title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=602 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Bird diversity-environment relationships in urban parks and cemeteries of the Neotropics during breeding and non-breeding seasons link: https://peerj.com/articles/14496 last-modified: 2022-12-14 description: BackgroundUrbanization will increase in the next decades, causing the loss of green areas and bird diversity within cities. There is a lack of studies at a continental scale analyzing the relationship between urban green areas, such as parks and cemeteries, and bird species richness in the Neotropical region. Bird diversity-environment relationships in urban parks and cemeteries may be influenced by latitudinal gradients or species-area relationships. However, the seasonal variation of species diversity- environment has not been analyzed at a continental scale in the Neotropics.MethodsBird surveys were conducted in 36 cemeteries and 37 parks within 18 Neotropical cities during non-breeding and breeding seasons. Bird diversity was assessed through Hill numbers, focusing on species richness, the effective number of species derived from Shannon index and the Simpson index. Environmental variables included latitude, altitude, and local scale variables such as area size, habitat diversity and pedestrian traffic.ResultsSpecies richness and Shannon diversity were higher during the breeding season, whereas Simpson diversity did not vary between seasons. During both seasons, species richness increased with area size, was negatively related to altitude, and was the highest at 20° latitude. Species richness was also positively related to habitat diversity, pedestrian traffic, and was highest in suburban areas during the non-breeding season. Shannon and Simpson diversity showed significant relationships with habitat diversity and area size during the breeding season. Bird diversity was similar between parks and cemeteries.DiscussionOur results showed that urban parks and cemeteries have similar roles in conserving urban bird diversity in Neotropical cities. However, species diversity-environment relations at the continental scale varied between seasons, highlighting the importance of conducting annual studies. creator: Lucas M. Leveau creator: Mariana Lucia Bocelli creator: Sergio Gabriel Quesada-Acuña creator: César González-Lagos creator: Pablo Gutiérrez Tapia creator: Gabriela Franzoi Dri creator: Carlos A. Delgado-V. creator: Álvaro Garitano-Zavala creator: Jackeline Campos creator: Yanina Benedetti creator: Rubén Ortega-Álvarez creator: Antonio Isain Contreras Rodríguez creator: Daniela Souza López creator: Carla Suertegaray Fontana creator: Thaiane Weinert da Silva creator: Sarah Sandri Zalewski Vargas creator: María Cecília Barbosa Toledo creator: Juan Andres Sarquis creator: Alejandro Giraudo creator: Ada Lilian Echevarria creator: María Elisa Fanjul creator: Maria Valeria Martínez creator: Josefina Haedo creator: Luis Gonzalo Cano Sanz creator: Yuri Peña creator: Viviana Fernandez creator: Verónica Marinero creator: Vinícius Abilhoa creator: Rafael Amorin creator: Juan Fernando Escobar Ibáñez creator: María Dolores Juri creator: Sergio Camín creator: Luis Marone creator: Augusto João Piratelli creator: Alexandre Gabriel Franchin creator: Larissa Crispim creator: Federico Morelli uri: https://doi.org/10.7717/peerj.14496 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Leveau et al. title: EcoCountHelper: an R package and analytical pipeline for the analysis of ecological count data using GLMMs, and a case study of bats in Grand Teton National Park link: https://peerj.com/articles/14509 last-modified: 2022-12-14 description: Here we detail the use of an R package, ‘EcoCountHelper’, and an associated analytical pipeline aimed at making generalized linear mixed-effects model (GLMM)-based analysis of ecological count data more accessible. We recommend a GLMM-based analysis workflow that allows the user to (1) employ selection of distributional forms (Poisson vs negative binomial) and zero-inflation (ZIP and ZINB, respectively) using AIC and variance-mean plots, (2) examine models for goodness-of-fit using simulated residual diagnostics, (3) interpret model results via easy to understand outputs of changes in predicted responses, and (4) compare the magnitude of predictor variable effects via effects plots. Our package uses a series of easy-to-use functions that can accept both wide- and long-form multi-taxa count data without the need for programming experience. To demonstrate the utility of this approach, we use our package to model acoustic bat activity data relative to multiple landscape characteristics in a protected area (Grand Teton National Park), which is threatened by encroaching disease—white nose syndrome. Global threats to bat conservation