title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=987 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Acoustic monitors and direct observations provide similar but distinct perspectives on bird assemblages in a lowland forest of eastern Ecuador link: https://peerj.com/articles/10565 last-modified: 2021-01-13 description: Bird communities in lowland Neotropical forests exhibit temporal and spatial variation in species composition and abundance at multiple scales. Detecting and explaining such variation requires adequate methods for sampling those bird communities but counting birds in highly diverse lowland forests of the Neotropics can be particularly challenging. Point counts are one of the most frequently used methods for counting birds in tropical forests but inter- and intra-observer variability in detecting and identifying sounds may cause problems. Acoustic monitors (passive acoustic monitors; autonomous recording units) provide an alternative and potentially effective method to sample bird communities by acting, in effect, as “point counts”, recording vocalizations at a given point for a set time. I used acoustic monitors to examine patterns of species richness, spatial distribution, and community composition of birds in a lowland forest in eastern Ecuador, one of the most diverse regions on earth. I deployed monitors at 25 locations, each separated by at least 200 m, on each of two 100-ha plots (Harpia, Puma) at Tiputini Biodiversity Station during January–February, 2013–2017. Monitors were set to record for 10 min followed by a 5-min break, from 0545 h to 0810 h (10 recording periods/morning). Recordings were later reviewed to identify species; no attempt was made to distinguish individuals or to estimate distance. Results were compared with contemporaneous direct observations along transects on the same plots. A total of 214 species were identified from recordings on both plots, combined, with slightly more on Harpia (208) than on Puma (188). Number per year ranged from 142 on Harpia in 2016 to 161 on Puma in 2015. Number per point was ~45 with an overall range of 29–68. Number of species detected in recordings was similar to but somewhat less than the number recorded during direct observations. Number of species recorded increased rapidly from the first period (0545–0555 h) to the third (0615–0625 h) but showed little subsequent change. Most species were recorded at relatively few points; the four most widely distributed species were the same on both plots (Patagioenas plumbea, Xiphorhynchus guttatus, Capito aurita, Ramphastos tucanus), all of which are relatively loud canopy or subcanopy species. Ordinations based on species composition illustrated differences between plots based on both recordings and direct observations; similarly, patterns of species composition differed between methods. Acoustic monitors can be an effective tool for sampling bird communities and may be particularly effective and efficient for sampling loud species with distinctive songs. Nonetheless, results from monitors may provide different perspectives on species composition when compared to direct observations. Which method is preferred likely will depend on the specific objectives of individual studies. creator: John G. Blake uri: https://doi.org/10.7717/peerj.10565 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Blake title: Reduced recognition of facial emotional expressions in global burnout and burnout depersonalization in healthcare providers link: https://peerj.com/articles/10610 last-modified: 2021-01-13 description: The healthcare provider profession strongly relies on the ability to care for others’ emotional experiences. To what extent burnout may relate to an actual alteration of this key professional ability has been little investigated. In an experimentally controlled setting, we investigated whether subjective experiences of global burnout or burnout depersonalization (the interpersonal component of burnout) relate to objectively measured alterations in emotion recognition and to what extent such alterations are emotion specific. Healthcare workers (n = 90) completed the Maslach Burnout Inventory and a dynamic emotion recognition task in which faces with neutral emotional expressions gradually changed to display a specific basic emotion (happiness, anger, fear, or sadness). Participants were asked to identify and then classify each displayed emotion. Before the task, a subsample of 46 participants underwent two salivary cortisol assessments. Individuals with global burnout were less accurate at recognizing others’ emotional expressions of anger and fear, tending to misclassify these as happiness, compared to individuals without global burnout. Individuals with high burnout depersonalization were more accurate in recognizing happiness and less accurate in recognizing all negative emotions, with a tendency to misclassify the latter as positive ones, compared to healthcare workers with moderate/low depersonalization. Moreover, individuals with high depersonalization—but not participants with global burnout—were characterized by higher cortisol levels. These results suggest that the subjective burnout experience relates to an actual, but selective, reduction in the recognition of facial emotional expressions, characterized by a tendency to misclassify negative emotional expressions as positive ones, perhaps due to an enhanced seeking of positive