title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1642 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A unified approach to model peripheral nerves across different animal species link: https://peerj.com/articles/4005 last-modified: 2017-11-10 description: Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related to the nature of the external stimuli, theoretical and computational tools were used to investigate their behaviour. In this work, a Yeoh-like polynomial strain energy function was used to reproduce the response of in vitro porcine nerve. Moreover, this approach was applied to different nervous structures coming from different animal species (rabbit, lobster, Aplysia) and tested for different amount of stretch (up to extreme ones). Starting from this theoretical background, in silico models of both porcine nerves and cerebro-abdominal connective of Aplysia were built to reproduce experimental data (R2 > 0.9). Finally, bi-dimensional in silico models were provided to reduce computational time of more than 90% with respect to the performances of fully three-dimensional models. creator: Elisabetta Giannessi creator: Maria Rita Stornelli creator: Pier Nicola Sergi uri: https://doi.org/10.7717/peerj.4005 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Giannessi et al. title: Anthropogenic water sources and the effects on Sonoran Desert small mammal communities link: https://peerj.com/articles/4003 last-modified: 2017-11-10 description: Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi) and white-throated woodrat (Neotoma albigula), had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture. creator: Aaron B. Switalski creator: Heather L. Bateman uri: https://doi.org/10.7717/peerj.4003 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Switalski and Bateman title: Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study link: https://peerj.com/articles/4027 last-modified: 2017-11-09 description: BackgroundCervical sagittal alignment plays an important role in the pathogenesis of cervical spondylotic myelopathy (CSM), but there are limited studies on the cervical sagittal parameters in CSM patients and their correlations with myelopathy. The aim of this study is to investigate the correlations among the preoperative cervical sagittal alignment parameters and their correlations with the development of myelopathy in patients with CSM.MethodsWe retrospectively collected 212 patients with CSM who underwent surgical interventions. Gender, age, modified Japanese Orthopedic Association score (mJOA), cervical lordosis (CL), C2–C7 sagittal vertical axis (C2–C7 SVA), T1 slope (T1S), neck tilt (NT) and thoracic inlet angle (TIA) were collected before operation. Interobserver and intraobserver reliability were calculated for all measurements (intraclass correlation coefficient, ICC). Data were analyzed with Pearson and Spearman correlation tests and multiple linear regression analysis.ResultsA total of 212 patients with CSM were included in this study (male: 136, female: 76) with an average age of 54.5 ± 10.1 years old. Intraobserver and interobserver reliability for all included radiographic parameters presented good to excellent agreement (ICC > 0.7). No significant differences in demographic and radiological parameters have been observed between males and females (P > 0.05). We found statistically significant correlations among the following parameters: age with CL (r = 0.135, P = 0.049), age with T1S (r = 0.222, P = 0.001), CL with T1S (r = 0.291, P < 0.001), CL with C2-C7 SVA (r =  − 0.395, P < 0.001), mJOA with age (r =  − 0.274, P < 0.001), mJOA with C2–C7 SVA (r =  − 0.219, P < 0.001) and mJOA with T1S(r =  − 0.171, p = 0.013). Linear regression analysis showed that C2–C7 SVA was the predictor of CL (adjusted R2 = 0.152, P < 0.001) and multiple linear regression showed that age combined with C2–C7 SVA was a sensitive predictor of mJOA (adjusted R2 = 0.106, P < 0.001).DiscussionThere were significant correlations among certain preoperative cervical sagittal parameters in CSM patients. CL was the only predictor of C2–C7 SVA. Age combined with C2–C7 SVA could predict the severity of myelopathy. creator: Wei Yuan creator: Yue Zhu creator: Haitao Zhu creator: Cui Cui creator: Lei Pei creator: Zhuxi Huang uri: https://doi.org/10.7717/peerj.4027 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yuan et al. title: The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle link: https://peerj.com/articles/4014 last-modified: 2017-11-09 description: The wood frog (Rana sylvatica) can endure freezing of up to 65% of total body water during winter. When frozen, wood frogs enter a dormant state characterized by a cessation of vital functions (i.e., no heartbeat, blood circulation, breathing, brain activity, or movement). Wood frogs utilize various behavioural and biochemical adaptations to survive extreme freezing and component anoxia and dehydration stresses, including a global suppression of metabolic functions and gene expression. The stress-responsive myocyte enhancer factor-2 (MEF2) transcription factor family regulates the selective expression of genes involved in glucose transport, protein quality control, and phosphagen homeostasis. This study examined the role of MEF2A and MEF2C proteins as well as select downstream targets (glucose transporter-4, calreticulin, and muscle and brain creatine kinase isozymes) in 40% dehydration and 24 h anoxia exposure at the