title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1104 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In or out: Response slowing across housing conditions as a measure of affect in three Western lowland gorillas (Gorilla gorilla gorilla) link: https://peerj.com/articles/9525 last-modified: 2020-07-10 description: BackgroundIndividuals experiencing negative affect have shown response slowing, a longer latency to respond in relation to baseline, when presented with aversive stimuli. We assessed response slowing in three male gorillas housed in a bachelor group as a function of daytime and nighttime housing arrangements.MethodsIn both experiments, three gorillas were rewarded for touching a single image (baseline, non-threatening gorilla or threatening gorilla) on a touchscreen. In Experiment One, they completed 48 50-trial sessions across combinations of three nested daytime and three nighttime conditions. In Experiment Two, they completed eight 50-trial sessions with novel stimuli across two daytime conditions, which were nested within two nighttime conditions. Housing conditions represented different amounts of space and degree of choice. We predicted that the gorillas would show response slowing to threatening stimuli when space and choice were restricted.ResultsWe did not observe response slowing in Experiment One, although daytime and nighttime conditions interacted to predict response latencies. The gorillas responded more slowly when they had access to indoors and outdoors overnight compared to when they were in their stalls or together in an indoor habitat, but only if they had been given access to both indoors and outdoors or locked in the indoor habitat the day before. In Experiment Two, the gorillas did show response slowing to threatening stimuli, but this pattern did not interact with housing conditions. Our results, although limited by a small sample, are somewhat consistent with those of a previous study that did not find significant response slowing for apes as a function of aversive testing conditions, although the procedure has been effective in identifying dysregulated fear (high fear in low threat conditions) in macaques. The utility of this paradigm for testing affect in apes awaits further evaluation. creator: Molly McGuire creator: Jennifer M. Vonk uri: https://doi.org/10.7717/peerj.9525 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 McGuire and Vonk title: Arthropod IGF, relaxin and gonadulin, putative orthologs of Drosophila insulin-like peptides 6, 7 and 8, likely originated from an ancient gene triplication link: https://peerj.com/articles/9534 last-modified: 2020-07-10 description: BackgroundInsects have several genes coding for insulin-like peptides and they have been particularly well studied in Drosophila. Some of these hormones function as growth hormones and are produced by the fat body and the brain. These act through a typical insulin receptor tyrosine kinase. Two other Drosophila insulin-like hormones are either known or suspected to act through a G-protein coupled receptor. Although insulin-related peptides are known from other insect species, Drosophila insulin-like peptide 8, one that uses a G-protein coupled receptor, has so far only been identified from Drosophila and other flies. However, its receptor is widespread within arthropods and hence it should have orthologs. Such putative orthologs were recently identified in decapods and have been called gonadulins.MethodologyIn an effort to identify gonadulins in other arthropods public genome assemblies and short-read archives from insects and other arthropods were explored for the presence of genes and transcripts coding insulin-like peptides and their putative receptors.ResultsGonadulins were detected in a number of arthropods. In those species for which transcriptome data from the gonads is available insect gonadulin genes are expressed in the ovaries and at least in some species also in the testes. In some insects differences in gonadulin expression in the ovary between actively reproducing and non-reproducing females differs more than 100-fold. Putative orthologs of Drosophila ilp 6 were also identified. In several non-Dipteran insects these peptides have C-terminally extensions that are alternatively spliced. The predicted peptides have been called arthropod insulin-like growth factors. In cockroaches, termites and stick insects genes coding for the arthropod insulin-like growth factors, gonadulin and relaxin, a third insulin-like peptide, are encoded by genes that are next to one another suggesting that they are the result of a local gene triplication. Such a close chromosomal association was also found for the arthropod insulin-like growth factor and gonadulin genes in spiders. Phylogenetic tree analysis of the typical insulin receptor tyrosine kinases from insects, decapods and chelicerates shows that the insulin signaling pathway evolved differently in these three groups. The G-protein coupled receptors that are related to the Drosophila ilp 8 receptor similarly show significant differences between those groups.ConclusionA local gene triplication in an early ancestor likely yielded three genes coding gonadulin, arthropod insulin-like growth factor and relaxin. Orthologs of these genes are now commonly present in arthropods and almost certainly