such as disease and deforestation have prompted extensive research to better understand bat ecology. Notwithstanding these efforts, managers operating on lands crucial to the persistence of bat populations are often equipped with too little information regarding local bat activity to make informed land-management decisions. In our case study in the Tetons, we found that an increased prevalence of porous buildings increases activity levels of Eptesicus fuscus and Myotis volans; Myotis lucifugus activity decreases as distance to water increases; and Myotis volans activity increases with the amount of forested area. By using GLMMs in tandem with ‘EcoCountHelper’, managers without advanced programmatic or statistical expertise can assess the effects of landscape characteristics on wildlife in a statistically-robust framework. creator: Hunter J. Cole creator: Dylan GE Gomes creator: Jesse R. Barber uri: https://doi.org/10.7717/peerj.14509 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cole et al. title: Transcriptomic analyses provide new insights into green and purple color pigmentation in Rheum tanguticum medicinal plants link: https://peerj.com/articles/14265 last-modified: 2022-12-13 description: BackgroundRheum tanguticum Maxim. ex Balf is a traditional Chinese medicinal plant that is commonly used to treat many ailments. It belongs to the Polygonacae family and grows in northwest and southwest China. At high elevations, the color of the plant’s young leaves is purple, which gradually changes to green during the growth cycle. Anthraquinone, which is known for various biological activities, is the main bioactive compound in R. tanguticum. Although a significant amount of research has been done on R. tanguticum in the past, the lack of transcriptome data limits our knowledge of the gene regulatory networks involved in pigmentation and in the metabolism of bioactive compounds in Rheum species.MethodsTo fill this knowledge gap, we generated high-quality RNA-seq data and performed multi-tissue transcriptomic analyses of R. tanguticum.ResultsWe found that three chlorophyll degradation enzymes (RtPPH, RtPao and RtRCCR) were highly expressed in purple samples, which suggests that the purple pigmentation is mainly due to the effects of chlorophyll degradation. Overall, these data may aid in drafting the transcriptional network in the regulation and biosynthesis of medicinally active compounds in the future. creator: Haixia Chen creator: Tsan-Yu Chiu creator: Sunil Kumar Sahu creator: Haixi Sun creator: Jiawen Wen creator: Jianbo Sun creator: Qiyuan Li creator: Yangfan Tang creator: Hong Jin creator: Huan Liu uri: https://doi.org/10.7717/peerj.14265 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Determination of PaO2/FiO2 after 24 h of invasive mechanical ventilation and ΔPaO2/FiO2 at 24 h as predictors of survival in patients diagnosed with ARDS due to COVID-19 link: https://peerj.com/articles/14290 last-modified: 2022-12-13 description: IntroductionAcute respiratory distress syndrome (ARDS) due to Coronavirus Disease 2019 (COVID-19) causes high mortality. The objective of this study is to determine whether the arterial pressure of oxygen/inspiratory fraction of oxygen (PaO2/FiO2) 24 h after invasive mechanical ventilation (IMV) and the difference between PaO2/FiO2 at 24 h after IMV and PaO2/FiO2 before admission to IMV (ΔPaO2/FiO2 24 h) are predictors of survival in patients with ARDS due to COVID-19.MethodsA retrospective cohort study was conducted that included patients with ARDS due to COVID-19 in IMV admitted to the intensive care unit (ICU) of a hospital in southern Peru from April 2020 to April 2021. The ROC curves and the Youden index were used to establish the cut-off point for PaO2/FiO2 at 24 h of IMV and ΔPaO2/FiO2 at 24 h associated with mortality. The association with mortality was determined by Cox regression, calculating the crude (cHR) and adjusted (aHR) risk ratios, with their respective 95% confidence intervals (95% CI).ResultsTwo hundred patients were analyzed. The average age was 54.29 years, 79% were men, and 25.5% (n = 51) died. The cut-off point calculated for PaO2/FiO2 24 h after IMV and ΔPaO2/FiO2 24 h was 222.5 and 109.5, respectively. Those participants with a value below the cut-off point of ΔPaO2/FiO2 24 h and PaO2/FiO2 24 h after IMV had higher mortality, aHR = 3.32 (CI 95% [1.82–6.07]) and aHR = 2.87 (CI 95% [1.48–5.57]) respectively.ConclusionPaO2/FiO2 24 h after IMV and ΔPaO2/FiO2 24 h in patients diagnosed with ARDS due to COVID-19 on IMV were associated with higher hospital mortality. These findings are helpful to identify those patients with a higher risk of dying on admission to the ICU. creator: Miguel Hueda-Zavaleta creator: Cesar Copaja-Corzo creator: Brayan Miranda-Chávez creator: Rodrigo Flores-Palacios creator: Jonathan