title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1094 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A cross-sectional assessment of the relationship between sedative medication and anticholinergic medication use and the movement behaviour of older adults living in residential aged care link: https://peerj.com/articles/9605 last-modified: 2020-07-24 description: ObjectivesMedications with anticholinergic or sedative effects are frequently used by older people but can increase risk of falls and adverse events; however, less is known about their effect on movement behaviour. Here we examine the cross-sectional association between medication use and movement behaviour in older adults living in residential aged care.Materials and MethodsTwenty-eight older adults living in residential aged care in metropolitan Australia participated. Medication data were collected from participants’ medical charts and sedative load and anticholinergic burden were determined. Seven-day movement behaviour was objectively assessed by a wrist-worn triaxial accelerometer. Raw accelerations were converted to sleep, sedentary time, and time in light, moderate, and moderate-to-vigorous physical activity. To explore the relationship between medication and movement behaviour, Spearman’s Rho correlations were conducted, as the data were not normally distributed.ResultsAnalyses indicated that while anticholinergic burden was not associated with movement behaviour, sedative load was negatively correlated with a number of variables, accounting for 14% variance in moderate-to-vigorous physical activity (MVPA), and 17% in the bout length of MVPA (p < .02).ConclusionThe findings of this study showed a negative association between sedative load, due to medicines, and an individual’s movement behaviour. The impact of this could be a reduction in the ability of this population to maintain or improve their functional mobility, which may overshadow any benefits of the medicine in some circumstances. creator: Gaynor Parfitt creator: Dannielle Post creator: Lisa Kalisch Ellett creator: Renly Lim creator: Alison Penington creator: Megan Corlis creator: Elizabeth Roughead uri: https://doi.org/10.7717/peerj.9605 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Parfitt et al. title: Disentangling biological variability and taphonomy: shape analysis of the limb long bones of the sauropodomorph dinosaur Plateosaurus link: https://peerj.com/articles/9359 last-modified: 2020-07-23 description: Sauropodomorph dinosaurs constitute a well-studied clade of dinosaurs, notably because of the acquisition of gigantism within this group. The genus Plateosaurus is one of the best-known sauropodomorphs, with numerous remains from various localities. Its tumultuous taxonomic history suggests the relevance of addressing its intrageneric shape variability, mixed with taphonomic modifications of the original bone shape. Here we investigate quantitatively the morphological variation of Plateosaurus occurring at the genus level by studying the shape variation of a sample of limb long bones. By means of 3D geometric morphometrics, the analysis of the uncorrelated variation permits separation of the variation estimated as obviously taphonomically influenced from the more biologically plausible variation. Beyond the dominant taphonomic signal, our approach permits interpretation of the most biologically plausible features, even on anatomical parts influenced by taphonomic deformations. Those features are thus found on a quantitative basis from the variation of samples containing fossil specimens, by taking the impact of taphonomy into account, which is paramount in order to avoid making biologically ambiguous interpretations. creator: Rémi Lefebvre creator: Ronan Allain creator: Alexandra Houssaye creator: Raphaël Cornette uri: https://doi.org/10.7717/peerj.9359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lefebvre et al. title: Morphological changes in the lower Lancang River due to extensive human activities link: https://peerj.com/articles/9471 last-modified: 2020-07-23 description: BackgroundMorphological changes in river beds determine the risk for soil erosion within floodplain areas. At present, little is known about river morphological changes in high-altitude mountainous area influenced by extensive human activities. The study has important reference value for clarifying the morphological changes of mountainous rivers due to extensive human activities.MethodsBased on the long-term multi-source remote sensing image data, we analyzed morphological changes in the lower Lancang River (LCR) in Southwest China at regional and local scales, and determined their influencing factors. Visual interpretation is used to extract the information and unify the interpretation standards of various localities, mainly including water bodies, sandbars, shorelines and beaches. Based on high-resolution remote sensing images, we analyzed the planforms, erosion and accretion conditions in Jinghongba (JHB) reach and Ganlanba (GLB) reach.ResultsOur results showed that: (1) during 1993–2016, the planforms of Jinghongba and Ganlanba in the wide valley of the lower LCR changed significantly, (2) In the interval 1993 to 2016, the JHB reach exhibited extensive erosion, with the right bank more eroded seriously than the left bank, and an erosion area of 0.36 km2. The erosion area of the GLB reach was 0.33 km2, with accretion area of 0.61 km2. The right bank was dominated by erosion, while the left bank by sedimentation; (3) Morphological changes in JHB and GLB reches were the result of the combined effects of cascade hydropower development, river regulation, and sand-mining in the river. The results improved the understanding of riverbed evolution, and could help guide sediment management in mountainous areas influenced by extensive human activities. creator: Peijia Wang creator: Kaidao Fu creator: Jiangcheng Huang creator: Xingwu Duan creator: Zaizhi Yang uri: https://doi.org/10.7717/peerj.9471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: The rule-based insensitivity effect: a systematic review link: https://peerj.com/articles/9496 last-modified: 2020-07-23 description: BackgroundAdherence to inaccurate rules has been viewed as a characteristic of human rule-following (i.e., the rule-based insensitivity effect; RBIE) and has been thought to be exacerbated in individuals suffering from clinical conditions. This review intended to systematically examine these claims in adult populations.MethodologyWe screened 1464 records which resulted in 21 studies that were deemed eligible for inclusion. Each of these studies was examined to determine: (1) if there is evidence for the RBIE in adults and (2) if this effect is larger in those suffering from psychological problems compared to their non-suffering counterparts. In addition, we investigated how (3) different operationalizations of the RBIE, and (4) the external validity and risks of bias of the experimental work investigating this effect, might influence the conclusions that can be drawn from the current systematic review.Results(1) Out of the 20 studies that were relevant for examining if evidence exists for the RBIE in adults, only 11 were eligible for vote counting. Results showed that after the contingency change, the rule groups were more inclined to demonstrate behavior that was reinforced before the change, compared to their non-instructed counterparts. Critically, however, none of these studies examined if their no-instructions group was an adequate comparison group. As a result, this made it difficult to determine whether the effects that were observed in the rule groups could be attributed to the rules or instructions that were manipulated in those experiments. (2) The single study that was relevant for examining if adults suffering from psychological problems demonstrated larger levels of the RBIE, compared to their non-clinical counterparts, was not eligible for vote counting. As a result, no conclusions could be drawn about the extent to which psychological problems moderated the RBIE in that study. (3) Similar procedures and tasks have been used to examine the RBIE, but their precise parameters differ across studies; and (4) most studies report insufficient information to evaluate all relevant aspects affecting their external validity and risks of bias.ConclusionsDespite the widespread appeal that the RBIE has enjoyed, this systematic review indicates that, at present, only preliminary evidence exists for the idea that adults demonstrate the RBIE and no evidence is available to assume that psychological problems exacerbate the RBIE in adults.The systematic review was registered in PROSPERO (CRD42018088210). creator: Ama Kissi creator: Colin Harte creator: Sean Hughes creator: Jan De Houwer creator: Geert Crombez uri: https://doi.org/10.7717/peerj.9496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kissi et al. title: Analysis of prognostic genes in the tumor microenvironment of lung adenocarcinoma link: https://peerj.com/articles/9530 last-modified: 2020-07-23 description: BackgroundPrognostic genes in the tumor microenvironment play an important role in immune biological processes and the response of cancer to immunotherapy. Thus, we aimed to assess new biomarkers that are associated with immune/stromal cells in lung adenocarcinomas (LUAD) using the ESTIMATE algorithm, which also significantly affects the prognosis of cancer.MethodsThe RNA sequencing (RNA-Seq) and clinical data of LUAD were downloaded from the the Cancer Genome Atlas (TCGA ). The immune and stromal scores were calculated for each sample using the ESTIMATE algorithm. The LUAD gene chip expression profile data and the clinical data (GSE37745, GSE11969, and GSE50081) were downloaded from the Gene Expression Omnibus (GEO) for subsequent validation analysis. Differentially expressed genes were calculated between high and low score groups. Univariate Cox regression analysis was performed on differentially expressed genes (DEGs) between the two groups