title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1048 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Connectivity of bacterial assemblages along the Loa River in the Atacama Desert, Chile link: https://peerj.com/articles/9927 last-modified: 2020-10-01 description: The Loa River is the only perennial artery that crosses the Atacama Desert in northern Chile. It plays an important role in the ecological and economic development of the most water-stressed region, revealing the impact of the mining industry, which exacerbate regional water shortages for many organisms and ecological processes. Despite this, the river system has remained understudied. To our knowledge, this study provides the first effort to attempt to compare the microbial communities at spatial scale along the Loa River, as well as investigate the physicochemical factors that could modulate this important biological component that still remains largely unexplored. The analysis of the spatial bacterial distribution and their interconnections in the water column and sediment samples from eight sites located in three sections along the river catchment (upper, middle and lower) was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. Among a total of 543 ASVs identified at the family level, over 40.5% were cosmopolitan in the river and distributed within a preference pattern by the sediment substrate with 162 unique ASVs, while only 87 were specific to the column water. Bacterial diversity gradually decreased from the headwaters, where the upper section had the largest number of unique families. Distinct groupings of bacterial communities often associated with anthropogenic disturbance, including Burkholderiaceae and Flavobacteriaceae families were predominant in the less-impacted upstream section. Members of the Arcobacteraceae and Marinomonadaceae were prominent in the agriculturally and mining-impacted middle sector while Rhodobacteraceae and Coxiellaceae were most abundant families in downstream sites. Such shifts in the community structure were also related to the influence of salinity, chlorophyll, dissolved oxygen and redox potential. Network analyses corroborated the strong connectivity and modular structure of bacterial communities across this desert river, shedding light on taxonomic relatedness of co-occurring species and highlighting the need for planning the integral conservation of this basin. creator: Ana Zárate creator: Cristina Dorador creator: Ruben Araya creator: Mariela Guajardo creator: July Z. Florez creator: Gonzalo Icaza creator: Diego Cornejo creator: Jorge Valdés uri: https://doi.org/10.7717/peerj.9927 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zárate et al. title: Persistent mosquito fogging can be detrimental to non-target invertebrates in an urban tropical forest link: https://peerj.com/articles/10033 last-modified: 2020-10-01 description: BackgroundHuman population growth has led to biodiversity declines in tropical cities. While habitat loss and fragmentation have been the main drivers of urban biodiversity loss, man-made interventions to reduce health risks have also emerged as an unintentional threat. For instance, insecticide fogging to control mosquito populations has become the most common method of preventing the expansion of mosquito-borne diseases such as Dengue. However, the effectiveness of fogging in killing mosquitoes has been called into question. One concern is the unintended effect of insecticide fogging on non-target invertebrates that are crucial for the maintenance of urban ecosystems. Here, we investigate the impacts of fogging on: (1) target invertebrate taxon (Diptera, including mosquitoes); (2) non-target invertebrate taxa; and (3) the foraging behavior of an invertebrate pollinator taxon (Lepidoptera) within an urban tropical forest.MethodsWe carried out fogging with Pyrethroid insecticide (Detral 2.5 EC) at 10 different sites in a forest situated in the state of Selangor, Peninsular Malaysia. Across the sites, we counted the numbers of knocked-down invertebrates and identified them based on morphology to different taxa. We constructed Bayesian hierarchical Poisson regression models to investigate the effects of fogging on: (1) a target invertebrate taxon (Diptera) 3-h post-fogging; (2) selected non-target invertebrate taxa 3-h post-fogging; and (3) an invertebrate pollinator taxon (Lepidoptera) 24-h post-fogging.ResultsA total of 1,874 invertebrates from 19 invertebrate orders were knocked down by the fogging treatment across the 10 sites. Furthermore, 72.7% of the invertebrates counted 3-h post-fogging was considered dead. Our regression models showed that given the data and prior information, the probability that fogging had a negative effect on invertebrate taxa 3-h post-fogging was 100%, with reductions to 11% of the pre-fogging count of live individuals for the target invertebrate taxon (Diptera), and between 5% and 58% of the pre-fogging count of live individuals for non-target invertebrate taxa. For the invertebrate pollinator, the probability that fogging had a negative effect 24-h post-fogging was also 100%, with reductions to 53% of the pre-fogging count of live individuals.DiscussionOur Bayesian models unequivocally demonstrate that fogging has detrimental effects on one pollinator order and non-target invertebrate orders, especially taxa that have comparatively lower levels of chitinisation. While fogging is effective in killing the target order (Diptera), no mosquitos were found dead in our experiment. In order to maintain urban biodiversity, we recommend that health authorities and the private sector move away from persistent insecticide fogging and to explore alternative measures to control adult mosquito populations. creator: Nicole S.M. Lee creator: Gopalasamy R. Clements creator: Adeline S.Y. Ting creator: Zhi H. Wong creator: Sze H. Yek uri: https://doi.org/10.7717/peerj.10033 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lee et al. title: Low-cost air pollution monitoring system—an opportunity for reducing the health risk associated with physical activity in polluted air link: https://peerj.com/articles/10041 last-modified: 2020-10-01 description: The issue of air pollution by particulate matter (PM) concerns many places in the world. At the same time, many residents undertake physical activity (recreation, rehabilitation, sport) in the open air. Generally, the amount of dust concentration depends on both the place (center or periphery of the city) and the time of day. In the present study we describe the outcome of monitoring of the state of air pollution by particle matter (PM10) in the Kraków agglomeration area in order to show that it can provide information concerning air quality in the area where people practice varied kinds of sports in the open air. The measurements of PM10 have been made by a few stations with identical construction working as one network. The details of the air pollution monitoring system and its data quality verification have been described. The network stations made multipoint observations across the Kraków Metropolitan Area during the year 2017 in eight locations. The locations selected represent a diverse spectrum of terrain conditions in which the Kraków agglomeration community undertakes physical activity. For most months of 2017, the minimum monthly average 4-hour PM10 concentrations were recorded between 10–14 h, regardless of location, whereas the maximum was between 18–22. We also noticed a huge differences in the average monthly value of PM10 in some locations within the Kraków agglomeration—ranging between 4.9–339.0 µg m−3. This indicates that some regions of the city are more suitable for performance of physical activity in the open air than others. In conclusion, we postulate that a low-cost air pollution monitoring system is capable of providing valuable information concerning air quality in a given region, which seems to be of importance also to people who practice varied sports activities in the open air. creator: Zenon Nieckarz creator: Jerzy A. Zoladz uri: https://doi.org/10.7717/peerj.10041 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nieckarz and Zoladz title: Brain hothubs and dark functional networks: correlation analysis between amplitude and connectivity for Broca’s aphasia link: https://peerj.com/articles/10057 last-modified: 2020-10-01 description: Source localization and functional brain network modeling are methods of identifying critical regions during cognitive tasks. The first activity estimates the relative differences of the signal amplitudes in regions of interest (ROI) and the second activity measures the statistical dependence among signal fluctuations. We hypothesized that the source amplitude–functional connectivity relationship decouples or reverses in persons having brain impairments. Five Broca’s aphasics with five matched cognitively healthy controls underwent overt picture-naming magnetoencephalography scans. The gamma-band (30–45 Hz) phase-locking values were calculated as connections among the ROIs. We calculated the partial correlation coefficients between the amplitudes and network measures and detected four node types, including hothubs with high amplitude and high connectivity, coldhubs with high connectivity but lower amplitude, non-hub hotspots, and non-hub coldspots. The results indicate that the high-amplitude regions are not necessarily highly connected hubs. Furthermore, the Broca aphasics utilized different hothub sets for the naming task. Both groups had dark functional networks composed of coldhubs. Thus, source amplitude–functional connectivity relationships could help reveal functional reorganizations in patients. The amplitude–connectivity combination provides a new perspective for pathological