title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1716 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A study of the progression of damage in an axially loaded Branta leucopsis femur using X-ray computed tomography and digital image correlation link: https://peerj.com/articles/3416 last-modified: 2017-06-23 description: This paper uses X-ray computed tomography to track the mechanical response of a vertebrate (Barnacle goose) long bone subjected to an axial compressive load, which is increased gradually until failure. A loading rig was mounted in an X-ray computed tomography system so that a time-lapse sequence of three-dimensional (3D) images of the bone’s internal (cancellous or trabecular) structure could be recorded during loading. Five distinct types of deformation mechanism were observed in the cancellous part of the bone. These were (i) cracking, (ii) thinning (iii) tearing of cell walls and struts, (iv) notch formation, (v) necking and (vi) buckling. The results highlight that bone experiences brittle (notch formation and cracking), ductile (thinning, tearing and necking) and elastic (buckling) modes of deformation. Progressive deformation, leading to cracking was studied in detail using digital image correlation. The resulting strain maps were consistent with mechanisms occurring at a finer-length scale. This paper is the first to capture time-lapse 3D images of a whole long bone subject to loading until failure. The results serve as a unique reference for researchers interested in how bone responds to loading. For those using computer modelling, the study not only provides qualitative information for verification and validation of their simulations but also highlights that constitutive models for bone need to take into account a number of different deformation mechanisms. creator: Zartasha Mustansar creator: Samuel A. McDonald creator: William Irvin Sellers creator: Phillip Lars Manning creator: Tristan Lowe creator: Philip J. Withers creator: Lee Margetts uri: https://doi.org/10.7717/peerj.3416 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Mustansar et al. title: Piwi1 is essential for gametogenesis in mollusk Chlamys farreri link: https://peerj.com/articles/3412 last-modified: 2017-06-23 description: Piwi (P-element induced wimpy testis) is an important gene involved in stem cell maintenance and gametogenesis in vertebrates. However, in most invertebrates, especially mollusks, the function of Piwi during gametogenesis remains largely unclear. To further understand the function of Piwi during gametogenesis, full-length cDNA of Piwi1 from scallop Chlamys farreri (Cf-Piwi1) was characterized, which consisted of a 2,637 bp open reading frame encoding an 878-amino acid protein. Cf-Piwi1 mRNA was mainly localized in the spermatogonia, spermatocytes, oogonia, oocytes of early development and intra-gonadal somatic cells. Additionally, the knockdown of Cf-Piwi1 by injection of Cf-Piwi1-dsRNA (double-stranded RNA) into scallop adductor led to a loss of germ cells in C. farreri gonads. Apoptosis was observed mainly in spermatocytes and oocytes of early development, as well as in a small number of spermatogonia and oogonia. Our findings indicate that Cf-Piwi1 is essential for gametogenesis in the scallop C. farreri. creator: Xiaoshi Ma creator: Aichang Ji creator: Zhifeng Zhang creator: Dandan Yang creator: Shaoshuai Liang creator: Yuhan Wang creator: Zhenkui Qin uri: https://doi.org/10.7717/peerj.3412 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ma et al. title: Two-headed butterfly vs. mantis: do false antennae matter? link: https://peerj.com/articles/3493 last-modified: 2017-06-22 description: The colour patterns and morphological peculiarities of the hindwings of several butterfly species result in the appearance of a head at the rear end of the insect’s body. Although some experimental evidence supports the hypothesis that the “false head” deflects predator attacks towards the rear end of the butterfly, more research is needed to determine the role of the different components of the “false head”. We explored the role of hindwing tails (presumably mimicking antennae) in predator deception in the “false head” butterfly Callophrys xami. We exposed butterflies with intact wings and with hindwing tails experimentally ablated to female mantises (Stagmomantis limbata). We found no differences in the number of butterflies being attacked and the number of butterflies escaping predation between both groups. However, our behavioural observations indicate that other aspects of the “false head” help C. xami survive some mantis attacks, supporting the notion that they are adaptations against predators. creator: Tania G. López-Palafox creator: Carlos R. Cordero uri: https://doi.org/10.7717/peerj.3493 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 López-Palafox and Cordero title: A simple electroelution