to obtain initial prognosis genes. These were verified by three independent LUAD cohorts from the GEO database. Multivariate Cox regression was used to identify overall survival-related DEGs. UALCAN and the Human Protein Atlas were used to analyze the mRNA /protein expression levels of the target genes. Immune cell infiltration was evaluated using the Tumor Immune Estimation Resource (TIMER) and CIBERSORT methods, and stromal cell infiltration was assessed using xCell.ResultsIn this study, immune scores and stromal scores are significantly associated with the clinical characteristics of LUAD, including T stage, M stage, pathological stage, and overall survival time. 530 DEGs (18 upregulated and 512 downregulated) were found to coexist in the difference analysis with the immune scores and stromal scores subgroup. Univariate Cox regression analysis showed that 286 of the 530 DEGs were survival-related genes (p < 0.05). Of the 286 genes initially identified, nine prognosis-related genes (CSF2RB, ITK, FLT3, CD79A, CCR4, CCR6, DOK2, AMPD1, and IGJ) were validated from three separate LUAD cohorts. In addition, functional analysis of DEGs also showed that various immunoregulatory molecular pathways, including regulation of immune response and the chemokine signaling pathways, were involved. Five genes (CCR6, ITK, CCR4, DOK2, and AMPD1) were identified as independent prognostic indicators of LUAD in specific data sets. The relationship between the expression levels of these genes and immune genes was assessed. We found that CCR6 mRNA and protein expression levels of LUAD were greater than in normal tissues. We evaluated the infiltration of immune cells and stromal cells in groups with high and low levels of expression of CCR6 in the TCGA LUAD cohort. In summary, we found a series of prognosis-related genes that were associated with the LUAD tumor microenvironment. creator: Zhan-yu Xu creator: Mengli Zhao creator: Wenjie Chen creator: Kun Li creator: Fanglu Qin creator: Wei-wei Xiang creator: Yu Sun creator: Jiangbo Wei creator: Li-qiang Yuan creator: Shi-kang Li creator: Sheng-hua Lin uri: https://doi.org/10.7717/peerj.9530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xu et al. title: Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) link: https://peerj.com/articles/9552 last-modified: 2020-07-23 description: Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323–25,369 bp each) separated by a large single-copy (LSC) region (86,510–86,716 bp) and a small single-copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65–0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species. creator: Furrukh Mehmood creator: Abdullah creator: Zartasha Ubaid creator: Iram Shahzadi creator: Ibrar Ahmed creator: Mohammad Tahir Waheed creator: Peter Poczai creator: Bushra Mirza uri: https://doi.org/10.7717/peerj.9552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mehmood et al. title: Outstanding performance of an invasive alien tree Bischofia javanica relative to native tree species and implications for management of insular primary forests link: https://peerj.com/articles/9573 last-modified: 2020-07-23 description: Invasive alien tree species can exert severe impacts, especially in insular biodiversity hotspots, but have been inadequately studied. Knowledge of the life history and population trends of an invasive alien tree species is essential for appropriate ecosystem management. The invasive tree Bischofia javanica has overwhelmed native trees on Haha-jima Island in the Ogasawara Islands, Japan. We explored forest community dynamics 2 years after a typhoon damaged the Sekimon primary forests on Haha-jima Island, and predicted the rate of population increase of B. javanica using a logistic model from forest dynamics data for 19 years. During the 2 years after the typhoon, only B. javanica increased in population size, whereas populations of native tree species decreased. Stem diameter growth of B. javanica was more rapid than that of other tree species, including native pioneer trees. Among the understory stems below canopy trees of other species, B. javanica grew most rapidly and B. javanica canopy trees decreased growth of the dominant native Ardisia sieboldii. These competitive advantages were indicated to be the main mechanism by which B. javanica replaces native trees. The logistic model predicted that B. javanica would reach 30% of the total basal area between 2017 (in the eastern plot adjacent to a former B. javanica plantation) and 2057 (in the western plot distant from the plantation site), which is a maximum percentage allowing to eradicate under the present guideline of the National Forest. The results suggest immediate removal of B. javanica is required to preserve native biodiversity in these forests. creator: Tetsuto Abe creator: Nobuyuki Tanaka creator: Yoshikazu Shimizu uri: https://doi.org/10.7717/peerj.9573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abe et al. title: WHONDRS-GUI: a web application for global survey of surface water