studies of the brain’s dark functional networks. creator: Feng Lin creator: Shao-Qiang Cheng creator: Dong-Qing Qi creator: Yu-Er Jiang creator: Qian-Qian Lyu creator: Li-Juan Zhong creator: Zhong-Li Jiang uri: https://doi.org/10.7717/peerj.10057 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lin et al. title: Iris sanguinea is conspecific with I. sibirica (Iridaceae) according to morphology and plastid DNA sequence data link: https://peerj.com/articles/10088 last-modified: 2020-10-01 description: A taxonomic revision of Iris subser. Sibiricae is provided based on morphological and molecular analyses and the study of protologues and original material. Two to three species have been recognized in this subseries by botanists. To address the question of species delimitations and relationships within this group, we analyzed four non-coding regions of plastid DNA (trnS–trnG, trnL–trnF, rps4–trnSGGA, and psbA–trnH) for samples from 26 localities across the distribution ranges of two currently recognized species, I. sanguinea and I. sibirica. Variance analysis, based on nine characters, revealed no separation between taxa. Moreover, no morphological character could be used to define clear boundaries between taxa. Our results strongly support that I. subser. Sibiricae is monotypic and comprises only I. sibirica, instead of two or three species. Iris sibirica is morphologically variable and one of the most widespread Eurasian species of Iridaceae. Previously accepted taxa, I. sanguinea and I. typhifolia, are synonymised with I. sibirica and also two names, I. orientalis and I. sibirica var. haematophylla, which are typified here, are placed in the synonymy of I. sibirica. Information on the distribution of I. sibirica and the main features used to distinguish between I. sibirica and I. subser. Chrysographes species are provided. creator: Eugeny Boltenkov creator: Elena Artyukova creator: Marina Kozyrenko creator: Andrey Erst creator: Anna Trias-Blasi uri: https://doi.org/10.7717/peerj.10088 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Boltenkov et al. title: Positive association between COVID-19 deaths and influenza vaccination rates in elderly people worldwide link: https://peerj.com/articles/10112 last-modified: 2020-10-01 description: BackgroundThe coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global health crisis, directly and indirectly impacting all spheres of human life. Some pharmacological measures have been proposed to prevent COVID-19 or reduce its severity, such as vaccinations. Previous reports indicate that influenza vaccination appears to be negatively correlated with COVID-19-associated mortality, perhaps as a result of heterologous immunity or changes in innate immunity. The understanding of such trends in correlations could prevent deaths from COVID-19 in the future. The aim of this study was therefore to analyze the association between COVID-19 related deaths and influenza vaccination rate (IVR) in elderly people worldwide.MethodsTo determine the association between COVID-19 deaths and influenza vaccination, available data sets from countries with more than 0.5 million inhabitants were analyzed (in total 39 countries). To accurately estimate the influence of IVR on COVID-19 deaths and mitigate effects of confounding variables, a sophisticated ranking of the importance of different variables was performed, including as predictor variables IVR and some potentially important geographical and socioeconomic variables as well as variables related to non-pharmaceutical intervention. The associations were measured by non-parametric Spearman rank correlation coefficients and random forest functions.ResultsThe results showed a positive association between COVID-19 deaths and IVR of people ≥65 years-old. There is a significant increase in COVID-19 deaths from eastern to western regions in the world. Further exploration is needed to explain these findings, and additional work on this line of research may lead to prevention of deaths associated with COVID-19. creator: Christian Wehenkel uri: https://doi.org/10.7717/peerj.10112 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wehenkel title: A strength-oriented exercise session required more recovery time than a power-oriented exercise session with equal work link: https://peerj.com/articles/10044 last-modified: 2020-09-30 description: The present randomized cross-over controlled study aimed to compare the rate of recovery from a strength-oriented exercise session vs. a power-oriented session with equal work. Sixteen strength-trained individuals conducted one strength-oriented session (five repetitions maximum (RM)) and one power-oriented session (50% of 5RM) in randomized order. Squat jump (SJ), countermovement jump (CMJ), 20-m sprint, and squat and bench press peak power and estimated 1RMs were combined with measures of rate of perceived exertion (RPE) and