title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1012 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Trends in summer presence of fin whales in the Western Mediterranean Sea Region: new insights from a long-term monitoring program link: https://peerj.com/articles/10544 last-modified: 2020-12-14 description: BackgroundThe Mediterranean subpopulation of fin whale Balaenoptera physalus (Linnaeus, 1758) has recently been listed as Vulnerable by the IUCN Red List of threatened species. The species is also listed as species in need of strict protection under the Habitat Directive and is one of the indicators for the assessment of Good Environmental Status under the MSFD. Reference values on population abundance and trends are needed in order to set the threshold values and to assess the conservation status of the population.MethodsYearly summer monitoring using ferries as platform of opportunity was performed since 2008 within the framework of the FLT Med Network. Data were collected along several fixed transects crossing the Western Mediterranean basin and the Adriatic and Ionian region. Species presence, expressed by density recorded along the sampled transects, was inspected for assessing interannual variability together with group size. Generalized Additive Models were used to describe density trends over a 11 years’ period (2008–2018). A spatial multi-scale approach was used to highlight intra-basin differences in species presence and distribution during the years.ResultsSummer presence of fin whales in the western Mediterranean area showed a strong interannual variability, characterized by the alternance of rich and poor years. Small and large groups of fin whales were sighted only during rich years, confirming the favorable feeding condition influencing species presence. Trends highlighted by the GAM can be summarized as positive from 2008 to 2013, and slightly negative from 2014 to 2018. The sub-areas analysis showed a similar pattern, but with a more stable trend during the second period in the Pelagos Sanctuary sub-area, and a negative one in the other two sub-areas. Our findings further confirm the need for an integrated approach foreseeing both, large scale surveys and yearly monitoring at different spatial scales to correct and interpret the basin wide abundance estimates, and to correlate spatial and temporal trends with the ecological and anthropogenic drivers. creator: Paola Tepsich creator: Ilaria Schettino creator: Fabrizio Atzori creator: Marta Azzolin creator: Ilaria Campana creator: Lara Carosso creator: Simone Cominelli creator: Roberto Crosti creator: Léa David creator: Nathalie Di-Méglio creator: Francesca Frau creator: Martina Gregorietti creator: Veronica Mazzucato creator: Clara Monaco creator: Aurelie Moulins creator: Miriam Paraboschi creator: Giuliana Pellegrino creator: Massimiliano Rosso creator: Marine Roul creator: Sébastien Saintignan creator: Antonella Arcangeli uri: https://doi.org/10.7717/peerj.10544 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tepsich et al. title: Portanini (Insecta: Hemiptera: Cicadellidae) from Peru: checklist with new records and descriptions of two new species link: https://peerj.com/articles/10222 last-modified: 2020-12-11 description: Portanini Linnavuori, 1959 is a small tribe of neotropical leafhoppers that includes two genera: Portanus Ball, 1932 and MetacephalusDeLong & Martinson, 1973. Herein, a checklist of portanines from Peru is given, including several new species records for the country, elevating the known diversity from nine to 22 species. In addition, four species have their department ranges expanded in Peru. Two new portanine species are also described: Metacephalus mamaquillasp. nov. and Portanus tambopatasp. nov. both from Tambopata National Reserve, Madre de Dios, Peru and we make available habitus photos of other Portanini species from this reserve. creator: Jádila Santos Prando creator: Clayton Corrêa Gonçalves creator: Daniela Maeda Takiya uri: https://doi.org/10.7717/peerj.10222 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Santos Prando et al. title: Driver versus navigator causation in biology: the case of insulin and fasting glucose link: https://peerj.com/articles/10396 last-modified: 2020-12-11 description: BackgroundIn biomedicine, inferring causal relation from experimental intervention or perturbation is believed to be a more reliable approach than inferring causation from cross-sectional correlation. However, we point out here that even in interventional inference there are logical traps. In homeostatic systems, causality in a steady state can be qualitatively different from that in a perturbed state. On a broader scale there is a need to differentiate driver causality from navigator causality. A driver is essential for reaching a destination but may not have any role in deciding the destination. A navigator on the other hand has a role in deciding the destination and the path but may not be able to drive the system to