metabolites link: https://peerj.com/articles/9277 last-modified: 2020-07-22 description: BackgroundThe Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created.ResultsThe web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811, which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server (https://xmlin.shinyapps.io/whondrs/). creator: Xinming Lin creator: Huiying Ren creator: Amy E. Goldman creator: James C. Stegen creator: Timothy D. Scheibe uri: https://doi.org/10.7717/peerj.9277 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Battelle Memorial Institute title: Antimicrobial stewardship in remote primary healthcare across northern Australia link: https://peerj.com/articles/9409 last-modified: 2020-07-22 description: BackgroundThe high burden of infectious disease and associated antimicrobial use likely contribute to the emergence of antimicrobial resistance in remote Australian Aboriginal communities. We aimed to develop and apply context-specific tools to audit antimicrobial use in the remote primary healthcare setting.MethodsWe adapted the General Practice version of the National Antimicrobial Prescribing Survey (GP NAPS) tool to audit antimicrobial use over 2–3 weeks in 15 remote primary healthcare clinics across the Kimberley region of Western Australia (03/2018–06/2018), Top End of the Northern Territory (08/2017–09/2017) and far north Queensland (05/2018–06/2018). At each clinic we reviewed consecutive clinic presentations until 30 presentations where antimicrobials had been used were included in the audit. Data recorded included the antimicrobials used, indications and treating health professional. We assessed the appropriateness of antimicrobial use and functionality of the tool.ResultsWe audited the use of 668 antimicrobials. Skin and soft tissue infections were the dominant treatment indications (WA: 35%; NT: 29%; QLD: 40%). Compared with other settings in Australia, narrow spectrum antimicrobials like benzathine benzylpenicillin were commonly given and the appropriateness of use was high (WA: 91%; NT: 82%; QLD: 65%). While the audit was informative, non-integration with practice software made the process manually intensive.ConclusionsPatterns of antimicrobial use in remote primary care are different from other settings in Australia. The adapted GP NAPS tool functioned well in this pilot study and has the potential for integration into clinical care. Regular stewardship audits would be facilitated by improved data extraction systems. creator: Will Cuningham creator: Lorraine Anderson creator: Asha C. Bowen creator: Kirsty Buising creator: Christine Connors creator: Kathryn Daveson creator: Joanna Martin creator: Stacey McNamara creator: Bhavini Patel creator: Rodney James creator: John Shanks creator: Kerr Wright creator: Trent Yarwood creator: Steven YC Tong creator: Jodie McVernon uri: https://doi.org/10.7717/peerj.9409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cuningham et al. title: Salivary proteome of a Neotropical primate: potential roles in host defense and oral food perception link: https://peerj.com/articles/9489 last-modified: 2020-07-22 description: BackgroundSaliva contains a very complex mixture of proteins for defense against microbiological pathogens and for oral food perception. Howler monkeys are Neotropical primates that can consume a mostly leaf diet. They are well known to thrive in highly disturbed habitats where they may cope with a diversity of dietary challenges and infection risks. We aimed to describe the salivary proteome of howlers to contribute to better understanding of their physiology.MethodsWe analyzed the salivary proteins of wild black howler monkeys (Alouatta pigra), by SDS-PAGE-1-D and Nano LC-MS/MS and categorized them by their function involved in host defense and oral food perception.ResultsOur proteomic analysis identified 156 proteins in howler saliva including a number of host defense peptides that are the first line of defense in mammals, such as defensin, cathelicidin, dermcidin, and lactotransferrin, and proteins with anti-bacterial, anti-fungal, and anti-viral capacity, such as IgA, IgG, IgM, BPI, salivary heat shock 70 kDa protein, beta-2-microbulin, and protein S-100. We also identified key proteins necessary for taste perception, including salivary carbonic anhydrase VI, cystatin D, IgA, and fatty acid-binding protein. Proteins to detect astringent foods were identifying, including four members of cystatins (A, B, C and D), lactoperoxidase, and histidine-rich proteins. No chitinase and amylase were identified as would be expected because howlers do not eat insects and little starch. These findings provide basic information to future studies in oral biology, ingestive physiology, and physiological ecology of mammals and non-human primates. creator: Fabiola Carolina Espinosa-Gómez creator: Eliel Ruíz-May creator: Juan Carlos Serio-Silva creator: Colin A. Chapman uri: https://doi.org/10.7717/peerj.9489 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Espinosa-Gómez et al.