perceived recovery status (PRS), before, immediately after and 24 and 48 h after exercise. Both sessions induced trivial to moderate performance decrements in all variables. Small reductions in CMJ height were observed immediately after both the strength-oriented session (7 ± 6%) and power-oriented session (5 ± 5%). Between 24 and 48 h after both sessions CMJ and SJ heights and 20 m sprint were back to baseline. However, in contrast to the power-oriented session, recovery was not complete 48 h after the strength-oriented session, as indicated by greater impairments in CMJ eccentric and concentric peak forces, SJ rate of force development (RFD) and squat peak power. In agreement with the objective performance measurements, RPE and PRS ratings demonstrated that the strength-oriented session was experienced more strenuous than the power-oriented session. However, these subjective measurements agreed poorly with performance measurements at the individual level. In conclusion, we observed a larger degree of neuromuscular impairment and longer recovery times after a strength-oriented session than after a power-oriented session with equal total work, measured by both objective and subjective assessments. Nonetheless, most differences were small or trivial after either session. It appears necessary to combine several tests and within-test analyses (e.g., CMJ height, power and force) to reveal such differences. Objective and subjective assessments of fatigue and recovery cannot be used interchangeably; rather they should be combined to give a meaningful status for an individual in the days after a resistance exercise session. creator: Christian Helland creator: Magnus Midttun creator: Fredrik Saeland creator: Lars Haugvad creator: Daniela Schäfer Olstad creator: Paul Andre Solberg creator: Gøran Paulsen uri: https://doi.org/10.7717/peerj.10044 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Helland et al. title: Metabolomics analysis identifies metabolites associated with systemic acquired resistance in Arabidopsis link: https://peerj.com/articles/10047 last-modified: 2020-09-30 description: BackgroundSystemic acquired resistance (SAR) is a type of plant defense response that provides a long-lasting resistance to broad-spectrum pathogens in uninfected distal tissues following an initial localized infection. However, little information is available at present on the biological basis of SAR at the molecular level, especially in uninfected distal leaves.MethodsIn the present work, we used two SAR-inducing pathogens, avirulent Pseudomonas syringae pv. maculicola ES4326 harboring avrRpm1 (Psm avrRpm1) and virulent P. syringae pv. maculicola ES4326 (Psm ES4326), to induce SAR in Arabidopsis ecotype Col-0. A metabolomics approach based on ultra-high-performance liquid chromatography (UPLC) coupled with mass spectrometry (MS) was used to identify SAR-related metabolites in infected local leaves, and in uninfected distal leaves.ResultsDifferentially accumulated metabolites were distinguished by statistical analyses. The results showed that both the primary metabolism and the secondary metabolism were significantly altered in infected local leaves and in uninfected distal leaves, including phenolic compounds, amino acids, nucleotides, organic acids, and many other metabolites.ConclusionsThe content of amino acids and phenolic compounds increased in uninfected distal leaves, suggesting their contribution to the establishment of SAR. In addition, 2′-hydroxy-4, 4′, 6′-trimethoxychalcone, phenylalanine, and p-coumaric acid were identified as potential components which may play important roles both in basic resistance and in SAR. This work provides a reference for understanding of the metabolic mechanism associated with SAR in plants, which will be useful for further investigation of the molecular basis of the systemic immunity. creator: Hang Gao creator: Qian Zhou creator: Liu Yang creator: Kaili Zhang creator: Yeye Ma creator: Zi-Qin Xu uri: https://doi.org/10.7717/peerj.10047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gao et al. title: Forest structure dependency analysis of L-band SAR backscatter link: https://peerj.com/articles/10055 last-modified: 2020-09-30 description: Forest structure plays an important role in forest biomass inversion using synthetic aperture radar (SAR) backscatter. Synthetic aperture radar (SAR) sensors with long-wavelength have the potentiality to provide reliable and timely forest biomass inversion for their ability of deep penetration into the forest. L-band SAR backscatter shows useful for forest above-ground biomass (AGB) estimation. However, the way that forest structure mediating the biomass-backscatter affects the improvement of the related biomass estimation accuracy. In this paper, we have investigated L-band SAR backscatter sensitivity to forests with different mean canopy density, mean tree height and mean DBH (diameter at breast height) at the sub-compartment level. The forest species effects on their relationship were also considered in this study. The linear correlation coefficient R, non-linear correlation parameter, Maximal Information Coefficient (MIC), and the determination coefficient R2 from linear function, Logarithmic function and Quadratic function were used in this study to analyze forest structural properties effects on L-band SAR backscatter. The HV channel, which is more sensitive than HH to forest structure parameters, was chosen as the representative of SAR backscatter. 