärzteblatt (DA), the journal of the German Medical Association, adapted this form and implemented it in early 2011. However, it is unclear whether changing COI forms leads to more positive COI statements.Material and Methods. In a controlled pre-post design, positive COI statements were analyzed at three German medical journals: one had changed its COI form (DA), two had not: Deutsche Medizinische Wochenschrift (DMW) and Nervenarzt (Ner), both of whom used open questions in their forms. At the levels of both authors and articles, respectively, the proportion of positive COI declarations in orignal and review articles was recorded for volumes 2010 (before implementation of the new COI form at DA) and 2012 (after). The change in positive COI disclosures at the journals was compared. Chi-square tests were used to compare the figures by journal in 2010 versus 2012 and among DA, DMW, and Ner.Results and Discussion. While positive COI statements more than doubled at DA, there was no meaningful change in either of the control journals: In 2010, 19.1% [95% CI: 15.4–23.2] of all DA-authors submitted positive COI declarations, relative to 39.6% [35.0–44.5] in 2012, a factor of 2.1. At the level of articles, positive COI statements increased from 32.3% [23.7–42.0] to 70.1% [60.5–78.6] (factor 2.2). At DMW, positive declarations rose by a factor of 1.3 to 12.1% [9.7–14.8] in 2012 at author level and by a factor of 1.3 to 19.4 [14.2–25.7] for articles. At Ner, figures fell: to 19.9% for authors [16.9–23.4] and 30.7% for articles [24.0–38.1] (both by a factor of 0.8). P-values for the comparison of positive COI statements between 2010 and 2012 were low at DA (p for both author and article level comparisons <0.00001) and considerably higher at DMW and Ner (all >0.05). Although this is not a randomized controlled study, the findings support the hypothesis that the steep increase in positive COI statements at DA from 2010 to 2012 is the result of its new COI form: Relative to two journals that had not modified their COI forms the effect size of the change was considerably higher at DA. Also, in contrast to DMW and Ner, p-values indicate that chance is unlikely to have played a major role in the change of positive COI statements at DA.Conclusions. COI forms employing closed questions based on clear definitions of conflicts of interests, such as those recommended by ICMJE and now used by Deutsches Ärzteblatt, seem to be superior to less structured forms. These results require confirmation with other COI forms and at other journals. creator: Christopher Baethge uri: https://doi.org/10.7717/peerj.128 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Baethge title: Physical fighting among Egyptian adolescents: social and demographic correlates among a nationally representative sample link: https://peerj.com/articles/125 last-modified: 2013-08-13 description: Introduction. Adolescent interpersonal violence is a global public health problem, yet gaps remain in the epidemiologic literature on adolescent violence in low- and middle-income countries (LMIC). Prevalence rates and risk and protective factors reported in high-income countries may be different from those reported in LMICs. Culturally-relevant epidemiologic data is important in efforts aimed at addressing adolescent interpersonal violence in these countries.Methods. A cross-sectional study of Egyptian adolescent involvement in violent behavior was conducted. Data collected from a 2006 school-based survey initiative were used; participants were adolescents aged 11–17 (N = 5, 249). Some participants were excluded from the dataset due to incomplete data (N = 111) resulting in a final sample of 5,138. Bivariate and logistic regression analyses were run to determine demographic and social variables associated with participation in physical fighting.Results. Thirty-one percent of adolescents reported being involved in a physical fight. Previously reported risk factors for violent behavior among adolescents such as depressive symptoms (OR = 1.29; CI = 1.11–1.50) and bullying victimization (OR = 2.44; CI = 2.12–2.83) were positively associated with violent behavior in the present study, while the more novel factor of sedentary behavior was also observed as having a positive association with violent behavior (OR = 1.43; CI = 1.21–1.69). Known protective factors such as helpful peers (OR = 0.75; CI = 0.62–0.90) and understanding parents (OR = 0.67; CI = 0.56–0.81) were found to have negative associations with violent behavior in the present study, in addition to the counterintuitive protective effect of having fewer friends (OR = 0.75; CI = 0.60–0.92).Conclusions. Prevalence rates of adolescent interpersonal violence in Egypt are similar to rates in other LMICs. The high reported rates of depressive symptomatology and bully victimization along with their positive association with physical fighting suggest that interventions aimed at treating and preventing these problems may help mitigate the likelihood of adolescents engaging in violent behavior; involvement in appropriate physical activity in a safe environment may be beneficial as