method for rapid protein purification: isolation and antibody production of alpha toxin from Clostridium septicum link: https://peerj.com/articles/3407 last-modified: 2017-06-22 description: Clostridium septicum produces a number of diseases in human and farm animals which, in most of the cases, are fatal without clinical intervention. Alpha toxin is an important agent and the unique lethal virulent factor produced by Clostridium septicum. This toxin is haemolytic, highly lethal and necrotizing activities but is being used as an antigen to develop animal vaccines. The aim of this study was to isolate the alpha toxin of Clostridium septicum and produce highly specific antibodies against it. In this work, we have developed a simple and efficient method for alpha toxin purification, based on electroelution that can be used as a time-saving method for purifying proteins. This technique avoids contamination by other proteins that could appear during other protein purification techniques such chromatography. The highly purified toxin was used to produce polyclonal antibodies. The specificity of the antibodies was tested by western blot and these antibodies can be applied to the quantitative determination of alpha toxin by slot blot. creator: Lorena Vázquez-Iglesias creator: Borja Estefanell-Ucha creator: Leticia Barcia-Castro creator: María Páez de la Cadena creator: Paula Álvarez-Chaver creator: Daniel Ayude-Vázquez creator: Francisco Javier Rodríguez-Berrocal uri: https://doi.org/10.7717/peerj.3407 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vázquez-Iglesias et al. title: Euphilomedes biacutidens (Ostracoda, Myodocopida, Philomedidae), a new species from China Sea link: https://peerj.com/articles/3488 last-modified: 2017-06-22 description: Ostracods are one of the major groups of marine benthos, inhabiting virtually all oceanic environments worldwide, and a total of 31 species have been recorded in genus EuphilomedesKornicker, 1967. In the present study, we describe a new species Euphilomedes biacutidens collected from the Taiwan Strait and South China Sea. E. biacutidens sp. nov. differs from the related species of the genus Euphilomedes in having a unique combination of the characteristics of spines on carapace, the filaments on sensory seta, the arrangement of setae on tip of the first antenna, the numbers of setae on appendages, the claws on fifth limb, the teeth on the comb of the seventh limb and furcal claws. It is particularly obvious that it has a bifurcated and pointed ventral corner of the rostrum, two spines on the posterior margin of right valve, a row of teeth along the inner margin of article 3 of the endopod of the second antenna, and some long claws instead of setae on the fifth limb. creator: Peng Xiang creator: Youyin Ye creator: Xiaoyin Chen creator: Ruixiang Chen creator: Mao Lin uri: https://doi.org/10.7717/peerj.3488 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Xiang et al. title: Diverse habitat use during two life stages of the critically endangered Bahama Oriole (Icterus northropi): community structure, foraging, and social interactions link: https://peerj.com/articles/3500 last-modified: 2017-06-22 description: Our ability to prevent extinction in declining populations often depends on effective management of habitats that are disturbed through wildfire, logging, agriculture, or development. In these disturbed landscapes, the juxtaposition of multiple habitat types can be especially important to fledglings and young birds, which may leave breeding grounds in human-altered habitat for different habitats nearby that provide increased foraging opportunities, reduced competition, and higher protection from predators. In this study, we evaluated the importance of three habitat types to two life stages of the critically endangered Bahama Oriole (Icterus northropi), a synanthropic songbird endemic to Andros, The Bahamas. First, we determined the avian species composition and relative abundance of I. northropi among three major vegetation types on Andros: Caribbean pine (Pinus caribaea) forest, coppice (broadleaf dry forest), and anthropogenic areas, dominated by nonnative vegetation (farmland and developed land). We then compared the foraging strategies and social interactions of two age classes of adult Bahama Orioles in relation to differential habitat use. Bird surveys late in the Bahama Oriole’s breeding season indicated the number of avian species and Bahama Oriole density were highest in coppice. Some bird species occurring in the coppice and pine forest were never observed in agricultural or residential areas, and may be at risk if human disturbance of pine forest and coppice increases, as is occurring at a rapid pace on Andros. During the breeding season, second-year (SY) adult Bahama Orioles foraged in all vegetation types, whereas after-second-year (ASY) adults were observed