6037 sub-compartment were involved in the analysis. Canopy density showed a great influence on L-band backscatter than mean forest height and DBH. All of the R between canopy density and L-band backscatter were greater than 0.7 during the forest growth cycle. The sensitivity of L-band backscatter to mean forest height depends on forest canopy density. When canopy density was lower than 0.4, R values between mean forest height are smaller than 0.5. In contrast, the values of R were greater than 0.8 if canopy density was higher than 0.4. The sensitivity SAR backscatter to DBH fluctuated with canopy density, but it only showed obvious sensitivity when canopy density equals to 0.6, where both the linear and non-liner correlation values are higher than others. However, their effects on L-bang HV backscatter are affected by forest species, the effects on three forest structural parameters depend on tree species. creator: Yongjie Ji creator: Jimao Huang creator: Yilin Ju creator: Shipeng Guo creator: Cairong Yue uri: https://doi.org/10.7717/peerj.10055 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ji et al. title: Social influence on the effectiveness of virtual fencing in sheep link: https://peerj.com/articles/10066 last-modified: 2020-09-30 description: Early virtual fencing trials have effectively contained small groups of sheep within set areas of a paddock when all animals were wearing manual electronic collars. With sheep farming commonly involving large flocks, a potential cost-effective application of virtual fencing would involve applying equipment to only a proportion of the flock. In this study, we tested the ability of virtual fencing to control a small flock of sheep with differing proportions of the group exposed to the virtual fence (VF). Thirty-six Merino sheep were identified as leaders, middle or followers by moving them through a laneway. The sheep were then allocated to groups balanced for order of movement. The groups (n = 9 per group) included applying the VF to the following proportions of animals within each group: (1) 100% (n = 9 VF) (2) 66% (n = 6 VF; n = 3 no VF) (3) 33% (n = 3 VF; n = 6 no VF) (4) 0% (no VF; free to roam the paddock). The groups were given access to their own paddock (80 × 20 m) for two consecutive days, six hours per day, with the VF groups prevented from entering an exclusion zone that covered 50% of the north side of the paddock. During these hours, VF interactions, behavioural time budgets, and body temperature were recorded as measures of stress, and location was tracked with GPS. Group 100% VF and Control were tested on the first two days and groups 33% VF and 66% VF were tested on the following two days. During VF implementation the 100% VF and 66% VF group were successfully prevented from entering the exclusion zone. Having only 33% of the flock exposed to the virtual fence was not successful, with the sheep pushing forward through the VF to join flock mates in the exclusion zone. For learning to respond to the audio cue, sheep in the 33% group received more electrical stimuli with a 0.51 proportion for the ratio of electrical stimuli to audio cue, compared to 0.22 and 0.28 for the 100% and 66% groups, respectively. There were small differences in behavioural patterns of standing and lying on both days of testing, with the 100% VF and 66% VF groups spending more time lying. Although stress-induced hyperthermia did not occur in any of the VF groups, body temperature differed in the 33% VF group. There were no differences in temperature measures between the control and 100% VF animals. This study demonstrates that for a short period, controlling two-thirds of the flock was equally as effective as virtually fencing all animals, while controlling one-third of a flock with a virtual fence was not effective. For the short term, it appears that implementing the VF to a proportion of the flock can be an effective method of containment. Due to the limitations of this study, these results warrant further testing with larger flocks and for longer periods. creator: Danila Marini creator: Tellisa Kearton creator: Jackie Ouzman creator: Rick Llewellyn creator: Sue Belson creator: Caroline Lee uri: https://doi.org/10.7717/peerj.10066 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Marini et al.