title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1052 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Earthworms accelerate rice straw decomposition and maintenance of soil organic carbon dynamics in rice agroecosystems link: https://peerj.com/articles/9870 last-modified: 2020-09-17 description: BackgroundTo promote straw degradation, we inoculated returned farmland straw with earthworms (Pheretima guillelmi). Increasing the number of earthworms may generally alter soil organic carbon (SOC) dynamics and the biological activity of agricultural soils.MethodsWe performed soil mesocosm experiments with and without earthworms to assess the decomposition and microbial mineralization of returned straw and soil enzyme activity across different time periods.ResultsWhen earthworms were present in soil, the surface residues were completely consumed during the first four weeks, but when earthworms were absent, most of the residues remained on the soil surface after 18 weeks. On day 28, the SOC content was significantly higher in the treatment where both earthworms and residue had been added. The SOC content was lower in the treatment where earthworms but no residue had been added. The organic carbon content in water-stable macroaggregates showed the same trend. During the first 14 weeks, the soil basal respiration was highest in the treatments with both residues and earthworms. From weeks 14 to 18, basal respiration was highest in the treatments with residues but without earthworms. We found a significant positive correlation between soil basal respiration and soil dissolved organic carbon content. Earthworms increased the activity of protease, invertase, urease and alkaline phosphatase enzymes, but decreased β-cellobiohydrolase, β-glucosidase and xylosidase activity, as well as significantly reducing ergosterol content.ConclusionThe primary decomposition of exogenous rice residues was mainly performed by earthworms. Over a short period of time, they converted plant carbon into soil carbon and increased SOC. The earthworms played a key role in carbon conversion and stabilization. In the absence of exogenous residues, earthworm activity accelerated the decomposition of original organic carbon in the soil, reduced SOC, and promoted carbon mineralization. creator: Ke Song creator: Lijuan Sun creator: Weiguang Lv creator: Xianqing Zheng creator: Yafei Sun creator: William Terzaghi creator: Qin Qin creator: Yong Xue uri: https://doi.org/10.7717/peerj.9870 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Song et al. title: Wild meat hunting and use by sedentarised Baka Pygmies in southeastern Cameroon link: https://peerj.com/articles/9906 last-modified: 2020-09-17 description: As a result of sedentarisation many Baka Pygmies have changed their mobility patterns away from nomadic lifestyles to living in roadside villages. These settled groups are increasingly dependent on cultivated foods but still rely on forest resources. The level of dependence on hunting of wild animals for food and cash, as well as the hunting profiles of sedentarised Pygmy groups is little known. In this study we describe the use of wild meat in 10 Baka villages along the Djoum-Mintom road in southeastern Cameroon. From data collected from 1,946 hunting trips by 121 hunters, we show that most trips are of around 13 hours and a median of eight hours. A mean ± SD of 1.15 ± 1.11 animal carcasses are taken in a single trip; there was a positive correlation between duration of trips and carcasses. A total of 2,245 carcasses of 49 species of 24 animal families were taken in the study; species diversity was similar in all villages except one. Most hunted animals were mammals, with ungulates contributing the highest proportion. By species, just over half of the animal biomass extracted by all hunters in the studied villages was provided by four mammal species. Most animals were trapped (65.77% ± 16.63), followed by shot with guns (22.56% ± 17.72), other methods (8.69% ± 6.96) and with dogs (2.96% ± 4.49). A mean of 7,569.7 ± 6,103.4 kg yr−1 (2,080.8–19,351.4) were extracted per village, giving 75,697 kg yr−1 in total, which is equivalent to 123 UK dairy cattle. In all villages, 48.07% ± 17.58 of animals hunted were consumed by the hunter and his family, around 32.73% ± 12.55, were sold, followed by a lower percentage of carcasses partially sold and consumed (19.21% ± 17.02). Between 60% and 80% of carcasses belonged to the “least concern” category, followed by “near threatened”, “vulnerable” and, rarely “endangered”. The only endangered species hunted was the chimpanzee (Pan troglodytes). We suggest that hunting is a critical activity that provides a vital source of food