the destination. The failure to differentiate between types of causalities is likely to have resulted into many misinterpretations in physiology and biomedicine.MethodsWe illustrate this by critically re-examining a specific case of the causal role of insulin in glucose homeostasis using five different approaches (1) Systematic review of tissue specific insulin receptor knock-outs, (2) Systematic review of insulin suppression and insulin enhancement experiments, (3) Differentiating steady state and post-meal state glucose levels in streptozotocin treated rats in primary experiments, (4) Mathematical and theoretical considerations and (5) Glucose-insulin relationship in human epidemiological data.ResultsAll the approaches converge on the inference that although insulin action hastens the return to a steady state after a glucose load, there is no evidence that insulin action determines the steady state level of glucose. Insulin, unlike the popular belief in medicine, appears to be a driver but not a navigator for steady state glucose level. It is quite likely therefore that the current line of clinical action in the field of type 2 diabetes has limited success largely because it is based on a misinterpretation of glucose-insulin relationship. The insulin-glucose example suggests that we may have to carefully re-examine causal inferences from perturbation experiments and set up revised norms for experimental design for causal inference. creator: Manawa Diwekar-Joshi creator: Milind Watve uri: https://doi.org/10.7717/peerj.10396 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Diwekar-Joshi and Watve title: Exogenous melatonin improves salt stress adaptation of cotton seedlings by regulating active oxygen metabolism link: https://peerj.com/articles/10486 last-modified: 2020-12-11 description: Melatonin is a small-molecule indole hormone that plays an important role in participating in biotic and abiotic stress resistance. Melatonin has been confirmed to promote the normal development of plants under adversity stress by mediating physiological regulation mechanisms. However, the mechanisms by which exogenous melatonin mediates salt tolerance via regulation of antioxidant activity and osmosis in cotton seedlings remain largely unknown. In this study, the regulatory effects of melatonin on reactive oxygen species (ROS), the antioxidant system, and osmotic modulators of cotton seedlings were determined under 0–500 µM melatonin treatments with salt stress induced by 150 mM NaCl treatment. Cotton seedlings under salt stress exhibited an inhibition of growth, excessive hydrogen peroxide (H2O2), superoxide anion (O2−), and malondialdehyde (MDA) accumulations in leaves, increased activity levels of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), and elevated ascorbic acid (AsA) and glutathione (GSH) content in leaves. However, the content of osmotic regulators (i.e., soluble sugars and proteins) in leaves was reduced under salt stress. This indicates high levels of ROS were produced, and the cell membrane was damaged. Additionally, osmotic regulatory substance content was reduced, resulting in osmotic stress, which seriously affected cotton seedling growth under salt stress. However, exogenous melatonin at different concentrations reduced the contents of H2O2, O2−, and MDA in cotton leaves, increased the activity of antioxidant enzymes and the content of reductive substances (i.e., AsA and GSH), and promoted the accumulation of osmotic regulatory substances in leaves under salt stress. These results suggest that melatonin can inhibit ROS production in cotton seedlings, improve the activity of the antioxidant enzyme system, raise the content of osmotic regulation substances, reduce the level of membrane lipid peroxidation, and protect the integrity of the lipid membrane under salt stress, which reduces damage caused by salt stress to seedlings and effectively enhances inhibition of salt stress on cotton seedling growth. These results indicate that 200 µM melatonin treatment has the best effect on the growth and salt tolerance of cotton seedlings. creator: Dan Jiang creator: Bin Lu creator: Liantao Liu creator: Wenjing Duan creator: Li Chen creator: Jin Li creator: Ke Zhang creator: Hongchun Sun creator: Yongjiang Zhang creator: Hezhong Dong creator: Cundong Li creator: Zhiying Bai uri: https://doi.org/10.7717/peerj.10486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jiang et al. title: Association analysis of Suboptimal health Status: a cross-sectional study in China link: https://peerj.com/articles/10508 last-modified: 2020-12-11 description: BackgroundSuboptimal health status (SHS) among urban residents is commonplace in China. However, factors influencing SHS have not been thoroughly explored, especially with regard to the effects of internal factors (e.g., personality and health awareness) on SHS.MethodsA cross-sectional study was conducted with a nationally representative sample of 5460 Chinese urban residents..SHS was measured