title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1746 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Modeling using clinical examination indicators predicts interstitial lung disease among patients with rheumatoid arthritis link: https://peerj.com/articles/3021 last-modified: 2017-02-21 description: Interstitial lung disease (ILD) is a severe extra-articular manifestation of rheumatoid arthritis (RA) that is well-defined as a chronic systemic autoimmune disease. A proportion of patients with RA-associated ILD (RA-ILD) develop pulmonary fibrosis (PF), resulting in poor prognosis and increased lifetime risk. We investigated whether routine clinical examination indicators (CEIs) could be used to identify RA patients with high PF risk. A total of 533 patients with established RA were recruited in this study for model building and 32 CEIs were measured for each of them. To identify PF risk, a new artificial neural network (ANN) was built, in which inputs were generated by calculating Euclidean distance of CEIs between patients. Receiver operating characteristic curve analysis indicated that the ANN performed well in predicting the PF risk (Youden index = 0.436) by only incorporating four CEIs including age, eosinophil count, platelet count, and white blood cell count. A set of 218 RA patients with healthy lungs or suffering from ILD and a set of 87 RA patients suffering from PF were used for independent validation. Results showed that the model successfully identified ILD and PF with a true positive rate of 84.9% and 82.8%, respectively. The present study suggests that model integration of multiple routine CEIs contributes to identification of potential PF risk among patients with RA. creator: Yao Wang creator: Wuqi Song creator: Jing Wu creator: Zhangming Li creator: Fengyun Mu creator: Yang Li creator: He Huang creator: Wenliang Zhu creator: Fengmin Zhang uri: https://doi.org/10.7717/peerj.3021 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Molecular and morphological data reveal three new cryptic species of Chiasmocleis (Mehely 1904) (Anura, Microhylidae) endemic to the Atlantic Forest, Brazil link: https://peerj.com/articles/3005 last-modified: 2017-02-21 description: Three new cryptic species of Chiasmocleis from the Atlantic Forest of Brazil are described. Two of these species occur in the northeastern states of Sergipe and Bahia, whereas the third species is found in the southeastern state of São Paulo. The new species can be distinguished from other congeneric species by the molecular data, as evidenced in the phylogeny, and by a combination of morphological characters including: size, foot webbing, dermal spines, and coloration patterns. Chiasmocleis species differ in osteological traits, therefore we also provide an osteological description of each new species and comparsions with data reported for other species in the genus. creator: Mauricio C. Forlani creator: João F.R. Tonini creator: Carlos A.G. Cruz creator: Hussam Zaher creator: Rafael O. de Sá uri: https://doi.org/10.7717/peerj.3005 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Forlani et al. title: A detailed observation of the ejection and retraction of defense tissue acontia in sea anemone (Exaiptasia pallida) link: https://peerj.com/articles/2996 last-modified: 2017-02-21 description: Acontia, located in the gastrovascular cavity of anemone, are thread-like tissue containing numerous stinging cells which serve as a unique defense tissue against predators of the immobile acontiarian sea anemone. Although its morphology and biological functions, such as defense and digestion, have been studied, the defense behavior and the specific events of acontia ejection and retraction are unclear. The aim of this study is to observe and record the detailed process of acontia control in anemones. Observations reveal that the anemone, Exaiptasia pallida, possibly controls a network of body muscles and manipulates water pressure in the gastrovascular cavity to eject and retract acontia. Instead of resynthesizing acontia after each ejection, the retraction and reuse of acontia enables the anemone to respond quickly at any given time, thus increasing its overall survivability. Since the Exaiptasia anemone is an emerging model for coral biology, this study provides a foundation to further investigate the biophysics, neuroscience, and defense biology of this marine model organism. creator: Julie Lam creator: Ya-Wen Cheng creator: Wan-Nan U. Chen creator: Hsing-Hui Li creator: Chii-Shiarng Chen creator: Shao-En Peng uri: https://doi.org/10.7717/peerj.2996 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lam et al. title: How patch size and refuge availability change interaction strength and population dynamics: a combined individual- and population-based modeling experiment link: https://peerj.com/articles/2993 last-modified: 2017-02-21 description: Knowledge on how functional responses (a measurement of feeding interaction strength) are affected by patch size and habitat complexity (represented by refuge availability) is crucial for understanding food-web stability and subsequently biodiversity. Due to their laborious character, it is almost impossible to carry out systematic empirical experiments on functional responses across wide gradients of patch sizes and refuge