Huanacuni-Ramos creator: Juan Mendoza-Laredo creator: Diana Minchón-Vizconde creator: Juan Carlos Gómez de la Torre creator: Vicente A. Benites-Zapata uri: https://doi.org/10.7717/peerj.14290 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hueda-Zavaleta et al. title: Predicting RNA secondary structure by a neural network: what features may be learned? link: https://peerj.com/articles/14335 last-modified: 2022-12-13 description: Deep learning is a class of machine learning techniques capable of creating internal representation of data without explicit preprogramming. Hence, in addition to practical applications, it is of interest to analyze what features of biological data may be learned by such models. Here, we describe PredPair, a deep learning neural network trained to predict base pairs in RNA structure from sequence alone, without any incorporated prior knowledge, such as the stacking energies or possible spatial structures. PredPair learned the Watson-Crick and wobble base-pairing rules and created an internal representation of the stacking energies and helices. Application to independent experimental (DMS-Seq) data on nucleotide accessibility in mRNA showed that the nucleotides predicted as paired indeed tend to be involved in the RNA structure. The performance of the constructed model was comparable with the state-of-the-art method based on the thermodynamic approach, but with a higher false positives rate. On the other hand, it successfully predicted pseudoknots. t-SNE clusters of embeddings of RNA sequences created by PredPair tend to contain embeddings from particular Rfam families, supporting the predictions of PredPair being in line with biological classification. creator: Elizaveta I. Grigorashvili creator: Zoe S. Chervontseva creator: Mikhail S. Gelfand uri: https://doi.org/10.7717/peerj.14335 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Grigorashvili et al. title: Experience of COVID-19 disease and fear of the SARS-CoV-2 virus among Polish students link: https://peerj.com/articles/14356 last-modified: 2022-12-13 description: BackgroundThe SARS-CoV-2 virus pandemic has significantly affected individuals and entire societies. It has caused a number of adverse consequences for public health. It has contributed to lower average life expectancy and significantly reduced the sense of health security. It has affected not only physical but also mental health. COVID-19 infections have become so common in many countries, including Poland, that almost every member of society has either experienced it themselves or has a family member or friend who have been affected by the disease. The investigations undertaken in the article concern the fear of COVID-19 infection among Polish university students, determined by the experience of the disease –whether direct or among loved ones.MethodsAn online survey was conducted with 851 students. It took place between 1 and 15 March 2021, a year after detection of the first case of infection with the virus in Poland. The aim of the study was to find out about the relationship between the experience of COVID-19 disease (whether direct or among people close to the respondent) and fear of this disease among university students in Poland. The analysis used intergroup comparison tests (Mann–Whitney U Test and t-test).ResultsThe results indicate that the level of fear of COVID-19 among Polish university students was low (M = 1.98; SD = .49), with women (M = 2.04; SD = .75) presenting statistically higher (t (620.46) = 3.05; p = .002) fear than men (M = 1.87; SD = .74). The situation of the respondent having had a close person fall ill with COVID-19 or die as a result of coronavirus infection was found to be significant for the level of experienced fear of COVID-19 in the studied group (t (469.46) = −2.98; p = .003).ConclusionsThe significantly higher level of fear in the group of young people who knew someone close with severe (fatal) COVID-19 disease indicates that psychological support may be more significant for such people than for individuals who have not experienced such a situation. A similar conclusion can be formulated taking into account the gender criterion, as the results make it possible to predict that women expect more support in a pandemic situation. creator: Elżbieta Turska creator: Natalia Stępień-Lampa creator: Paweł Grzywna uri: https://doi.org/10.7717/peerj.14356 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Turska et al. title: Animal movement ecology in India: insights from 2011–2021 and prospective for the future link: https://peerj.com/articles/14401 last-modified: 2022-12-13 description: The field of animal movement ecology has advanced by leaps and bounds in the past few decades with the advent of sophisticated technology, advanced analytical tools, and multiple frameworks and