include the Drosophila insulin-like peptides 6, 7 and 8. creator: Jan A. Veenstra uri: https://doi.org/10.7717/peerj.9534 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Veenstra title: From the index case to global spread: the global mobility based modelling of the COVID-19 pandemic implies higher infection rate and lower detection ratio than current estimates link: https://peerj.com/articles/9548 last-modified: 2020-07-10 description: BackgroundSince the outbreak of the COVID-19 pandemic, multiple efforts of modelling of the geo-temporal transmissibility of the virus have been undertaken, but none describes the pandemic spread at the global level. The aim of this research is to provide a high-resolution global model of the pandemic that overcomes the problem of biased country-level data on the number of infected cases. To achieve this we propose a novel SIR-type metapopulation transmission model and a set of analytically derived model parameters. We used them to perform a simulation of the disease spread with help of the Global Epidemic and Mobility (GLEAM) framework embedding actual population densities, commute patterns and long-range travel networks. The simulation starts on 17 November 2019 with the index case (presymptomatic, yet infectious) in Wuhan, China, and results in an accurate prediction of the number of diagnosed cases after 154 days in multiple countries across five continents. In addition, the model outcome shows high compliance with the results of a random screening test conducted on pregnant women in the New York area.MethodsWe have built a modified SIR metapopulation transmission model and parameterized it analytically either by setting the values of the parameters based on the literature, or by assuming their plausible values. We compared our results with the number of diagnosed cases in twenty selected countries, ones which provide reliable statistics but differ substantially in terms of strength and speed of undertaken Non-Drug Interventions. The obtained 95% confidence intervals for the predictions are in agreement with the empirical data.ResultsThe parameters that successfully model the pandemic are: the basic reproduction number R0, 4.4; a latent non-infectious period of 1.1. days followed by 4.6 days of the presymptomatic infectious period; the probability of developing severe symptoms, 0.01; the probability of being diagnosed when presenting severe symptoms of 0.6; the probability of diagnosis for cases with mild symptoms or asymptomatic, 0.001.DiscussionParameters that successfully reproduce the observed number of cases indicate that both R0 and the prevalence of the virus might be underestimated. This is in concordance with the newest research on undocumented COVID-19 cases. Consequently, the actual mortality rate is putatively lower than estimated. Confirmation of the pandemic characteristic by further refinement of the model and screening tests is crucial for developing an effective strategy for the global epidemiological crisis. creator: Marian Siwiak creator: Pawel Szczesny creator: Marlena Siwiak uri: https://doi.org/10.7717/peerj.9548 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Siwiak et al. title: Identifying hub genes of papillary thyroid carcinoma in the TCGA and GEO database using bioinformatics analysis link: https://peerj.com/articles/9120 last-modified: 2020-07-09 description: BackgroundThyroid carcinoma (THCA) is a common endocrine malignant tumor. Papillary carcinoma with low degree of malignancy and good prognosis is the most common. It can occur at any age, but it is more common in young adults. Although the mortality rate is decreased due to early diagnosis, the survival rate varies depending on the type of tumor. Therefore, the purpose of this study is to identify hub biomarkers and novel therapeutic targets for THCA.MethodsThe GSE3467, GSE3678, GSE33630 and GSE53157 were obtained from the GEO database, including 100 thyroid tumors and 64 normal tissues to obtain the intersection of differentially expressed genes, and a protein-protein interaction network was constructed to obtain the HUB gene. The corresponding overall survival information from The Cancer Genome Atlas Project-THCA was then included in this research. The signature mechanism was studied by analyzing the gene ontology and the Kyoto Encyclopedia of Genes and Genome database.ResultsIn this research, we identified eight candidate genes (FN1, CCND1, CDH2, CXCL12, MET, IRS1, DCN and FMOD) from the network. Also, expression verification and survival analysis of these candidate genes based on the TCGA database indicate the robustness of the above results. Finally, our hospital samples validated the expression levels of these genes.ConclusionThe research identified eight mRNA (four up–regulated and four down–regulated) which serve as signatures and could be a potential prognostic marker of THCA. creator: Ying Wan creator: Xiaolian Zhang creator: Huilin Leng creator: Weihua Yin creator: Wenxing Zeng creator: Congling Zhang uri: https://doi.org/10.7717/peerj.9120 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wan et al. title: Environmentally relevant levels of four psychoactive compounds vary in their effects on freshwater fish condition: a brain concentration evidence approach link: https://peerj.com/articles/9356 last-modified: 2020-07-09 