for our study communities. Measured wild meat extraction levels are likely to be sustainable if hunter densities do not increase. creator: Eva Avila Martin creator: Guillermo Ros Brull creator: Stephan M. Funk creator: Luca Luiselli creator: Robert Okale creator: Julia E. Fa uri: https://doi.org/10.7717/peerj.9906 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Avila Martin et al. title: Estimating the impact of lock-down, quarantine and sensitization in a COVID-19 outbreak: lessons from the COVID-19 outbreak in China link: https://peerj.com/articles/9933 last-modified: 2020-09-17 description: In recent history, COVID-19 is one of the worst infectious disease outbreaks currently affecting humanity globally. Using real data on the COVID-19 outbreak from 22 January 2020 to 30 March 2020, we developed a mathematical model to investigate the impact of control measures in reducing the spread of the disease. Analyses of the model were carried out to determine the dynamics. The results of the analyses reveal that, using the data from China, implementing all possible control measures best reduced the rate of secondary infections. However, quarantine (isolation) of infectious individuals is shown to have the most dominant effect. This possibility emphasizes the need for extensive testing due to the possible prevalence of asymptomatic COVID-19 cases. creator: Obiora C. Collins creator: Kevin J. Duffy uri: https://doi.org/10.7717/peerj.9933 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Collins and Duffy title: Cocoa colonic phenolic metabolites are related to HDL-cholesterol raising effects and methylxanthine metabolites and insoluble dietary fibre to anti-inflammatory and hypoglycemic effects in humans link: https://peerj.com/articles/9953 last-modified: 2020-09-17 description: BackgroundIn many cocoa intervention studies, health outcomes are related to cocoa components without taking into account the bioavailability of the main bioactive components: phenolic compounds and methylxanthines.MethodsThe present work associates the results of bioavailability and randomised controlled crossover studies in humans carried out with similar cocoa products, so that the main phenol and methylxanthine metabolites observed in plasma and urine are associated to the health effects observed in the chronic studies. We outstand that doses of cocoa and consumption rate used are realistic. In the bioavailability study, a conventional (CC) and a methylxanthine-polyphenol rich (MPC) cocoa product were used, whereas in the chronic study a dietary fibre-rich (DFC) and a polyphenol-rich (PC) product were studied in healthy and cardiovascular risk subjects.Results and DiscussionThe main phenolic metabolites formed after CC and MPC intake, 5-(4′-hydroxyphenyl)-γ-valerolactone-3′-sulfate, 3′-methyl-epicatechin-5-sulfate, 4-hydroxy-5-(4′-hydroxyphenyl)valeric acid-sulfate, 5-phenyl-γ-valerolactone--sulfate and 5-(4′-hydroxyphenyl)-γ-valerolactone-3′-glucuronide, may contribute to the changes in cholesterol (and indirectly HDL-cholesterol) observed after the regular intake of both DFC and PC, in healthy and cardiovascular risk subjects, whereas 7-methylxanthine (the main cocoa methylxanthine metabolite) and theobromine, together with its content in insoluble dietary fibre, may be responsible for the decrease of IL-1β and hypoglycemic effects observed with DFC. With both phenolic and methylxanthine metabolites a strong dose–response effect was observed.ConclusionAfter the regular consumption of both DFC and PC, positive changes were observed in volunteer’s lipid profile, which may be related to the long-lasting presence of colonic phenolic metabolites in blood. In contrast, the anti-inflammatory and hypoglycemic effects were only observed with DFC, and these may be related to methylxanthine metabolites, and it is likely that insoluble dietary fibre may have also played a role. creator: Beatriz Sarriá creator: Miren Gomez-Juaristi creator: Sara Martínez López creator: Joaquín García Cordero creator: Laura Bravo creator: Mª Raquel Mateos Briz uri: https://doi.org/10.7717/peerj.9953 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sarriá et al. title: Role of reactive oxygen species and isoflavonoids in soybean resistance to the attack of the southern green stink bug link: https://peerj.com/articles/9956 last-modified: 2020-09-17 description: Southern green stink bugs (Nezara viridula L.) are one of the major pests in many soybean producing areas. They cause a decrease in yield and affect seed quality by reducing viability and vigor. Alterations have been reported in the oxidative response and in the secondary metabolites in different plant species due to insect