paradigms to address key ecological problems. Unlike the longer history and faster growth of the field in North America, Europe, and Africa, movement ecology in Asia has only recently been gaining momentum. Here, we provide a review of the field from studies based in India over the last 11 years (2011–2021) curated from the database, Scopus, and search engine, Google Scholar. We identify current directions in the research objectives, taxa studied, tracking technology and the biogeographic regions in which animals were tracked, considering the years since the last systematic review of movement ecology research in the country. As an indication of the growing interest in this field, there has been a rapid increase in the number of publications over the last decade. Class Mammalia continues to dominate the taxa tracked, with tiger and leopard being the most common species studied across publications. Invertebrates and other small and medium-sized animals, as well as aquatic animals, in comparison, are understudied and remain among the important target taxa for tracking in future studies. As in the previous three decades, researchers have focussed on characterising home ranges and habitat use of animals. There is, however, a notable shift to examine the movement decision of animals in human-modified landscapes, although efforts to use movement ecology to understand impacts of climate change remain missing. Given the biogeographic and taxonomic diversity of India, and the fact that the interface between anthropogenic activity and wildlife interactions is increasing, we suggest ways in which the field of movement ecology can be expanded to facilitate ecological insights and conservation efforts. With the advancement of affordable technologies and the availability of analytical tools, the potential to expand the field of movement ecology, shift research foci, and gain new insights is now prime. creator: Harish Prakash creator: R. Suresh Kumar creator: Bibhuti Lahkar creator: Raman Sukumar creator: Abi T. Vanak creator: Maria Thaker uri: https://doi.org/10.7717/peerj.14401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Prakash et al. title: Hygiene of housing conditions and proinflammatory signals alter gene expressions in porcine adipose tissues and blood cells link: https://peerj.com/articles/14405 last-modified: 2022-12-13 description: Adipose tissue is an organ with metabolic, endocrine and immune functions. In this tissue, the expressions of genes associated with several metabolic pathways, including lipid metabolism, have been shown to be affected by genetic selection for feed efficiency, an important trait to consider in livestock. We hypothesized that the stimulation of immune system caused by poor hygiene conditions of housing impacts the molecular and cellular features of adipose tissue and that the impact may differ between pigs that diverge in feed efficiency. At the age of 12 weeks, Large White pigs from two genetic lines divergent for residual feed intake (RFI) were housed in two contrasting hygiene conditions (good vs poor). After six weeks of exposure, pigs were slaughtered (n = 36). Samples of blood, subcutaneous (SCAT) and perirenal (PRAT) adipose tissues were collected for cell response and gene expression investigations. The decrease in the relative weight of PRAT was associated with a decline in mRNA levels of FASN, ME, LCN2 and TLR4 (P < 0.05) in pigs housed in poor conditions compared with pigs housed in good conditions for both RFI lines. In SCAT, the expressions of only two key genes (PPARG and TLR4) were significantly affected by the hygiene of housing conditions. Besides, the mRNA levels of both LCN2 and GPX3 were influenced by the RFI line (P < 0.05). Because we suspected an effect of poor hygiene at the cellular levels, we investigated the differentiation of stromal vascular cells isolated from SCAT in vitro in the absence or presence of a pro-inflammatory cytokine, Tumor Necrosis Factor-α (TNF-α). The ability of these cells to differentiate in the absence or presence of TNF-α did not differ among the four groups of animals (P > 0.05). We also investigated the expressions of genes involved in the immune response and lipid metabolism in whole blood cells cultured in the absence and presence of LPS. The hygiene conditions had no effect but, the relative expression of the GPX3 gene was higher (P < 0.001) in high RFI than in low RFI pigs while the expressions of IL-10 (P = 0.027), TGFβ1 (P = 0.023) and ADIPOR2 (P = 0.05) genes were lower in high RFI than in low RFI pigs. Overall, the current study indicates that the hygiene of housing had similar effects on both RFI lines on the expression of genes in adipose tissues and on the features of SCAT adipose cells and whole blood cells in response to TNF-α and LPS. It further demonstrates that the number