well. More research is needed to understand the observed protective factor of having fewer friends. creator: Karen L. Celedonia creator: Michael L. Wilson creator: Hanan A. El Gammal creator: Abeer M. Hagras uri: https://doi.org/10.7717/peerj.125 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Celedonia et al. title: How age influences phonotaxis in virgin female Jamaican field crickets (Gryllus assimilis) link: https://peerj.com/articles/130 last-modified: 2013-08-08 description: Female mating preference can be a dominant force shaping the evolution of sexual signals. However, females rarely have consistent mating preferences throughout their lives. Preference flexibility results from complex interactions of predation risk, social and sexual experience, and age. Because residual reproductive value should theoretically decline with age, older females should not be as choosy as younger females. We explored how age influences phonotaxis towards a standard mate attraction signal using a spherical treadmill (trackball) and a no-choice experimental protocol. Female Jamaican field crickets, Gryllus assimilis, were highly variable in their phonotaxis; age explained up to 64% of this variation. Females 10 days post imaginal eclosion and older oriented toward the mate attraction signal, with 10- and 13-day females exhibiting the greatest movement in the direction of the signal. Our study suggests 10- and 13-day old females would be most responsive when quantifying the preference landscape for G. assimilis sexual signals. creator: Karen Pacheco creator: Jeff W. Dawson creator: Michael Jutting creator: Susan M. Bertram uri: https://doi.org/10.7717/peerj.130 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Pacheco et al. title: Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree link: https://peerj.com/articles/126 last-modified: 2013-08-08 description: Human protein kinases play fundamental roles mediating the majority of signal transduction pathways in eukaryotic cells as well as a multitude of other processes involved in metabolism, cell-cycle regulation, cellular shape, motility, differentiation and apoptosis. The human protein kinome contains 518 members. Most studies that focus on the human kinome require, at some point, the visualization of large amounts of data. The visualization of such data within the framework of a phylogenetic tree may help identify key relationships between different protein kinases in view of their evolutionary distance and the information used to annotate the kinome tree. For example, studies that focus on the promiscuity of kinase inhibitors can benefit from the annotations to depict binding affinities across kinase groups. Images involving the mapping of information into the kinome tree are common. However, producing such figures manually can be a long arduous process prone to errors. To circumvent this issue, we have developed a web-based tool called Kinome Render (KR) that produces customized annotations on the human kinome tree. KR allows the creation and automatic overlay of customizable text or shape-based annotations of different sizes and colors on the human kinome tree. The web interface can be accessed at: http://bcb.med.usherbrooke.ca/kinomerender. A stand-alone version is also available and can be run locally. creator: Matthieu Chartier creator: Thierry Chénard creator: Jonathan Barker creator: Rafael Najmanovich uri: https://doi.org/10.7717/peerj.126 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Chartier et al. title: Bile acids induce apoptosis selectively in androgen-dependent and -independent prostate cancer cells link: https://peerj.com/articles/122 last-modified: 2013-08-08 description: Prostate cancer is a prevalent age-related disease in North America, accounting for about 15% of all diagnosed cancers. We have previously identified lithocholic acid (LCA) as a potential chemotherapeutic compound that selectively kills neuroblastoma cells while sparing normal human neurons. Now, we report that LCA inhibits the proliferation of androgen-dependent (AD) LNCaP prostate cancer cells and that LCA is the most potent bile acid with respect to inducing apoptosis in LNCaP as well as androgen-independent (AI) PC-3 cells, without killing RWPE-1 immortalized normal prostate epithelial cells. In LNCaP and PC-3 cells, LCA triggered the extrinsic pathway of apoptosis and cell death induced by LCA was partially dependent on the activation of caspase-8 and -3. Moreover, LCA increased cleavage of Bid and Bax, down-regulation of Bcl-2, permeabilization of the mitochondrial outer membrane and activation of caspase-9. The cytotoxic actions of LCA occurred despite the inability of this bile acid to enter the prostate cancer cells with about 98% of the nominal test concentrations present in the extracellular culture medium. With our findings, we provide evidence to support a mechanism of action underlying the broad anticancer activity of LCA in various human tissues. creator: Alexander A. Goldberg creator: Vladimir I. Titorenko creator: Adam Beach creator: J. Thomas Sanderson uri: https://doi.org/10.7717/peerj.122 