damage. However, there is little information available on soybean-stink bug interactions. In this study we compare the response of undamaged and damaged seeds by Nezara viridula in two soybean cultivars, IAC-100 (resistant) and Davis (susceptible), grown under greenhouse conditions. Pod hardness, H2O2 generation, enzyme activities in guaiacol peroxidase (GPOX), catalase (CAT) and superoxide dismutase (SOD) as well as lipoxygenase expression and isoflavonoid production were quantified. Our results showed a greater resistance of IAC-100 to pod penetration, a decrease in peroxide content after stink bug attack, and higher GPOX, CAT and SOD activities in seeds due to the genotype and to the genotype-interaction with the herbivory treatment. Induction of LOX expression in both cultivars and higher production of isoflavonoids in IAC-100 were also detected. It was then concluded that the herbivory stink bug induces pathways related to oxidative stress and to the secondary metabolites in developing seeds of soybean and that differences between cultivars hold promise for a plant breeding program. creator: Ivana Sabljic creator: Jesica A. Barneto creator: Karina B. Balestrasse creator: Jorge A. Zavala creator: Eduardo A. Pagano uri: https://doi.org/10.7717/peerj.9956 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sabljic et al. title: Comparable behaviour of ring and little fingers due to an artificial reduction in thumb contribution to hold objects link: https://peerj.com/articles/9962 last-modified: 2020-09-17 description: BackgroundThe human hand plays a crucial role in accomplishing activities of daily living. The contribution of each finger in the human hand is remarkably unique in establishing object stabilization. According to the mechanical advantage hypothesis, the little finger tends to exert a greater normal force than the ring finger during a supination moment production task to stabilize the object. Similarly, during pronation, the index finger produces more normal force when compared with the middle finger. Hence, the central nervous system employs the peripheral fingers for torque generation to establish the equilibrium as they have a mechanical advantage of longer moment arms for normal force. In our study, we tested whether the mechanical advantage hypothesis is supported in a task in which the contribution of thumb was artificially reduced. We also computed the safety margin of the individual fingers and thumb.MethodologyFifteen participants used five-finger prismatic precision grip to hold a custom-built handle with a vertical railing on the thumb side. A slider platform was placed on the railing such that the thumb sensor could move either up or down. There were two experimental conditions. In the “Fixed” condition, the slider was mechanically fixed, and hence the thumb sensor could not move. In the “Free” condition, the slider platform on which the thumb sensor was placed could freely move. In both conditions, the instruction was to grasp and hold the handle (and the platform) in static equilibrium. We recorded tangential and normal forces of all the fingers.ResultsThe distribution of fingertip forces and moments changed depending on whether the thumb platform was movable (or not). In the free condition, the drop in the tangential force of thumb was counteracted by an increase in the normal force of the ring and little finger. Critically, the normal forces of the ring and little finger were statistically equivalent. The safety margin of the index and middle finger did not show a significant drop in the free condition when compared to fixed condition.ConclusionWe conclude that our results does not support the mechanical advantage hypothesis at least for the specific mechanical task considered in our study. In the free condition, the normal force of little finger was comparable to the normal force of the ring finger. Also, the safety margin of the thumb and ring finger increased to prevent slipping of the thumb platform and to maintain the handle in static equilibrium during the free condition. However, the rise in the safety margin of the ring finger was not compensated by a drop in the safety margin of the index and middle finger. creator: Banuvathy Rajakumar creator: Varadhan SKM uri: https://doi.org/10.7717/peerj.9962 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rajakumar and SKM title: One becomes two: second species of the Euwallacea fornicatus (Coleoptera: Curculionidae: Scolytinae) species complex is established on two Hawaiian Islands link: https://peerj.com/articles/9987 last-modified: 2020-09-17 description: The cryptic species that make up the Euwallacea fornicatus species complex can be readily