of genes with expression impacted by housing conditions was higher in PRAT than in SCAT. It suggests a depot-specific response of adipose tissue to the current challenge. creator: Audrey Quéméner creator: Marie-Hélène Perruchot creator: Frédéric Dessauge creator: Annie Vincent creator: Elodie Merlot creator: Nathalie Le Floch creator: Isabelle Louveau uri: https://doi.org/10.7717/peerj.14405 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Quéméner et al. title: Transcriptome and metabolome analyses reveal anthocyanins pathways associated with fruit color changes in plum (Prunus salicina Lindl.) link: https://peerj.com/articles/14413 last-modified: 2022-12-13 description: Plum (Prunus salicina Lindl.) is one of the most widely cultivated and important fruit trees in temperate and cold regions. Fruit color is a significant trait relating to fruit quality in plum. However, its development mechanism has not been studied from the aspects of transcriptional regulation and metabolomic progress. To reveal the mechanism of fruit color developments in plums, we selected the fruits of two plum cultivars, ‘Changli84’ (Ch84, red fruit) and ‘Dahuangganhe’ (D, yellow fruit) as plant materials for transcriptome sequencing and metabolomic analysis were performed. Based on the data of transcriptome and metabolome at three fruit developmental stages, young fruit stage, color-change stage, and maturation stage, we identified 2,492 differentially expressed genes (DEGs) and 54 differential metabolites (DMs). The KEGG analysis indicated that “Flavonoid biosynthesis” was significantly enriched during three fruit development stages. Some DEGs in the “Flavonoid biosynthesis” pathway, had opposite trends between Ch84 and D, including chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR) and flavonol synthase (FLS). Also, the genes encoding MYB–bHLH–WD (MBW) protein complexes, especially MYBs and bHLHs, showed a close relationship with plum fruit color. In the current study, DMs like procyanidin B1, cyanidin 3-glucoside, and cyanidin-3-O-alpha-arabinopyranoside were key pigments (or precursors), while the carotene and carotenoids did not show key relationships with fruit color. In conclusion, the anthocyanins dominate the color change of plum fruit. Carotenes and carotenoids might be related to the color of plum fruit, but do not play a dominate role. creator: Lei Chen creator: Xuesong Wang creator: Long Cui creator: Yuebo Li creator: Yinghai Liang creator: Shanshan Wang creator: Yubo Chen creator: Lan Zhou creator: Yanbo Zhang creator: Feng Li uri: https://doi.org/10.7717/peerj.14413 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Diversification and historical demography of Haloxylon ammodendron in relation to Pleistocene climatic oscillations in northwestern China link: https://peerj.com/articles/14476 last-modified: 2022-12-13 description: The influence of aridification and climatic oscillations on the genetic diversity and evolutionary processes of organisms during the Quaternary in northwestern China is examined using Haloxylon ammodendron. Based on the variation of two cpDNA regions (trnS-trnG and trnV) and one nDNA sequence (ITS1-ITS4) in 420 individuals from 36 populations, the spatial genetic structure and demographic history of H. ammodendron in arid China is examined. Median-joining network and Bayesian inference trees enabled the identification of three diverged lineages within H. ammodendron from 24 different haplotypes and 16 ribotypes, distributed across western (Xinjiang), eastern (Gansu and Inner Mongolia) and southern (Qinghai) regions. AMOVA analysis demonstrated that more than 80% of observed genetic variation related to lineage split was based on cpDNA and nDNA variation. Allopatric divergence among the three groups was mainly triggered by geographical isolation due to Xingxingxia rock and uplift of the Qilian Mountains during the Quaternary. Local adaptive differentiation among western, eastern and southern groups occurred due to gene flow obstruction resulting from arid landscape fragmentation accompanied by local environmental heterogeneity of different geographical populations. The southern margin of the Junggar Basin and the Tengger Desert possibly served as two independent glacial refugia for H. ammodendron. The distribution of genetic variation, coupled with SDMs and LCP results, indicated that H. ammodendron probably moved northward along the Junggar Basin and westward along Tengger Desert at the end of the last glacial maximum; postglacial re-colonization was probably westward and southward along the Hexi Corridor. creator: Yuting Chen creator: Songmei Ma creator: Dan Zhang creator: Bo Wei creator: Gang Huang creator: Yunling Zhang creator: Benwei Ge uri: https://doi.org/10.7717/peerj.14476 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al.