description: BackgroundThe aquatic environment has been contaminated with various anthropogenic pollutants, including psychoactive compounds that may alter the physiology and behavior of free-living organisms. The present study focused on the condition and related mortality of the juvenile chub (Squalius cephalus). The aim of the study was to test whether the adverse effects of the antidepressants sertraline and citalopram, the analgesic tramadol and the illicit drug methamphetamine, on fish condition exist under environmentally relevant concentrations and whether these effects persist after a depuration period. Innovative analyses of the fish brain concentrations of these compounds were performed with the aim to show relationship between compound brain tissue concentration and fish condition.MethodsThe laboratory experiment consisted of 42 days of exposure and a subsequent 14-day depuration period with regular monitoring of the condition and mortality of exposed and control fish. Identical methodology, including individual brain concentration analyses for the tested compounds, was applied for all substances. Additional study on feeding under sertraline exposure was also conducted. The feeding was measured from the 28th day of the exposure, three times in a week, by observation of food intake during 15 minutes in social environment.ResultsThe effects of particular psychoactive compounds on chub condition varied. While sertraline induced a lower condition and increased mortality, the effects of methamphetamine were inverse, and tramadol and citalopram had no significant effect at all. Individual brain concentrations of the tested compounds showed that the effects of sertraline and methamphetamine on fish condition were increased with brain concentration increases. Additionally, the food intake was reduced in case of sertraline. In contrast, there was no relationship between tramadol and citalopram brain tissue concentration and fish condition, suggesting that the concentration-dependent effect is strongly compound-specific. Methamphetamine was the only compound with a persistent effect after the depuration period. Our results demonstrate the suitability of the brain concentration evidence approach and suggest that changes in fish condition and other related parameters can be expected in freshwater ecosystems polluted with specific psychoactive compounds. creator: Pavla Hubená creator: Pavel Horký creator: Roman Grabic creator: Kateřina Grabicová creator: Ondřej Slavík creator: Tomáš Randák uri: https://doi.org/10.7717/peerj.9356 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hubená et al. title: Access to scientific literature by the conservation community link: https://peerj.com/articles/9404 last-modified: 2020-07-09 description: Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ∼97% need to use the scientific literature in order to support their IUCN-related conservation work, with ∼50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and sex (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ∼50% in Asia and Latin America, and ∼40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide. creator: Daisy Larios creator: Thomas M. Brooks creator: Nicholas B.W. Macfarlane creator: Sugoto Roy uri: https://doi.org/10.7717/peerj.9404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Larios et al. title: Molecular phylogenetics and evolutionary history of the endemic land snail genus Everettia in northern Borneo link: https://peerj.com/articles/9416 last-modified: 2020-07-09 description: Borneo has gone through dramatic changes in geology and topography from the early Eocene until the early Pliocene and experienced climatic cycling during the Pleistocene. However, how these changes have shaped the present-day patterns of high diversity and complex distribution are still poorly understood. In this study, we use integrative approaches by estimating phylogenetic relationships, divergence time, and current and past niche suitability for the Bornean endemic land snail genus Everettia to provide additional insight into the evolutionary history of this genus in northern Borneo in the light of the geological vicariance events and climatic fluctuations in the Pleistocene. Our results show that northern Borneo Everettia species belong to two deeply divergent lineages: one contains the species that inhabit high elevation at the central mountain range, while the other contains lowland species. Species diversification in these lineages has taken place before the Pliocene. Climate changes during the Pleistocene did not play a significant role in species diversification but could have shaped contemporary species distribution patterns. Our results also show that the species-rich highland habitats have acted as interglacial refugia for highland species. This study of a relatively sedentary invertebrate supports and enhances the growing understanding of the evolutionary history of Borneo. Species diversification in Everettia is caused by geological vicariance events between the early Miocene and the Pliocene, and the distribution patterns were subsequently determined by climatic fluctuations in the Pleistocene. creator: Thor-Seng Liew creator: Mohammad Effendi Marzuki creator: Menno Schilthuizen creator: Yansen Chen creator: Jaap J. Vermeulen creator: Jayasilan Mohd-Azlan