distinguished via their DNA sequences. Until recently, it was believed that the Hawaiian Islands had been invaded by only one of these cryptic species, E. perbrevis (tea shot hole borer; TSHB). However, following the 2016 deposition of a DNA sequence in the public repository GenBank, it became evident that another species, E. fornicatus (polyphagous shot hole borer; PSHB), had been detected in macadamia orchards on Hawaiʻi Island (the Big Island). We surveyed the two most-populous islands of Hawaiʻi, Big Island and Oʻahu, and herein confirm that populations of TSHB and PSHB are established on both. Beetles were collected using a variety of techniques in macadamia orchards and natural areas. Individual specimens were identified to species using a high-resolution melt assay, described herein and validated by subsequent sequencing of specimens. It remains unclear how long each species has been present in the state, and while neither is currently recognized as causing serious economic or ecological damage in Hawaiʻi, the similarity of the newly-confirmed PSHB population to other damaging invasive PSHB populations around the world is discussed. Although the invasive PSHB populations in Hawaiʻi and California likely have different geographic origins within the beetle’s native range, they share identical Fusarium and Graphium fungal symbionts, neither of which have been isolated from PSHB in that native range. creator: Paul F. Rugman-Jones creator: Michelle Au creator: Valeh Ebrahimi creator: Akif Eskalen creator: Conrad P.D.T. Gillett creator: David Honsberger creator: Deena Husein creator: Mark G. Wright creator: Fazila Yousuf creator: Richard Stouthamer uri: https://doi.org/10.7717/peerj.9987 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rugman-Jones et al. title: Adaptive Metropolis-coupled MCMC for BEAST 2 link: https://peerj.com/articles/9473 last-modified: 2020-09-16 description: With ever more complex models used to study evolutionary patterns, approaches that facilitate efficient inference under such models are needed. Metropolis-coupled Markov chain Monte Carlo (MCMC) has long been used to speed up phylogenetic analyses and to make use of multi-core CPUs. Metropolis-coupled MCMC essentially runs multiple MCMC chains in parallel. All chains are heated except for one cold chain that explores the posterior probability space like a regular MCMC chain. This heating allows chains to make bigger jumps in phylogenetic state space. The heated chains can then be used to propose new states for other chains, including the cold chain. One of the practical challenges using this approach, is to find optimal temperatures of the heated chains to efficiently explore state spaces. We here provide an adaptive Metropolis-coupled MCMC scheme to Bayesian phylogenetics, where the temperature difference between heated chains is automatically tuned to achieve a target acceptance probability of states being exchanged between individual chains. We first show the validity of this approach by comparing inferences of adaptive Metropolis-coupled MCMC to MCMC on several datasets. We then explore where Metropolis-coupled MCMC provides benefits over MCMC. We implemented this adaptive Metropolis-coupled MCMC approach as an open source package licenced under GPL 3.0 to the Bayesian phylogenetics software BEAST 2, available from https://github.com/nicfel/CoupledMCMC. creator: Nicola F. Müller creator: Remco R. Bouckaert uri: https://doi.org/10.7717/peerj.9473 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Müller and Bouckaert title: Density and diversity of macroinvertebrates in Colombian Andean streams impacted by mining, agriculture and cattle production link: https://peerj.com/articles/9619 last-modified: 2020-09-16 description: BackgroundMining, agriculture and cattle production are activities that threaten the quality and quantity of water resources in the Colombian Andes. However, many drainage basins in this region have not been subjected to simultaneous evaluation of the impact these activities have on the density, diversity and composition of aquatic macroinvertebrates (AMI). The first two of these ecological variables are expected to decrease drastically from zones with no apparent impact towards areas with anthropogenic activity, which areas with mining will present the most impoverished AMI community.MethodsWe evaluated the density, diversity and composition dissimilarity of AMI in streams impacted by gold mining, agriculture and cattle production. Two reference streams were also studied. Six benthic samplings were conducted bimonthly (Feb 2014–Feb 2015) using a Surber net. Water samples were taken in order to make environmental evaluation among the