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Goldberg et al. title: The variability of inner ear orientation in saurischian dinosaurs: testing the use of semicircular canals as a reference system for comparative anatomy link: https://peerj.com/articles/124 last-modified: 2013-08-06 description: The vestibular system of the inner ear houses three semicircular canals—oriented on three nearly-orthogonal planes—that respond to angular acceleration stimuli. In recent years, the orientation of the lateral semicircular canal (LSC) has been regularly used to determine skull orientations for comparative purposes in studies of non-avian dinosaurs. Such orientations have been inferred based on fixing the LSC to a common set of coordinates (parallel to the Earth’s horizon), given that the orientation to gravity of this sensory system is assumed constant among taxa. Under this assumption, the LSC is used as a baseline (a reference system) both to estimate how the animals held their heads and to describe craniofacial variation among dinosaurs. However, the available data in living birds (extant saurischian dinosaurs) suggests that the orientation of the LSC in non-avian saurischian dinosaurs could have been very variable and taxon-specific. If such were the case, using the LSC as a comparative reference system would cause inappropriate visual perceptions of craniofacial organization, leading to significant descriptive inconsistencies among taxa. Here, we used Procrustes methods (Geometric Morphometrics), a suite of analytical tools that compares morphology on the basis of shared landmark homology, to show that the variability of LSC relative to skull landmarks is large (ca. 50°) and likely unpredictable, thus making it an inconsistent reference system for comparing and describing the skulls of saurischian (sauropodomorph and theropod) dinosaurs. In light of our results, the lateral semicircular canal is an inconsistent baseline for comparative studies of craniofacial morphology in dinosaurs. creator: Jesús Marugán-Lobón creator: Luis M. Chiappe creator: Andrew A. Farke uri: https://doi.org/10.7717/peerj.124 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Marugan-Lobon et al. title: Lacosamide adjunctive therapy for partial-onset seizures: a meta-analysis link: https://peerj.com/articles/114 last-modified: 2013-08-06 description: Background. The relative efficacy and safety of lacosamide as adjunctive therapy compared to other antiepileptic drugs has not been well established.Objective. To determine if lacosamide provides improved efficacy and safety, reduced length of hospital stay and improved quality of life compared with other anti-epileptic therapies for adults with partial-onset seizures.Data Sources. A systematic review of the medical literature using Medline (1946–Week 4, 2012), EMBASE (1980–Week 3, 2012), Cochrane Central Register of Controlled Trials (Issue 1 of 12, January 2012). Additional studies were identified (through to February 7, 2012) by searching bibliographies, the FDA drug approval files, clinical trial registries and major national and international neurology meeting abstracts. No restrictions on publication status or language were applied.Study Selection. Randomized controlled trials of lacosamide in adults with partial-onset seizures were included.Data Extraction. Study selection, extraction and risk of bias assessment were performed independently by two authors. Authors of studies were contacted for missing data.Data Synthesis. All pooled analyses used the random effects model.Results. Three trials (1311 patients) met inclusion criteria. Lacosamide increased the 50% responder rate compared to placebo (RR 1.68 [95% CI 1.36 to 2.08]; I2 = 0%). Discontinuation due to adverse events was statistically significantly higher in the lacosamide arm (RR3.13 [95% CI 1.94 to 5.06]; I2 = 0%). Individual adverse events (ataxia, dizziness, fatigue, and nausea) were also significantly higher in the lacosamide group.Limitations. All dosage arms from the included studies were pooled to make a single pair-wise comparison to placebo. Selective reporting of outcomes was found in all of the included RCTs.Conclusions. Lacosamide as adjunctive therapy in patients with partial-onset seizures increases the 50% responder rate but with significantly more adverse events compared to the placebo. creator: Sonja C. Sawh creator: Jennifer J. Newman creator: Santosh Deshpande creator: Philip M. Jones uri: https://doi.org/10.7717/peerj.114 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Sawh et al. title: Adding propensity scores to pure prediction models fails to improve predictive performance link: https://peerj.com/articles/123 last-modified: 2013-08-01 description: Background. Propensity score usage seems to be growing in popularity leading researchers to question the possible role of propensity scores in prediction modeling, despite the lack of a theoretical rationale. It is suspected that such requests are due to the lack of differentiation regarding the goals of predictive modeling versus causal inference modeling. Therefore, the purpose of this study is to formally examine