using the Suboptimal Health Mesurement Scale Version 1.0. Demographic information, and information pertaining to lifestyle behaviors, environmental factors, and internal factors were abtained through a questionnaire. The associations between demographic information, lifestyle behaviors, environmental factors, internal factors and SHS were assessed using logistic regression.ResultsOf the 5460 participants (with a mean age of 41.56 ±  16.14 years), 2640 (48.4 %) were men. Out of 36 variables, 23 were significantly associated with SHS: age (odds ratio [OR]: 1.014), an education level of high school/junior college (OR: 1.443) , marital status (OR: 1.899), area of registered permanent residence (OR: 0.767), monthly household income (p < 0.001) , exposure to second-hand smoke (p = 0.001), alcohol drinking (OR: 1.284), bad eating habits (OR: 1.717), not sleeping before 11 p.m. every day (p = 0.002), spending time online more than five hours a day (OR: 1.526), having a good relationship with parents during one’s growth period (OR: 0.602), living with good quality air (OR:0.817), living in not crowded conditions (OR:0.636), having a harmonious neighborhood (OR:0.775), having adequate fitness facilities (OR:0.783), one’s health being affected by two-child policy (OR: 1.468) and medical policies (OR: 1.265) , high adverse quotient (OR: 0.488), many (≥3 kinds) interests and hobbies (OR: 0.617), mature and steady personality traits (OR: 0.469) , a high attention to one’s health (OR: 0.833), and effective health promotion induced by leading a leisurely lifestyle (OR: 0.466) were significantly associated with SHS.ConclusionsAll these variables were included demographic information, lifestyle behaviors, environmental factors and internal factors. Our study supports the benefits of controlling both internal and external factors in preventing suboptimal health. creator: Yunlian Xue creator: Zhuomin Huang creator: Guihao Liu creator: Yefang Feng creator: Mengyao Xu creator: Lijie Jiang creator: Jun Xu uri: https://doi.org/10.7717/peerj.10508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xue et al. title: Detection and estimating the blood accumulation volume of brain hemorrhage in a human anatomical skull using a RF single coil link: https://peerj.com/articles/10416 last-modified: 2020-12-10 description: ObjectiveAn experimental study for testing a simple robust algorithm on data derived from an electromagnetic radiation device that can detect small changes in the tissue/fluid ratio in a realistic head configuration.MethodsChanges in the scattering parameters (S21) of an inductive coil resulting from injections of chicken blood in the 0–18 ml range into calf brain tissue in a human anatomical skull were measured over a 100–1,000 MHz frequency range.ResultsAn algorithm that combines amplitude and phase results was found to detect changes in the tissue/fluid ratio with 90% accuracy. An algorithm that estimated the injected blood volume was found to have a 1–4 ml average error. This demonstrates the possibility of the inductive coil-based device to possess a practical ability to detect a change in the tissue/fluid ratio in the head.SignificanceThis study is an important step towards the goal of building an inexpensive and safe device that can detect an early brain hemorrhagic stroke. creator: Moshe Oziel creator: Boris Rubinsky creator: Rafi Korenstein uri: https://doi.org/10.7717/peerj.10416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Oziel et al. title: Multi-year pair-bonding in Murray cod (Maccullochella peelii) link: https://peerj.com/articles/10460 last-modified: 2020-12-10 description: Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes—in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes. creator: Alan J. Couch creator: Fiona Dyer creator: Mark Lintermans uri: https://doi.org/10.7717/peerj.10460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Couch et al. title: Determinants of behavioural and biological risk factors for cardiovascular diseases from state level STEPS survey (2017–19) in Madhya Pradesh link: https://peerj.com/articles/10476 last-modified: 2020-12-10 description: BackgroundNational and statewide assessment of cardiovascular risk factors needs to be conducted periodically in order to inform public health policy and prioritise allocation of funds, especially in LMICs. Although there have been studies from India which have explored the determinants of cardiovascular risk factors, they have mostly been from high epidemiological transition states. The present study assessed the determinants of cardiovascular (CVD) risk factors in a low epidemiological transition state (Madhya Pradesh) using the WHO STEPwise approach to surveillance (STEPS).MethodsA total of 5,680 persons aged 18–69 years were selected from the state of Madhya Pradesh through multi-stage cluster random sampling. Key CVD risk factors we sought to evaluate were from behavioural (tobacco, alcohol, physical activity, diet) and biological domains (overweight