foraging only in anthropogenic areas, where the species nested largely in introduced coconut palms (Cocos nucifera). Additionally, SY adults foraging in anthropogenic areas were often observed with an ASY adult, suggesting divergent habitat use for younger, unpaired birds. Other aspects of foraging (vegetation features, food-gleaning behavior, and food items) were similar for the two age classes. Older Bahama Orioles exhibited relatively higher rates of social interactions (intraspecific and interspecific pooled) in anthropogenic areas, and won more interaction outcomes compared to younger adults. Our findings concur with those of other studies indicating dry broadleaf forest is vitally important to migrating, wintering, and resident birds, including the critically endangered Bahama Oriole, which appears to depend heavily on this vegetation type during certain life stages. creator: Melissa R. Price creator: William K. Hayes uri: https://doi.org/10.7717/peerj.3500 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Price and Hayes title: Time to cash in on positive interactions for coral restoration link: https://peerj.com/articles/3499 last-modified: 2017-06-22 description: Coral reefs are among the most biodiverse and productive ecosystems on Earth, and provide critical ecosystem services such as protein provisioning, coastal protection, and tourism revenue. Despite these benefits, coral reefs have been declining precipitously across the globe due to human impacts and climate change. Recent efforts to combat these declines are increasingly turning to restoration to help reseed corals and speed-up recovery processes. Coastal restoration theory and practice has historically favored transplanting designs that reduce potentially harmful negative species interactions, such as competition between transplants. However, recent research in salt marsh ecosystems has shown that shifting this theory to strategically incorporate positive interactions significantly enhances restoration yield with little additional cost or investment. Although some coral restoration efforts plant corals in protected areas in order to benefit from the facilitative effects of herbivores that reduce competitive macroalgae, little systematic effort has been made in coral restoration to identify the entire suite of positive interactions that could promote population enhancement efforts. Here, we highlight key positive species interactions that managers and restoration practitioners should utilize to facilitate the restoration of corals, including (i) trophic facilitation, (ii) mutualisms, (iii) long-distance facilitation, (iv) positive density-dependence, (v) positive legacy effects, and (vi) synergisms between biodiversity and ecosystem function. As live coral cover continues to decline and resources are limited to restore coral populations, innovative solutions that increase efficiency of restoration efforts will be critical to conserving and maintaining healthy coral reef ecosystems and the human communities that rely on them. creator: Elizabeth C. Shaver creator: Brian R. Silliman uri: https://doi.org/10.7717/peerj.3499 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shaver and Silliman title: Utility of a time frame in assessing psychological pain and suicide ideation link: https://peerj.com/articles/3491 last-modified: 2017-06-22 description: BackgroundAssessing psychological pain has been recommended as an integral part of a comprehensive suicide risk assessment. The Psychache Scale, an established measure of psychological pain, does not specify a time frame for when pain is experienced, which may inadvertently increase the likelihood of identifying individuals as being at elevated suicide risk when they complete the Psychache Scale based on psychological pain experienced at some undefined time in the past.MethodsWe conducted a national general population survey among United States adults to determine whether addition of a time frame to the instructions of the Psychache Scale would more accurately reflect current psychological pain and more effectively identify people with current suicide ideation. A between-subjects design was used where respondents were randomized to complete the original Psychache scale or a modified scale with time frame. Data were collected online from September 2015 to June 2016. A total of 242 respondents had complete psychological pain data: 133 completed the original Psychache Scale and 109 completed the Psychache Scale with time frame.ResultsAddition of a time frame did not result in differences in psychological pain scores. However, when screening for participants with current suicide ideation, 13% fewer false positives were observed with the modified scale at higher cut-off values than previously reported (38 vs. 24). The substantial increase in positive predictive value suggests that a time frame is a worthwhile addition