the effect of propensity scores on predictive performance. Our hypothesis is that a multivariable regression model that adjusts for all covariates will perform as well as or better than those models utilizing propensity scores with respect to model discrimination and calibration.Methods. The most commonly encountered statistical scenarios for medical prediction (logistic and proportional hazards regression) were used to investigate this research question. Random cross-validation was performed 500 times to correct for optimism. The multivariable regression models adjusting for all covariates were compared with models that included adjustment for or weighting with the propensity scores. The methods were compared based on three predictive performance measures: (1) concordance indices; (2) Brier scores; and (3) calibration curves.Results. Multivariable models adjusting for all covariates had the highest average concordance index, the lowest average Brier score, and the best calibration. Propensity score adjustment and inverse probability weighting models without adjustment for all covariates performed worse than full models and failed to improve predictive performance with full covariate adjustment.Conclusion. Propensity score techniques did not improve prediction performance measures beyond multivariable adjustment. Propensity scores are not recommended if the analytical goal is pure prediction modeling. creator: Amy S. Nowacki creator: Brian J. Wells creator: Changhong Yu creator: Michael W. Kattan uri: https://doi.org/10.7717/peerj.123 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Nowacki et al. title: Towards objectively quantifying sensory hypersensitivity: a pilot study of the “Ariana effect” link: https://peerj.com/articles/121 last-modified: 2013-08-01 description: Background. Normally one habituates rapidly to steady, faint sensations. People with sensory hypersensitivity (SH), by contrast, continue to attend to such stimuli and find them noxious. SH is common in Tourette syndrome (TS) and autism, and methods to quantify SH may lead to better understanding of these disorders. In an attempt to objectively quantify SH severity, the authors tested whether a choice reaction time (CRT) task was a sensitive enough measure to detect significant distraction from a steady tactile stimulus, and to detect significantly greater distraction in subjects with more severe SH.Methods. Nineteen ambulatory adult volunteers with varying scores on the Adult Sensory Questionnaire (ASQ), a clinical measure of SH, completed a CRT task in the alternating presence and absence of tactile stimulation.Results. Tactile stimulation interfered with attention (i.e., produced longer reaction times), and this effect was significantly greater in participants with more SH (higher ASQ scores). Accuracy on the CRT was high in blocks with and without stimulation. Habituation within stimulation blocks was not detected.Conclusion. This approach can detect distraction from a cognitive task by a steady, faint tactile stimulus that does not degrade response accuracy. The method was also sensitive to the hypothesized enhancement of this effect by SH. These results support the potential utility of this approach to quantifying SH, and suggest possible refinements for future studies. creator: Vassilis N. Panagopoulos creator: Deanna J. Greene creator: Meghan C. Campbell creator: Kevin J. Black uri: https://doi.org/10.7717/peerj.121 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Black et al. title: Playing with heart and soul…and genomes: sports implications and applications of personal genomics link: https://peerj.com/articles/120 last-modified: 2013-08-01 description: Whether the integration of genetic/omic technologies in sports contexts will facilitate player success, promote player safety, or spur genetic discrimination depends largely upon the game rules established by those currently designing genomic sports medicine programs. The integration has already begun, but there is not yet a playbook for best practices. Thus far discussions have focused largely on whether the integration would occur and how to prevent the integration from occurring, rather than how it could occur in such a way that maximizes benefits, minimizes risks, and avoids the exacerbation of racial disparities. Previous empirical research has identified members of the personal genomics industry offering sports-related DNA tests, and previous legal research has explored the impact of collective bargaining in professional sports as it relates to the employment protections of the Genetic Information Nondiscrimination Act (GINA). Building upon that research and upon participant observations with specific sports-related DNA tests purchased from four direct-to-consumer companies in 2011 and broader personal genomics (PGx) services, this anthropological, legal, and ethical (ALE) discussion highlights fundamental issues that must be addressed by those developing personal genomic sports medicine programs, either independently or through collaborations with commercial providers. For example, the vulnerability of student-athletes