social cues. This study adds to the understanding of emotional processing in burnout and paves the way for more nuanced studies on the role of altered processing of threat signals in the development and/or persistence of burnout. creator: Valentina Colonnello creator: Luca Carnevali creator: Paolo Maria Russo creator: Cristina Ottaviani creator: Valeria Cremonini creator: Emanuele Venturi creator: Katia Mattarozzi uri: https://doi.org/10.7717/peerj.10610 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Colonnello et al. title: Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species link: https://peerj.com/articles/10618 last-modified: 2021-01-13 description: This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera HomalosilphaStål, 1874 and MimosilphaBey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided. creator: Shuran Liao creator: Yishu Wang creator: Duting Jin creator: Rong Chen creator: Zongqing Wang creator: Yanli Che uri: https://doi.org/10.7717/peerj.10618 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Liao et al. title: Economic contribution and attitude towards alien freshwater ornamental fishes of pet store owners in Klang Valley, Malaysia link: https://peerj.com/articles/10643 last-modified: 2021-01-13 description: Malaysia is one of the top ten countries in the world that produce freshwater ornamental fishes. This industry can offer better livelihood opportunities to many poor households. However, most of the produced ornamental fishes are alien to Malaysia. In this study, we explore the contribution of alien freshwater fishes to the income of ornamental fish store owners and their attitude towards alien freshwater fishes within Klang Valley, Malaysia. Using a structured questionnaire, we surveyed 70 pet stores out of which 54 (81.42%) store owners responded. Most of the pet store owners were male (72%), Chinese (83%), and the highest educational level was at the secondary level (79%). Most of the pet store owners reported a monthly income of RM 2001–RM 5000 (78%) and were married (73%). Using Chi-square (χ2) test, significant relationships (p < 0.05) existed between the attitude of store owners towards alien ornamental fish species versus educational level (χ2 = 16.424, p = 0.007) and contribution of alien ornamental fishes to the pet store owners’ income (χ2 = 27.266, p = 0.003). Fish sales as the main income source also related significantly with the impact of fish selling business on income level (χ2 = 10.448, p = 0.007). This study showed that the ornamental fish sales contributed over half of the income (51–100%) from the businesses of store owners. Almost half of the respondents (42%) reported that alien ornamental fish was the highest contributor to their income from the ornamental fish sale. While the mismanagement of alien ornamental fishes could give various negative ecological impacts, the socio-economic benefits of these fishes cannot be denied. creator: Abdulwakil Olawale Saba creator: Ahmad Ismail creator: Syaizwan Zahmir Zulkifli creator: Shamarina Shohaimi creator: Mohammad Noor Amal Azmai uri: https://doi.org/10.7717/peerj.10643 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Saba et al. title: Modeling the bidirectional glutamine/ammonium conversion between cancer cells and cancer-associated fibroblasts link: https://peerj.com/articles/10648 last-modified: 2021-01-13 description: Like in an ecosystem, cancer and other cells residing in the tumor microenvironment engage in various modes of interactions to buffer the negative effects of environmental changes. One such change is the consumption of common nutrients (such as glutamine/Gln) and the consequent accumulation of toxic metabolic byproducts (such as ammonium/NH4). Ammonium is a waste product of cellular metabolism whose accumulation causes cell stress. In tumors, it is known that it can be recycled into nutrients by cancer associated fibroblasts (CAFs). Here we present monoculture and coculture growth of cancer cells and CAFs on different substrates: glutamine and ammonium. We propose a mathematical model to aid our understanding. We find that cancer cells are able to survive on ammonium and recycle it to glutamine for limited periods of time. CAFs are able to even grow on ammonium. In coculture, the presence of CAFs results in an improved survival of cancer cells compared to their monoculture when exposed to ammonium. Interestingly, the ratio between the two cell populations is maintained under various concentrations of NH4, suggesting the ability of the mixed cell system to survive temporary metabolic stress and sustain the size and cell composition as a stable entity. creator: Peter Hinow creator: Gabriella Pinter creator: Wei Yan creator: Shizhen Emily Wang uri: https://doi.org/10.7717/peerj.10648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hinow et al. title: Ballroom dancers exhibit a dispositional need for arousal and elevated cerebral cortical activity during preferred melodic recall link: https://peerj.com/articles/10658 last-modified: 2021-01-13 description: BackgroundAlthough the association of human temperament and preference has been studied previously, few investigations have examined cerebral cortical activation to assess brain dynamics associated with the motivation to engage in performance. The present study adopted a personality and cognitive neuroscience approach to investigate if participation in ballroom dancing is