availabilities. Here we overcame this issue by using an individual-based model (IBM) to simulate feeding experiments. The model is based on empirically measured traits such as body-mass dependent speed and capture success. We simulated these experiments in patches ranging from sizes of petri dishes to natural patches in the field. Moreover, we varied the refuge availability within the patch independently of patch size, allowing for independent analyses of both variables. The maximum feeding rate (the maximum number of prey a predator can consume in a given time frame) is independent of patch size and refuge availability, as it is the physiological upper limit of feeding rates. Moreover, the results of these simulations revealed that a type III functional response, which is known to have a stabilizing effect on population dynamics, fitted the data best. The half saturation density (the prey density where a predator consumes half of its maximum feeding rate) increased with refuge availability but was only marginally influenced by patch size. Subsequently, we investigated how patch size and refuge availability influenced stability and coexistence of predator-prey systems. Following common practice, we used an allometric scaled Rosenzweig–MacArthur predator-prey model based on results from our in silico IBM experiments. The results suggested that densities of both populations are nearly constant across the range of patch sizes simulated, resulting from the constant interaction strength across the patch sizes. However, constant densities with decreasing patch sizes mean a decrease of absolute number of individuals, consequently leading to extinction of predators in the smallest patches. Moreover, increasing refuge availabilities also allowed predator and prey to coexist by decreased interaction strengths. Our results underline the need for protecting large patches with high habitat complexity to sustain biodiversity. creator: Yuanheng Li creator: Ulrich Brose creator: Katrin Meyer creator: Björn C. Rall uri: https://doi.org/10.7717/peerj.2993 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Li et al. title: Counting complete? Finalising the plant inventory of a global biodiversity hotspot link: https://peerj.com/articles/2984 last-modified: 2017-02-21 description: The Cape Floristic Region—the world’s smallest and third richest botanical hotspot—has benefited from sustained levels of taxonomic effort and exploration for almost three centuries, but how close is this to resulting in a near-complete plant species inventory? We analyse a core component of this flora over a 250-year period for trends in taxonomic effort and species discovery linked to ecological and conservation attributes. We show that >40% of the current total of species was described within the first 100 years of exploration, followed by a continued steady rate of description. We propose that <1% of the flora is still to be described. We document a relatively constant cohort of taxonomists, working over 250 years at what we interpret to be their ‘taxonomic maximum.’ Rates of description of new species were independent of plant growth-form but narrow-range taxa have constituted a significantly greater proportion of species discoveries since 1950. This suggests that the fraction of undiscovered species predominantly comprises localised endemics that are thus of high conservation concern. Our analysis provides important real-world insights for other hotspots in the context of global strategic plans for biodiversity in informing considerations of the likely effort required in attaining set targets of comprehensive plant inventories. In a time of unprecedented biodiversity loss, we argue for a focused research agenda across disciplines to increase the rate of species descriptions in global biodiversity hotspots. creator: Martina Treurnicht creator: Jonathan F. Colville creator: Lucas N. Joppa creator: Onno Huyser creator: John Manning uri: https://doi.org/10.7717/peerj.2984 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Treurnicht et al. title: Patient satisfaction with doctor-patient interaction and its association with modifiable cardiovascular risk factors among moderately-high risk patients in primary healthcare link: https://peerj.com/articles/2983 last-modified: 2017-02-21 description: BackgroundThe outcomes of the physician-patient discussion intervene in the satisfaction of cardiovascular disease risk patients. Adherence to treatment, provision of continuous care, clinical management of the illness and patients’ adjustment are influenced by satisfaction with physician-patient interaction. This study aims to determine patient satisfaction with doctor-patient interactions and, over six months after following prevention counselling, its associations with modifiable cardiovascular risk factors amongst moderately-high risk patients in a primary healthcare clinic in Kelantan, Malaysia.MethodsA prospective survey was conducted amongst patients with moderately-high cardiovascular risk. A total of 104 moderately-high risk patients were recruited and underwent structured prevention counselling based on the World Health Organization guideline, and their satisfaction with the doctor-patient interaction was assessed using ‘Skala Kepuasan Interaksi Perubatan-11,’ the Malay version of the Medical