creates a number of issues that require careful, deliberate consideration. More broadly, however, this ALE discussion highlights potential sports-related implications (that ultimately might mitigate or, conversely, exacerbate racial disparities among athletes) of whole exome/genome sequencing conducted by biomedical researchers and clinicians for non-sports purposes. For example, the possibility that exome/genome sequencing of individuals who are considered to be non-patients, asymptomatic, normal, etc. will reveal the presence of variants of unknown significance in any one of the genes associated with hypertrophic cardiomyopathy (HCM), long QT syndrome (LQTS), Marfan’s syndrome, and other conditions is not inconsequential, and how this information is reported, interpreted, and used may ultimately prevent the individual from participation in competitive sports. Due to the distribution of genetic diversity that reflects our evolutionary and demographic history (including the discernible effects of restricted gene flow and genetic drift associated with cultural constructs of race) and in recognition of previous policies for “leveling” the playing field in competitive sports based on “natural” athletic abilities, preliminary recommendations are provided to discourage genetic segregation of sports and to develop best practice guidelines for genomic sports medicine programs that will facilitate player success, promote player safety, and avoid genetic discrimination within and beyond the program. creator: Jennifer K. Wagner uri: https://doi.org/10.7717/peerj.120 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Wagner title: Microsaccades restore the visibility of minute foveal targets link: https://peerj.com/articles/119 last-modified: 2013-08-01 description: Stationary targets can fade perceptually during steady visual fixation, a phenomenon known as Troxler fading. Recent research found that microsaccades—small, involuntary saccades produced during attempted fixation—can restore the visibility of faded targets, both in the visual periphery and in the fovea. Because the targets tested previously extended beyond the foveal area, however, the ability of microsaccades to restore the visibility of foveally-contained targets remains unclear. Here, subjects reported the visibility of low-to-moderate contrast targets contained entirely within the fovea during attempted fixation. The targets did not change physically, but their visibility varied intermittently during fixation, in an illusory fashion (i.e., foveal Troxler fading). Microsaccade rates increased significantly before the targets became visible, and decreased significantly before the targets faded, for a variety of target contrasts. These results support previous research linking microsaccade onsets to the visual restoration of peripheral and foveal targets, and extend the former conclusions to minute targets contained entirely within the fovea. Our findings suggest that the involuntary eye movements produced during attempted fixation do not always prevent fading—in either the fovea or the periphery—and that microsaccades can restore perception, when fading does occur. Therefore, microsaccades are relevant to human perception of foveal stimuli. creator: Francisco M. Costela creator: Michael B. McCamy creator: Stephen L. Macknik creator: Jorge Otero-Millan creator: Susana Martinez-Conde uri: https://doi.org/10.7717/peerj.119 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Costela et al. title: Rapid quantitative pharmacodynamic imaging by a novel method: theory, simulation testing and proof of principle link: https://peerj.com/articles/117 last-modified: 2013-08-01 description: Pharmacological challenge imaging has mapped, but rarely quantified, the sensitivity of a biological system to a given drug. We describe a novel method called rapid quantitative pharmacodynamic imaging. This method combines pharmacokinetic-pharmacodynamic modeling, repeated small doses of a challenge drug over a short time scale, and functional imaging to rapidly provide quantitative estimates of drug sensitivity including EC50 (the concentration of drug that produces half the maximum possible effect). We first test the method with simulated data, assuming a typical sigmoidal dose-response curve and assuming imperfect imaging that includes artifactual baseline signal drift and random error. With these few assumptions, rapid quantitative pharmacodynamic imaging reliably estimates EC50 from the simulated data, except when noise overwhelms the drug effect or when the effect occurs only at high doses. In preliminary fMRI studies of primate brain using a dopamine agonist, the observed noise level is modest compared with observed drug effects, and a quantitative EC50 can be obtained from some regional time-signal curves. Taken together, these results suggest that research and clinical applications for rapid quantitative pharmacodynamic imaging are realistic. creator: Kevin J. Black creator: Jonathan M. Koller creator: Brad D. Miller uri: https://doi.org/10.7717/peerj.117 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Black et al.