associated with sensation-seeking temperament and elevated cerebral cortical arousal during freely chosen musical recall.MethodsPreferred tempo, indicated by tapping speed during melodic recall, and a measure of fundamental disposition or temperament were assessed in 70 ballroom dancers and 71 nondancers. All participants completed a trait personality inventory (i.e., the Chen Huichang 60 Temperaments Inventory) to determine four primary types: choleric, sanguine, phlegmatic and melancholic. Participants separately recalled their favorite musical piece and tapped to it with their index finger for 40 beats using a computer keyboard. A subset of 59 participants (29 ballroom dancers and 30 nondancers) also repeated the same tapping task while electroencephalographic (EEG) activity was recorded.ResultsThe results revealed that the dancers were more extraverted, indicative of a heightened need for arousal, exhibited a preference for faster musical tempo, and exhibited elevated EEG beta power during the musical recall task relative to nondancers. Paradoxically, dancers also showed elevated introversion (i.e., melancholic score) relative to nondancers, which can be resolved by consideration of interactional personality theory if one assumes reasonably that dance performance environment is perceived in a stimulating manner.ConclusionThe results are generally consistent with arousal theory, and suggest that ballroom dancers seek elevated stimulation and, thereby, choose to engage with active and energetic rhythmic auditory stimulation, thus providing the nervous system with the requisite stimulation for desired arousal. These results also suggest an underlying predisposition for engagement in ballroom dance and support the gravitational hypothesis, which propose that personality traits and perception lead to the motivation to engage in specific forms of human performance. creator: Xinhong Jin creator: Yingzhi Lu creator: Bradley D. Hatfield creator: Xiaoyu Wang creator: Biye Wang creator: Chenglin Zhou uri: https://doi.org/10.7717/peerj.10658 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jin et al. title: Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics link: https://peerj.com/articles/10670 last-modified: 2021-01-13 description: MotivationAnalysis of singe cell RNA sequencing (scRNA-seq) typically consists of different steps including quality control, batch correction, clustering, cell identification and characterization, and visualization. The amount of scRNA-seq data is growing extremely fast, and novel algorithmic approaches improving these steps are key to extract more biological information. Here, we introduce: (i) two methods for automatic cell type identification (i.e., without expert curator) based on a voting algorithm and a Hopfield classifier, (ii) a method for cell anomaly quantification based on isolation forest, and (iii) a tool for the visualization of cell phenotypic landscapes based on Hopfield energy-like functions. These new approaches are integrated in a software platform that includes many other state-of-the-art methodologies and provides a self-contained toolkit for scRNA-seq analysis.ResultsWe present a suite of software elements for the analysis of scRNA-seq data. This Python-based open source software, Digital Cell Sorter (DCS), consists in an extensive toolkit of methods for scRNA-seq analysis. We illustrate the capability of the software using data from large datasets of peripheral blood mononuclear cells (PBMC), as well as plasma cells of bone marrow samples from healthy donors and multiple myeloma patients. We test the novel algorithms by evaluating their ability to deconvolve cell mixtures and detect small numbers of anomalous cells in PBMC data.AvailabilityThe DCS toolkit is available for download and installation through the Python Package Index (PyPI). The software can be deployed using the Python import function following installation. Source code is also available for download on Zenodo: DOI 10.5281/zenodo.2533377.Supplementary informationSupplemental Materials are available at PeerJ online. creator: Sergii Domanskyi creator: Alex Hakansson creator: Thomas J. Bertus creator: Giovanni Paternostro creator: Carlo Piermarocchi uri: https://doi.org/10.7717/peerj.10670 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Domanskyi et al. title: The association between serum uric acid and diabetic complications in patients with type 2 diabetes mellitus by gender: a cross-sectional study link: https://peerj.com/articles/10691 last-modified: 2021-01-13 description: BackgroundThe relationship between serum uric acid (SUA) and several diabetic complications or co-morbidities remains a matter of debate. The study aims to explore the association between SUA levels and the prevalence of non-alcoholic fatty liver disease (NAFLD), diabetic retinopathy (DR), diabetic nephropathy (DN) and diabetic peripheral neuropathy (DPN) in patients with type 2 diabetes mellitus (T2DM).MethodsA total of 2,809 participants (1,784 males and 1,025 females) were included in this cross-sectional study. Clinical characteristics and the prevalence of each of the four diseases were analyzed based on gender-specific quartiles of SUA levels. The Pearson correlation analysis and linear-regression analysis were used to access the correlation between SUA levels and clinical characteristics. Furthermore, a binary logistic regression analysis was carried out to determine