or obese, Hypertension, Diabetes, and Raised serum cholesterol). Key socio-demographic factors of interest were the caste and tribe groups, and rural vs urban location, in addition to known influencers of CVD risk such as age, gender and education levelResultsThose belonging to the scheduled tribes were more at risk of consuming tobacco (OR 2.13 (95% CI [1.52–2.98]), and a diet with less than five servings of fruits and vegetables (OR 2.78 (95% CI [1.06–7.24]), but had had the least risk of physical inactivity (OR 0.31 (95% CI [0.02–0.54]). Residence in a rural area also reduced the odds of physical inactivity (OR 0.65 (95% CI [0.46–0.92])). Lack of formal education was a risk factor for both tobacco consumption and alcohol intake (OR 1.40 (95% CI [1.08–1.82]) for tobacco use; 1.68 (95% CI [1.14–2.49]) for alcohol intake). Those belonging to schedules tribes had much lower risk of being obese (OR 0.25; 95% CI [0.17–0.37]), but were at similar risk of all other clinical CVD risk factors as compared to other caste groups.ConclusionIn the current study we explored socio-demographic determinants of behavioural and biological CVD risks, and found that in Madhya Pradesh, belonging to a scheduled tribe or living in a rural location, protects against being physically inactive or being overweight or obese. Increasing age confers a greater CVD-risk in all domains. Being a male, and lack of formal education confers a greater risk for behavioural domains, but not for most clinical risk domains. Future efforts at curbing CVDs should be therefore two pronged –a population-based strategy targeting biological risk factors, and a more focussed approach directed at those displaying risky behaviour. creator: Arun M. Kokane creator: Rajnish Joshi creator: Ashwin Kotnis creator: Anirban Chatterjee creator: Kriti Yadav creator: G Revadi creator: Ankur Joshi creator: Abhijit P. Pakhare uri: https://doi.org/10.7717/peerj.10476 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kokane et al. title: miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts link: https://peerj.com/articles/10502 last-modified: 2020-12-10 description: BackgroundRadiation exposure of the thorax is associated with a greatly increased risk of cardiac morbidity and mortality even after several decades of advancement in the field. Although many studies have demonstrated the damaging influence of ionizing radiation on cardiac fibroblast (CF) structure and function, myocardial fibrosis, the molecular mechanism behind this damage is not well understood. miR-21, a small microRNA, promotes the activation of CFs, leading to cardiac fibrosis. miR-21 is overexpressed after irradiation; however, the relationship between increased miR-21 and myocardial fibrosis after irradiation is unclear. This study was conducted to investigate gene expression after radiation-induced CF damage and the role of miR-21 in this process in rats.MethodsWe sequenced irradiated rat CFs and performed weighted correlation network analysis (WGCNA) combined with differentially expressed gene (DEG) analysis to observe the effect on the expression profile of CF genes after radiation.ResultsDEG analysis showed that the degree of gene changes increased with the radiation dose. WGCNA revealed three module eigengenes (MEs) associated with 8.5-Gy-radiation—the Yellow, Brown, Blue modules. The three module eigengenes were related to apoptosis, G2/M phase, and cell death and S phase, respectively. By blocking with the cardiac fibrosis miRNA miR-21, we found that miR-21 was associated with G2/M blockade in the cell cycle and was mainly involved in regulating extracellular matrix-related genes, including Grem1, Clu, Gdf15, Ccl7, and Cxcl1. Stem-loop quantitative real-time PCR was performed to verify the expression of these genes. Five genes showed higher expression after 8.5 Gy-radiation in CFs. The target genes of miR-21 predicted online were Gdf15 and Rsad2, which showed much higher expression after treatment with antagomir-miR-21 in 8.5-Gy-irradiated CFs. Thus, miR-21 may play the role of fibrosis and G2/M blockade in regulating Grem1, Clu, Gdf15, Ccl7, Cxcl1, and Rsad2 post-irradiation. creator: Huan Guo creator: Xinke Zhao creator: Haixiang Su creator: Chengxu Ma creator: Kai Liu creator: Shanshan Kong creator: Kedan Liu creator: Haining Li creator: Juan Chang creator: Tao Wang creator: Hongyun Guo creator: Huiping Wei creator: Zhaoyuan Fu creator: Xinfang Lv creator: Yingdong Li uri: https://doi.org/10.7717/peerj.10502 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease link: https://peerj.com/articles/10513 last-modified: 2020-12-10 description: We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein–protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD. creator: Jie Zhang creator: Changli Zhu creator: Hong Gao creator: Xun Liang creator: Xiaoqian Fan creator: Yulong Zheng creator: Song Chen creator: Yufeng Wan uri: https://doi.org/10.7717/peerj.10513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al.