uri: https://doi.org/10.7717/peerj.9416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liew et al. title: A collection of hexactinellids (Porifera) from the deep South Atlantic and North Pacific: new genus, new species and new records link: https://peerj.com/articles/9431 last-modified: 2020-07-09 description: This article describes or redescribes four hexactinellid sponges, namely Poliopogon amadou, Euplectella sanctipauli sp. nov., Bolosoma perezi sp. nov. and Advhena magnifica gen. et sp. nov. P. amadou, E. sanctipauli sp. nov. and B. perezi sp. nov. represent new findings for the South Atlantic deep-sea fauna, including the first record of Bolosoma for this ocean. Advhena magnifica gen. et sp. nov., on the other hand, was collected by NOAA oceanographic expeditions in the North Pacific (Pigafetta Guyot). creator: Cristiana Castello-Branco creator: Allen G. Collins creator: Eduardo Hajdu uri: https://doi.org/10.7717/peerj.9431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Castello-Branco et al. title: Sharing for science: high-resolution trophic interactions revealed rapidly by social media link: https://peerj.com/articles/9485 last-modified: 2020-07-09 description: Discrete, ephemeral natural phenomena with low spatial or temporal predictability are incredibly challenging to study systematically. In ecology, species interactions, which constitute the functional backbone of ecological communities, can be notoriously difficult to characterise especially when taxa are inconspicuous and the interactions of interest (e.g., trophic events) occur infrequently, rapidly, or variably in space and time. Overcoming such issues has historically required significant time and resource investment to collect sufficient data, precluding the answering of many ecological and evolutionary questions. Here, we show the utility of social media for rapidly collecting observations of ephemeral ecological phenomena with low spatial and temporal predictability by using a Facebook group dedicated to collecting predation events involving reptiles and amphibians in sub-Saharan Africa. We collected over 1900 independent feeding observations using Facebook from 2015 to 2019 involving 83 families of predators and 129 families of prey. Feeding events by snakes were particularly well-represented with close to 1,100 feeding observations recorded. Relative to an extensive literature review spanning 226 sources and 138 years, we found that social media has provided snake dietary records faster than ever before in history with prey being identified to a finer taxonomic resolution and showing only modest concordance with the literature due to the number of novel interactions that were detected. Finally, we demonstrate that social media can outperform other citizen science image-based approaches (iNaturalist and Google Images) highlighting the versatility of social media and its ability to function as a citizen science platform. creator: Robin A. Maritz creator: Bryan Maritz uri: https://doi.org/10.7717/peerj.9485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Maritz and Maritz title: Prognostic value of complementary biomarkers of neurodegeneration in a mixed memory clinic cohort link: https://peerj.com/articles/9498 last-modified: 2020-07-09 description: BackgroundBiomarkers of neurodegeneration, e.g. MRI brain atrophy and [18F]FDG-PET hypometabolism, are often evaluated in patients suspected of neurodegenerative disease.ObjectiveOur primary objective was to investigate prognostic properties of atrophy and hypometabolism.MethodsFrom March 2015-June 2016, 149 patients referred to a university hospital memory clinic were included. The primary outcome was progression/stable disease course as assessed by a clinician at 12 months follow-up. Intracohort defined z-scores of baseline MRI automatic quantified volume and [18F]FDG-PET standardized uptake value ratios were calculated for all unilaterally defined brain lobes and dichotomized as pronounced atrophy (+A)/ pronounced hypometabolism (+H) at z-score <0. A logistic regression model with progression status as the outcome was carried out with number of lobes with the patterns +A/-H, -A/+H, +A/+H respectively as predictors. The model was mutually adjusted along with adjustment for age and sex. A sensitivity analysis with a z-score dichotomization at −0.1 and −0.5 and dichotomization regarding number of lobes affected at one and three lobes was done.ResultsMedian follow-up time was 420 days [IQR: 387-461 days] and 50 patients progressed. Patients with two or more lobes affected by the pattern +A/+H compared to patients with 0–1 lobes affected had a statistically significant increased risk of progression (odds ratio, 95 % confidence interval: 4.33, 1.90–9.86) in a multivariable model. The model was partially robust to the applied sensitivity analysis.ConclusionCombined atrophy and hypometabolism as assessed by MRI and [18F]FDG-PET in patients under suspicion of neurodegenerative disease predicts progression over 1 year. creator: Mathias Holsey Gramkow creator: Le Gjerum creator: Juha Koikkalainen creator: Jyrki Lötjönen creator: Ian Law creator: Steen Gregers Hasselbalch creator: Gunhild Waldemar creator: Kristian Steen Frederiksen uri: https://doi.org/10.7717/peerj.9498 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gramkow et al.