to the Psychache Scale.DiscussionWe recommend using the Psychache Scale with a time frame and testing the cut-off score for suicide ideation in population samples that reflect the general population more accurately. Psychological pain cut-off scores in clinical samples have yet to be established. creator: Esther L. Meerwijk creator: Sandra J. Weiss uri: https://doi.org/10.7717/peerj.3491 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Meerwijk and Weiss title: Sea star Henricia spiculifera (Clark, 1901) in the northwestern Pacific: one species or three? link: https://peerj.com/articles/3489 last-modified: 2017-06-22 description: Three species of the sea stars are reported from the waters of the northwestern Pacific. These species were referred by earlier authors as Henricia spiculifera or H. leviuscula spiculifera. Two of them, H. lineata and H. uluudax, were recently described from the Aleutian Islands. These species are reported for the first time from the western Pacific (southeastern Kamchatka shore, Commander Islands, and the northern Kurile Islands). The third species, H. olga sp. n. is herein described from the northern Sea of Japan. It is very likely that similar sea stars recorded in Yellow Sea and the southern Kurile Islands belong to H. olga sp. n. These three species are a part of a phylogenetic clade within the subgenus Setihenricia, which also includes H. sanguinolenta, H. multispina, and several undescribed species occurring in the northeastern Pacific. creator: Anton Chichvarkhin uri: https://doi.org/10.7717/peerj.3489 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chichvarkhin title: Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections link: https://peerj.com/articles/3487 last-modified: 2017-06-22 description: BackgroundThe microbiome of built environment surfaces is impacted by the presence of humans. In this study, we tested the hypothesis that analysis of surface swabs from clinic toilet/bathroom yields results correlated with sexually transmitted infection (STI) notifications from corresponding human populations. We extended a previously reported study in which surfaces in toilet/bathroom facilities in primary health clinics in the Australian Northern Territory (NT) were swabbed then tested for nucleic acid from the STI agents Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis. This was in the context of assessing the potential for such nucleic acid to contaminate specimens collected in such facilities. STIs are notifiable in the NT, thus allowing comparison of swab and notification data.MethodsAn assumption in the design was that while absolute built environment loads of STI nucleic acids will be a function of patient traffic density and facility cleaning protocols, the relative loads of STI nucleic acids from different species will be largely unaffected by these processes. Another assumption was that the proportion of swabs testing positive for STIs provides a measure of surface contamination. Accordingly, “STI profiles” were calculated. These were the proportions that each of the three STIs of interest contributed to the summed STI positive swabs or notifications. Three comparisons were performed, using swab data from clinics in remote Indigenous communities, clinics in small-medium towns, and a single urban sexual health clinic. These data were compared with time and place-matched STI notifications.ResultsThere were significant correlations between swab and notifications data for the both the remote Indigenous and regional data. For the remote Indigenous clinics the p values ranged from 0.041 to 0.0089, depending on data transformation and p value inference method. Further, the swab data appeared to strongly indicate known higher relative prevalence of gonorrhoeae in central Australia than in northern Australia. Similarly, the regional clinics yielded p values from 0.0088–0.0022. In contrast, swab and notifications data from the sexual health clinic were not correlated.DiscussionStrong correlations between swab and notifications were observed. However, there was evidence for limitations of this approach. Despite the correlation observed with the regional clinics data, one clinic yielded zero positive swabs for C. trachomatis, although this STI constituted 25.1% of the corresponding notifications. This could be ascribed to stochastic effects. The lack of correlation observed for sexual health clinic data was also likely due to stochastic effects. It was concluded that toilet/bathroom surface swab sampling has considerable potential for public health surveillance. The approach may be applicable in situations other than primary health clinics, and for targets other than STIs. creator: Philip M. Giffard creator: Jiunn-Yih Su creator: Patiyan Andersson creator: Deborah C. Holt uri: https://doi.org/10.7717/peerj.3487 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Giffard et al.