title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=671 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Catch composition and risk assessment of two fishing gears used in small-scale fisheries of Bandon Bay, the Gulf of Thailand link: https://peerj.com/articles/13878 last-modified: 2022-08-16 description: We examined catch compositions and vulnerability of target and bycatch species in two fishing gears, namely the bottom-set gillnet and collapsible crab trap, used in small-scale fisheries of Bandon Bay, Suratthani Province, Thailand. Both gears mainly target the blue swimming crab (BSC) Portunus pelagicus, and together contribute about half of Thailand’s annual BSC catch of around 2.5 thousand tonnes. Field sampling was conducted from January to November of 2018. Specimens from bottom-set gillnets and collapsible crab traps comprised 111 and 118 taxa, respectively. Of these, 26 and 27 crab species and 41 and 46 fish species were collected by gillnets and traps, respectively. The index of relative importance of BSC was higher in gillnets (48.8 ± 16.6%) than in traps (25.0 ± 15.5%), where another swimming crab (Charybdis affinis) was more common. Cluster analysis revealed that catch compositions were seasonal and differed between the two monsoonal seasons, i.e., northeast monsoon (October to February) and southwest monsoon (May to September), and the transition period (March and April). Potential impact from both fishing gears on various stocks was assessed by standard productivity and susceptibility analysis (PSA). Vulnerability scores of the BSC stock as the main target species suggested it was at moderate risk, as assessed by PSA. The impacts of both gears to stocks of the other species in Bandon Bay showed either low or moderate risk. Ten fish stocks, including two stingrays, six species of sole and two other bony fishes, were near the threshold of high risk from gillnet fishing. creator: Tuantong Jutagate creator: Amonsak Sawusdee uri: https://doi.org/10.7717/peerj.13878 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jutagate and Sawusdee title: Rainforest conversion to rubber and oil palm reduces abundance, biomass and diversity of canopy spiders link: https://peerj.com/articles/13898 last-modified: 2022-08-16 description: Rainforest canopies, home to one of the most complex and diverse terrestrial arthropod communities, are threatened by conversion of rainforest into agricultural production systems. However, little is known about how predatory arthropod communities respond to such conversion. To address this, we compared canopy spider (Araneae) communities from lowland rainforest with those from three agricultural systems in Jambi Province, Sumatra, Indonesia, i.e., jungle rubber (rubber agroforest) and monoculture plantations of rubber and oil palm. Using canopy fogging, we collected 10,676 spider specimens belonging to 36 families and 445 morphospecies. The four most abundant families (Salticidae N = 2,043, Oonopidae N = 1,878, Theridiidae N = 1,533 and Clubionidae N = 1,188) together comprised 62.2% of total individuals, while the four most speciose families, Salticidae (S = 87), Theridiidae (S = 83), Araneidae (S = 48) and Thomisidae (S = 39), contained 57.8% of all morphospecies identified. In lowland rainforest, average abundance, biomass and species richness of canopy spiders was at least twice as high as in rubber or oil palm plantations, with jungle rubber showing similar abundances as rainforest, and intermediate biomass and richness. Community composition of spiders was similar in rainforest and jungle rubber, but differed from rubber and oil palm, which also differed from each other. Canonical Correspondence Analysis showed that canopy openness, aboveground tree biomass and tree density together explained 18.2% of the variation in spider communities at family level. On a morphospecies level, vascular plant species richness and tree density significantly affected the community composition but explained only 6.8% of the variance. While abundance, biomass and diversity of spiders declined strongly with the conversion of rainforest into monoculture plantations of rubber and oil palm, we also found that a large proportion of the rainforest spider community can thrive in extensive agroforestry systems such as jungle rubber. Despite being very different from rainforest, the canopy spider communities in rubber and oil palm plantations may still play a vital role in the biological control of canopy herbivore species, thus contributing important ecosystem services. The components of tree and palm canopy structure identified as major determinants of canopy spider communities may aid in decision-making processes toward establishing cash-crop plantation management systems which foster herbivore control by spiders. creator: Daniel Ramos creator: Tamara R. Hartke creator: Damayanti Buchori creator: Nadine Dupérré creator: Purnama Hidayat creator: Mayanda Lia creator: Danilo Harms creator: Stefan Scheu creator: Jochen Drescher uri: https://doi.org/10.7717/peerj.13898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ramos et al. title: Building a synthesis of economic costs of biological invasions in New Zealand link: https://peerj.com/articles/13580 last-modified: 2022-08-15 description: Biological invasions are a major component of anthropogenic environmental change, incurring substantial economic costs across all sectors of society and ecosystems. There have been recent syntheses of costs for a number of countries using the newly compiled InvaCost database, but New Zealand—a country renowned for its approach to invasive species management—has so far not been examined. Here we analyse reported economic damage and management costs incurred by biological invasions in New Zealand from 1968 to 2020. In total, US$69 billion (NZ$97 billion) is currently reported over this ∼50-year period, with approximately US$9 billion of this considered highly reliable, observed (c.f. projected) costs. Most (82%) of these observed economic costs are associated with damage, with comparatively