aforementioned streams, including hydrological, physicochemical and bacteriological parameters (HPCB). Diversity was evaluated as the effective number of RTUs—recognizable taxonomic units—by comparing the richness, typical diversity, and effective number of the most abundant RTUs. Compositional dissimilarity was examined with nMDS and CCA analysis.ResultsA total of 7,483 organisms were collected: 14 orders, 42 families and 71 RTUs. Our prediction regarding the density and diversity of AMI (Reference > Cattle production > Agriculture > Mining) was partially fulfilled, since the agriculture-dominated stream presented a more impoverished AMI community than that of the gold mining stream. However, these streams presented lower diversity than the cattle production and reference streams, and the AMI density only differed significantly between one reference stream and the agriculture stream. The AMI composition in the agriculture-dominated stream clearly differed from that of the other streams.DiscussionThe observation of a more impoverished AMI community in agricultural production areas compared to those with mining or cattle production may reflect the importance of the remaining riparian vegetation, which was scarce at the stream with agricultural activity. Moreover, the low diversity, and mainly the reduced AMI richness, in the agriculture stream coincided with the absence of insect genera are intolerant to deterioration of the biological and physicochemical conditions of the water (e.g. Anacroneuria).ConclusionsThe results suggest that the local impact of agricultural activities may be of equal or greater magnitude than that of mining in terms of AMI density, diversity and composition, in the Colombian Andean riverscape. Future studies should systematically evaluate, throughout the annual cycle, the relative effects of the productive land use, the remaining native vegetation cover and the consequent changes in the HPCB parameters of the water on AMI communities in Colombian Andean basins. creator: Ana M. Meza-Salazar creator: Giovany Guevara creator: Lucimar Gomes-Dias creator: Carlos A. Cultid-Medina uri: https://doi.org/10.7717/peerj.9619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Meza-Salazar et al. title: Psychometric properties of the Automatic Thoughts Questionnaire-8 in two Spanish nonclinical samples link: https://peerj.com/articles/9747 last-modified: 2020-09-16 description: BackgroundThe ATQ is a widely used instrument consisting of 30 items that assess the frequency of negative automatic thoughts. However, the extensive length of the ATQ could compromise its measurement efficiency in survey research. Consequently, an 8-item shortened version of the ATQ has been developed. This study aims to analyze the validity of the ATQ-8 in two Spanish samples.MethodThe ATQ-8 was administered to a total sample of 1,148 participants (302 undergraduates and 846 general online population). To analyze convergent construct validity, the questionnaire package also included the Dysfunctional Attitude Scale-Revised (DAS-R), Depression Anxiety and Stress Scale-21 (DASS-21), Acceptance Action Questionnaire-II (AAQ-II), Cognitive Fusion Questionnaire (CFQ), Generalized Pliance Questionnaire (GPQ), and Satisfaction with Life Scale (SWLS). To analyze internal consistency, we computed Cronbach’s alpha and McDonald’s omega. A confirmatory factor analysis was conducted to test the one-factor structure of the ATQ-8. In so doing, a robust diagonally weighted least square estimation method (Robust DWLS) was adopted using polychoric correlations. Afterward, we analyzed measurement invariance across samples, gender, groupage, and education level. Lastly, we evaluated convergent construct validity by computing Pearson correlations between the ATQ-8 and the remaining instruments.ResultsThe internal consistency across samples was adequate (alpha and omega = .89). The one-factor model demonstrated a good fit to the data (RMSEA = 0.10, 90% CI [0.089, 0.112], CFI = 0.98, NNFI = 0.97, and SRMR = 0.048). The ATQ-8 showed scalar metric invariance across samples, gender, groupage, and education level. The ATQ-8 scores were significantly associated with emotional symptoms (DASS-21), satisfaction with life (SWLS), dysfunctional schemas (DAS-R), cognitive fusion (CFQ), experiential avoidance (AAQ-II), and generalized pliance (GPQ). In conclusion, the Spanish version of the ATQ-8 demonstrated adequate psychometric properties in Spanish samples. creator: Francisco J. Ruiz creator: Miguel A. Segura-Vargas creator: Paula Odriozola-González creator: Juan C. Suárez-Falcón uri: https://doi.org/10.7717/peerj.9747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ruiz et al.