transcriptional, translational, and post-translational levels using qRT-PCR, immunoblotting, and subcellular localization. Mef2a/c transcript levels remained constant during dehydration and anoxia. Total, cytoplasmic, and nuclear MEF2A/C and phospho-MEF2A/C protein levels remained constant during dehydration, whereas a decrease in total MEF2C levels was observed during rehydration. Total and phospho-MEF2A levels remained constant during anoxia, whereas total MEF2C levels decreased during 24 h anoxia and P-MEF2C levels increased during 4 h anoxia. In contrast, cytoplasmic MEF2A levels and nuclear phospho-MEF2A/C levels were upregulated during anoxia. MEF2 downstream targets remained constant during dehydration and anoxia, with the exception of glut4 which was upregulated during anoxia. These results suggest that the upregulated MEF2 response reported in wood frogs during freezing may in part stem from their cellular responses to surviving prolonged anoxia, rather than dehydration, leading to an increase in GLUT4 expression which may have an important role during anoxia survival. creator: Myriam P. Hoyeck creator: Hanane Hadj-Moussa creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4014 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hoyeck et al. title: The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert link: https://peerj.com/articles/4007 last-modified: 2017-11-09 description: BackgroundSoil microbial communities (SMC) play a central role in the structure and function of desert ecosystems. However, the high variability of annual precipitation could results in the alteration of SMC and related biological processes depending on soil water potential. The nature of the physiological adjustments made by SMC in order to obtain energy and nutrients remains unclear under different soil resource availabilities in desert ecosystems. In order to examine this dynamic, the present study examined the effects of variation in annual precipitation on physiological adjustments by the SMC across two vegetation-soil systems of different soil organic matter input in an oligotrophic desert ecosystem.MethodsWe collected soil samples in the Cuatro Ciénegas Basin (Mexico) under two vegetation covers: rosetophylous scrub (RS) and grassland (G), that differ in terms of quantity and quality of organic matter. Collections were conducted during the years 2011, 2012, 2013 and 2014, over which a noticeable variation in the annual precipitation occurred. The ecoenzymatic activity involved in the decomposition of organic matter, and the concentration of dissolved, available and microbial biomass nutrients, were determined and compared between sites and years.ResultsIn 2011, we observed differences in bacterial taxonomic composition between the two vegetation covers. The lowest values of dissolved, available and microbial nutrients in both cover types were found in 2012. The G soil showed higher values of dissolved and available nutrients in the wet years. Significant positive correlations were detected between precipitation and the ratios Cmic:Nmic and Cmic:Pmic in the RS soil and Cmic:Pmic and Nmic:Pmic in the G soil. The slopes of the regression with Cmic and Nmic were higher in the G soil and lower in the RS soil. Moreover, the SMC under each vegetation cover were co-limited by different nutrients and responded to the sum of water stress and nutrient limitation.DiscussionSoil community within both sites (RS and G) may be vulnerable to drought. However, the community of the site with lower resources (RS) is well adapted to acquire P resources by ecoenzyme upregulation during years with adequate precipitation, suggesting that this community is resilient after drought occurs. Under the Global Climate Change scenarios for desert ecosystems that predict reduced annual precipitation and an increased intensity and frequency of torrential rains and drought events, the soil microbial communities of both sites could be vulnerable to drought through C and P co-limitation and reallocation of resources to physiological acclimatization strategies in order to survive. creator: Cristina Montiel-González creator: Yunuen Tapia-Torres creator: Valeria Souza creator: Felipe García-Oliva uri: https://doi.org/10.7717/peerj.4007 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Montiel-González et al. title: Mobile acoustic transects miss rare bat species: implications of survey method and spatio-temporal sampling for monitoring bats link: https://peerj.com/articles/3940 last-modified: 2017-11-09 description: Due to increasing threats facing bats, long-term monitoring protocols are needed to inform conservation strategies. Effective monitoring should be easily repeatable while capturing spatio-temporal variation. Mobile acoustic driving transect surveys (‘mobile transects’) have been touted as a robust, cost-effective method to monitor bats; however, it is not clear how well mobile transects represent dynamic bat communities, especially when used as the sole survey approach. To assist biologists who must select a single survey method due to resource limitations, we assessed the effectiveness of three acoustic survey methods at detecting species richness in a vast protected area (Everglades National Park): (1) mobile transects, (2) stationary surveys that were strategically located by sources of open water and (3) stationary surveys that were replicated spatially across the landscape. We found that mobile transects underrepresented bat species