Interview Satisfaction Scale-21. Systolic blood pressure, total cholesterol and high-density lipoprotein cholesterol were measured at baseline and at a follow-up visit at six months. Descriptive analysis, paired t test and linear regression analyses were performed.ResultsA total of 102 patients responded, giving a response rate of 98.1%. At baseline, 76.5% of the respondents were satisfied with the relation with their doctor, with the favourable domain of distress relief (85.3%) and rapport/confidence (91.2%). The unfavourable domain was interaction outcome, with satisfaction in only 67.6% of the respondents. Between the two visits, changes had occurred in total cholesterol (P = 0.022) and in systolic blood pressure (P < 0.001). Six months after the initial visits, no relationship existed between patient satisfaction scores and changes in modifiable cardiovascular risks.DiscussionThe ‘Skala Kepuasan Interaksi Perubatan-11’ which represents a component of the interpersonal doctor-patient relationship can be used to assess improvements of the medical skills and in medical training to enhance the quality of therapeutic communication. creator: Mohd Noor Norhayati creator: Abd Aziz Masseni creator: Ishak Azlina uri: https://doi.org/10.7717/peerj.2983 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Norhayati et al. title: Bax-inhibitor-1 knockdown phenotypes are suppressed by Buffy and exacerbate degeneration in a Drosophila model of Parkinson disease link: https://peerj.com/articles/2974 last-modified: 2017-02-21 description: BackgroundBax inhibitor-1 (BI-1) is an evolutionarily conserved cytoprotective transmembrane protein that acts as a suppressor of Bax-induced apoptosis by regulation of endoplasmic reticulum stress-induced cell death. We knocked down BI-1 in the sensitive dopa decarboxylase (Ddc) expressing neurons of Drosophila melanogaster to investigate its neuroprotective functions. We additionally sought to rescue the BI-1-induced phenotypes by co-expression with the pro-survival Buffy and determined the effect of BI-1 knockdown on the neurodegenerative α-synuclein-induced Parkinson disease (PD) model.MethodsWe used organismal assays to assess longevity of the flies to determine the effect of the altered expression of BI-1 in the Ddc-Gal4-expressing neurons by employing two RNAi transgenic fly lines. We measured the locomotor ability of these RNAi lines by computing the climbing indices of the climbing ability and compared them to a control line that expresses the lacZ transgene. Finally, we performed biometric analysis of the developing eye, where we counted the number of ommatidia and calculated the area of ommatidial disruption.ResultsThe knockdown of BI-1 in these neurons was achieved under the direction of the Ddc-Gal4 transgene and resulted in shortened lifespan and precocious loss of locomotor ability. The co-expression of Buffy, the Drosophila anti-apoptotic Bcl-2 homologue, with BI-1-RNAi resulted in suppression of the reduced lifespan and impaired climbing ability. Expression of human α-synuclein in Drosophila dopaminergic neurons results in neuronal degeneration, accompanied by the age-dependent loss in climbing ability. We exploited this neurotoxic system to investigate possible BI-1 neuroprotective function. The co-expression of α-synuclein with BI-1-RNAi results in a slight decrease in lifespan coupled with an impairment in climbing ability. In supportive experiments, we employed the neuron-rich Drosophila compound eye to investigate subtle phenotypes that result from altered gene expression. The knockdown of BI-1 in the Drosophila developing eye under the direction of the GMR-Gal4 transgene results in reduced ommatidia number and increased disruption of the ommatidial array. Similarly, the co-expression of BI-1-RNAi with Buffy results in the suppression of the eye phenotypes. The expression of α-synuclein along with the knockdown of BI-1 resulted in reduction of ommatidia number and more disruption of the ommatidial array.ConclusionKnockdown of BI-1 in the dopaminergic neurons of Drosophila results in a shortened lifespan and premature loss in climbing ability, phenotypes that appear to be strongly associated with models of PD in Drosophila, and which are suppressed upon overexpression of Buffy and worsened by co-expression with α-synuclein. This suggests that BI-1 is neuroprotective and its knockdown can be counteracted by the overexpression of the pro-survival Bcl-2 homologue. creator: P. Githure M’Angale creator: Brian E. Staveley uri: https://doi.org/10.7717/peerj.2974 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 M’Angale & Staveley title: Intersexual differences of heat shock response between two amphipods (Eulimnogammarus verrucosus and Eulimnogammarus cyaneus) in Lake Baikal link: https://peerj.com/articles/2864 last-modified: 2017-02-21 description: Acute temperature fluctuations are common in surface waters, and aquatic organisms may manifest physiological responses to punctuated temperature spikes long before behavioral responses. Ectotherms, especially cryophilic stenotherms such as those endemic to Lake Baikal (Siberia), may demonstrate specialized physiological responses to acute temperature increases because their proteomes have evolved to function most efficiently at lower temperatures (e.g., <10 °C). Therefore, our study questioned the nature and degree of variation in physiological response to acute thermal stress in two congenerous, endemic Baikal amphipod species, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus. We hypothesized that because interspecific and intersexual thermosensitivity varies significantly among ectotherms, there would be divergent intersexual and interspecific strategies to withstand acute thermal stress, manifested in different protein compositions and concentrations. We exposed individuals to the species’ respective LT50 for one hour followed by a three-hour recovery period. We then performed 1D-PAGE, Western blotting, 2D-PAGE, and Mass Spectrometry techniques and assessed relative intersexual and interspecific changes in proteomic composition and heat shock protein 70 level. Our results demonstrate that females tend to be more sensitive to an acute thermal stimulus than males, most likely because females allocate significant energy to reproduction and less to heat shock response, evidenced by females’ significantly lower LT50time. Lower level of Hsp70 was found in females of the thermosensitive E. verrucosus compared to males of this species. No intersexual differences were found in Hsp70 level in thermotolerant E. cyaneus. Higher levels of hemocyanin subunits and arginine kinase were found in E. cyaneus females after heat shock and recovery compared to males, which was not found for E. verrucosus, suggesting interspecific mechanisms for E. cyaneus’s higher thermotolerance. These differing responses between species and sexes of Baikal amphipods may reflect more general strategies for maintaining homeostatic conditions during acute thermal stress. As mean surface water temperatures increase worldwide, the net efficiency and efficacy of these strategies could give rise to long term changes in physiology, behavior, and interactions with other species, potentially precipitating population and community level alterations. creator: Daria Bedulina creator: Michael F. Meyer creator: Anton Gurkov creator: Ekaterina Kondratjeva creator: Boris Baduev creator: Roman Gusdorf creator: Maxim A. Timofeyev uri: https://doi.org/10.7717/peerj.2864 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bedulina et al. title: Species coexistence and the superior ability of an invasive species to exploit a facilitation cascade habitat link: https://peerj.com/articles/2848 last-modified: 2017-02-21 description: Facilitation cascades generated by co-occurring foundation species can enhance the abundance and diversity of associated organisms. However, it remains poorly understood how differences among native and invasive species in their ability to exploit these positive interactions contribute to emergent patterns of community structure and biotic acceptance. On intertidal shorelines in New England, we examined the patterns of coexistence between the native mud crabs and the invasive Asian shore crab in and out of a facilitation cascade habitat generated by mid intertidal cordgrass and ribbed mussels. These crab species co-occurred in low intertidal cobbles adjacent to the cordgrass–mussel beds, despite experimental findings that the dominant mud crabs can kill and displace Asian shore crabs and thereby limit their successful recruitment to their shared habitat. A difference between the native and invasive species in their utilization of the facilitation cascade likely contributes to this pattern. Only the Asian shore crabs inhabit the cordgrass–mussel beds, despite experimental evidence that both species can similarly benefit from stress amelioration in the beds. Moreover, only Asian shore crabs settle in the beds, which function as a nursery habitat free of lethal mud crabs, and where their recruitment rates are particularly high (nearly an order of magnitude higher than outside beds). Persistence of invasive adult Asian shore crabs among the dominant native mud crabs in the low cobble zone is likely enhanced by a spillover effect of the facilitation cascade in which recruitment-limited Asian shore crabs settle in the mid intertidal cordgrass–mussel beds and subsidize their vulnerable populations in the adjacent low cobble zone. This would explain why the abundances of Asian shore crabs in cobbles are doubled when adjacent to facilitation cascade habitats. The propensity for this exotic species to utilize habitats created by facilitation cascades, despite the lack of a shared evolutionary history, contributes to species coexistence and the acceptance of invasives into a diverse community. creator: Andrew H. Altieri creator: Andrew D. Irving uri: https://doi.org/10.7717/peerj.2848 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Altieri and Irving title: Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies link: https://peerj.com/articles/2988 last-modified: 2017-02-16 description: BackgroundDe novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved.ResultsWe built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts.ConclusionTranscriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap. creator: Cédric Cabau creator: Frédéric Escudié creator: Anis Djari creator: Yann Guiguen creator: Julien Bobe creator: Christophe Klopp uri: https://doi.org/10.7717/peerj.2988 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cabau et al.