whether SUA was an independent risk factor for each of the four complications.ResultsSUA levels were positively correlated to BMI, BUN, Scr and TG, but negatively associated with eGFR, HDL, FBG, 2h-PG and HbA1c% for the patients with T2DM. The prevalence of NAFLD and DN, but not DR or DPN, were increased with SUA levels from the first to the fourth quartile. Binary logistic regression further disclosed that SUA was an independent risk factor for NAFLD (ORs Male = 1.002, ∗P = 0.0013; ORs Female = 1.002, ∗P = 0.015) and DN (ORs Male = 1.006, ∗P < 0.001; ORs Female = 1.005, ∗P < 0.001), but not for DR and DPN. After adjustment for the confounders, SUA levels were significantly associated with NAFLD within the 3rd (ORs = 1.829, P = 0.004) and 4th quartile (ORs = 2.064, P = 0.001) for women, but not independently associated with SUA for man. On the other hand, our results revealed increased prevalence of DN for SUA quartile 2 (ORs = 3.643, P = 0.039), quartile 3 (ORs = 3.967, P = 0.024) and quartile 4 (ORs = 9.133, P < 0.001) in men; however, SUA quartiles were significantly associated with DN only for quartile 4 (ORs = 4.083, P = 0.042) in womenConclusionFor patients with T2DM, elevated SUA concentration is an independent risk factor for the prevalence of NAFLD and DN after adjustment for other indicators, but not DR or DPN. creator: Yimeng Hu creator: Qinge Li creator: Rui Min creator: Yingfeng Deng creator: Yancheng Xu creator: Ling Gao uri: https://doi.org/10.7717/peerj.10691 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hu et al. title: Improved salt tolerance of Chenopodium quinoa Willd. contributed by Pseudomonas sp. strain M30-35 link: https://peerj.com/articles/10702 last-modified: 2021-01-13 description: BackgroundPlant-growth-promoting rhizobacteria (PGPR) can promote plant growth and enhance plant tolerance to salt stress. Pseudomonas sp. strain M30-35 might confer abiotic stress tolerance to its host plants. We evaluated the effects of M30-35 inoculation on the growth and metabolite accumulation of Chenopodium quinoa Willd. during salt stress growth conditions.MethodsThe effects of M30-35 on the growth of C. quinoa seedlings were tested under salt stress. Seedling growth parameters measured included chlorophyll content, root activity, levels of plant- phosphorus (P), and saponin content.ResultsM30-35 increased biomass production and root activity compared to non-inoculated plants fertilized with rhizobia and plants grown under severe salt stress conditions. The photosynthetic pigment content of chlorophyll a and b were higher in M30-35-inoculated C. quinoa seedlings under high salt stress conditions compared to non-inoculated seedlings. The stability of P content was also maintained. The content of saponin, an important secondary metabolite in C. quinoa, was increased by the inoculation of M30-35 under 300 mM NaCl conditions.ConclusionInoculation of M30-35 rescues the growth diminution of C. quinoa seedlings under salt stress. creator: Deyu Cai creator: Ying Xu creator: Fei Zhao creator: Yan Zhang creator: Huirong Duan creator: Xiaonong Guo uri: https://doi.org/10.7717/peerj.10702 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cai et al. title: Consistency of dark skeletal muscles in Thai native black-bone chickens (Gallus gallus domesticus) link: https://peerj.com/articles/10728 last-modified: 2021-01-13 description: Black-bone chickens (Gallus gallus domesticus) have become economically valuable, particularly in Southeast Asia as a consequence of popular traditional Chinese medical practices. Chickens with whole body organ darkness are considered to have higher value and are, therefore, more often requested. This research study aimed to investigate the darkness in 34 skeletal muscles of 10 Thai black-bone chickens (five males and five females). The evaluation of muscle darkness was done on two levels: (i) a color chart was employed at the macroanatomical level and (ii) by using melanin pigment to evaluate the structure at the microanatomy level. The results revealed that the accumulation of melanin pigment in the muscle tissue was observed in the endomysium, perimysium and epimysium. With respect to the results of the color chart test, iliotibialis lateralis pars preacetabularis, gastrocnemius, fibularis longus and puboischiofemoralis pars medialis showed the highest degree of darkness, while serratus profundus, pectoralis, iliotibialis cranialis, flexor cruris lateralis, and flexor cruris medialis appeared to be the least dark. In addition, we found that the highest and lowest amounts of melanin pigment was noted in the flexor carpi ulnaris and pectoralis (p < 0.05), respectively; however, there was no significant difference (p > 0.05) observed between the sexes. These results reveal that the 34 specified muscles of black-bone chickens showed uneven distribution of darkness due to the differing accumulations of melanin pigments of each muscle.This information may provide background knowledge for a better understanding of melanin accumulation and lead to breeding improvements in Thai black-bone chickens. creator: Wannapimol Kriangwanich creator: Promporn Piboon creator: Wirakorn Sakorn creator: Kittisak Buddhachat creator: Varankpicha Kochagul creator: Kidsadagon Pringproa creator: Supamit Mekchay creator: Korakot Nganvongpanit uri: https://doi.org/10.7717/peerj.10728 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kriangwanich et al.