richness compared to stationary surveys across all major vegetation communities and in two distinct seasons (dry/cool and wet/warm). Most critically, mobile transects failed to detect three rare bat species, one of which is federally endangered. Spatially replicated stationary surveys did not estimate higher species richness than strategically located stationary surveys, but increased the rate at which species were detected in one vegetation community. The survey strategy that detected maximum species richness and the highest mean nightly species richness with minimal effort was a strategically located stationary detector in each of two major vegetation communities during the wet/warm season. creator: Elizabeth C. Braun de Torrez creator: Megan A. Wallrichs creator: Holly K. Ober creator: Robert A. McCleery uri: https://doi.org/10.7717/peerj.3940 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Braun de Torrez et al. title: HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities link: https://peerj.com/articles/4015 last-modified: 2017-11-08 description: The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM. creator: Weizhi Song creator: Kerrin Steensen creator: Torsten Thomas uri: https://doi.org/10.7717/peerj.4015 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Song et al. title: Indicators for the use of robotic labs in basic biomedical research: a literature analysis link: https://peerj.com/articles/3997 last-modified: 2017-11-08 description: Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs could be applicable in current experimental practice. We do this by text mining 1,628 papers for occurrences of methods that are supported by commercial robotic labs. Using two different concept recognition tools, we find that 86%–89% of the papers have at least one of these methods. This and our other results provide indications that robotic labs can serve as the foundation for performing many lab-based experiments. creator: Paul Groth creator: Jessica Cox uri: https://doi.org/10.7717/peerj.3997 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Groth and Cox title: Character drawing style in cartoons on empathy induction: an eye-tracking and EEG study link: https://peerj.com/articles/3988 last-modified: 2017-11-08 description: In its most basic form, empathy refers to the ability to understand another person’s feelings and emotions, representing an essential component of human social interaction. Owing to an increase in the use of mass media, which is used to distribute high levels of empathy-inducing content, media plays a key role in individual and social empathy induction. We investigated empathy induction in cartoons using eye movement, EEG and behavioral measures to explore whether empathy factors correlate with character drawing styles. Two different types of empathy-inducing cartoons that consisted of three stages and had the same story plot were used. One had an iconic style, while the other was realistic style. Fifty participants were divided into two groups corresponding to the individual cartoon drawing styles and were presented with only one type of drawing style. We found that there were no significant differences of empathy factors between iconic and realistic style. However, the Induced Empathy Score (IES) had a close relationship with subsequent attentional processing (total fixation length for gaze duration). Furthermore, iconic style suppressed the fronto-central area more than realistic style in the gamma power band. These results suggest that iconic cartoons have the advantage of abstraction during empathy induction, because the iconic cartoons induced the same level of empathy as realistic cartoons while using the same story plot (top-down process), even though lesser time and effort were required by the cartoon artist to draw them. This also means that the top-down process (story plot) is more important than the bottom-up process (drawing style) in empathy induction when viewing cartoons creator: Yong-il Lee creator: Yeojeong Choi creator: Jaeseung Jeong uri: https://doi.org/10.7717/peerj.3988 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lee et al. title: Visual and acoustic components of courtship in the bird-of-paradise genus Astrapia (Aves: Paradisaeidae) link: https://peerj.com/articles/3987 last-modified: 2017-11-08 description: The distinctive and divergent courtship phenotypes of the birds-of-paradise make them an important group for gaining insights into the evolution of sexually selected phenotypic evolution. The genus Astrapia includes five long-tailed species that inhabit New Guinea’s montane forests. The visual and acoustic components of courtship among Astrapia species are very poorly known. In this study, we use audiovisual data from a natural history collection of animal behavior to fill gaps in knowledge about the visual and acoustic components of Astrapia courtship. We report seven distinct male behaviors and two female specific behaviors along with distinct vocalizations and wing-produced sonations for all five species. These results provide the most complete assessment of courtship in the genus Astrapia to date and provide a valuable baseline for future research, including comparative and evolutionary studies among these and other bird-of-paradise species. creator: Edwin Scholes creator: Julia M. Gillis creator: Timothy G. Laman uri: https://doi.org/10.7717/peerj.3987 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Scholes et al.