little invested in management (18%). Reported costs are increasing over time, with damage averaging US$120 million per year and exceeding management expenditure in all decades. Where specified, most reported costs are from terrestrial plants and animals, with damages principally borne by primary industries such as agriculture and forestry. Management costs are more often associated with interventions by authorities and stakeholders. Relative to other countries present in the InvaCost database, New Zealand was found to spend considerably more than expected from its Gross Domestic Product on pre- and post-invasion management costs. However, some known ecologically (c.f. economically) impactful invasive species are notably absent from estimated damage costs, and management costs are not reported for a number of game animals and agricultural pathogens. Given these gaps for known and potentially damaging invaders, we urge improved cost reporting at the national scale, including improving public accessibility through increased access and digitisation of records, particularly in overlooked socioeconomic sectors and habitats. This also further highlights the importance of investment in management to curtail future damages across all sectors. creator: Thomas W. Bodey creator: Zachary T. Carter creator: Phillip J. Haubrock creator: Ross N. Cuthbert creator: Melissa J. Welsh creator: Christophe Diagne creator: Franck Courchamp uri: https://doi.org/10.7717/peerj.13580 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bodey et al. title: Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction link: https://peerj.com/articles/13848 last-modified: 2022-08-15 description: BackgroundEfficient identification of microbe-drug associations is critical for drug development and solving problem of antimicrobial resistance. Traditional wet-lab method requires a lot of money and labor in identifying potential microbe-drug associations. With development of machine learning and publication of large amounts of biological data, computational methods become feasible.MethodsIn this article, we proposed a computational model of neighborhood-based inference (NI) and restricted Boltzmann machine (RBM) to predict potential microbe-drug association (NIRBMMDA) by using integrated microbe similarity, integrated drug similarity and known microbe-drug associations. First, NI was used to obtain a score matrix of potential microbe-drug associations by using different thresholds to find similar neighbors for drug or microbe. Second, RBM was employed to obtain another score matrix of potential microbe-drug associations based on contrastive divergence algorithm and sigmoid function. Because generalization ability of individual method is poor, we used an ensemble learning to integrate two score matrices for predicting potential microbe-drug associations more accurately. In particular, NI can fully utilize similar (neighbor) information of drug or microbe and RBM can learn potential probability distribution hid in known microbe-drug associations. Moreover, ensemble learning was used to integrate individual predictor for obtaining a stronger predictor.ResultsIn global leave-one-out cross validation (LOOCV), NIRBMMDA gained the area under the receiver operating characteristics curve (AUC) of 0.8666, 0.9413 and 0.9557 for datasets of DrugVirus, MDAD and aBiofilm, respectively. In local LOOCV, AUCs of 0.8512, 0.9204 and 0.9414 were obtained for NIRBMMDA based on datasets of DrugVirus, MDAD and aBiofilm, respectively. For five-fold cross validation, NIRBMMDA acquired AUC and standard deviation of 0.8569 ± −0.0027, 0.9248 ± −0.0014 and 0.9369 ± −0.0020 on the basis of datasets of DrugVirus, MDAD and aBiofilm, respectively. Moreover, case study for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed that 13 out of the top 20 predicted drugs were verified by searching literature. The other two case studies indicated that 17 and 17 out of the top 20 predicted microbes for the drug of ciprofloxacin and minocycline were confirmed by identifying published literature, respectively. creator: Xiaolong Cheng creator: Jia Qu creator: Shuangbao Song creator: Zekang Bian uri: https://doi.org/10.7717/peerj.13848 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cheng et al. title: The role of autophagy in high-fat diet-induced insulin resistance of adipose tissues in mice link: https://peerj.com/articles/13867 last-modified: 2022-08-15 description: AimsStudies have observed changes in autophagic flux in the adipose tissue of type 2 diabetes patients with obesity. However, the role of autophagy in obesity-induced insulin resistance is unclear. We propose to confirm the effect of a high-fat diet (HFD) on autophagy and insulin signaling transduction from adipose tissue to clarify whether altered autophagy-mediated HFD induces insulin resistance, and to elucidate the possible mechanisms in autophagy-regulated adipose insulin sensitivity.MethodsEight-week-old male C57BL/6 mice were fed with HFD to confirm the effect of HFD on autophagy and insulin signaling transduction from adipose tissue. Differentiated 3T3-L1 adipocytes were treated with 1.2 mM fatty acids (FAs) and 50 nM Bafilomycin A1 to determine the autophagic flux. 2.5 mg/kg body weight dose of Chloroquine (CQ) in PBS was locally injected into mouse epididymal adipose (10 and 24 h) and 40 µM of CQ to 3T3-L1 adipocytes for 24 h to evaluate the role of autophagy in insulin signaling transduction.ResultsThe HFD treatment resulted in a significant increase in SQSTM1/p62, Rubicon expression, and C/EBP homologous protein (CHOP) expression, yet the insulin capability to induce Akt (Ser473) and GSK3β (Ser9) phosphorylation were reduced. PHLPP1 and PTEN remain unchanged after CQ injection. In differentiated 3T3-L1 adipocytes treated with CQ, although the amount of phospho-Akt stimulated by insulin in the CQ-treated group was significantly lower, CHOP expressions and cleaved caspase-3 were increased and bafilomycin A1 induced less accumulation of LC3-II protein.ConclusionLong-term high-fat diet promotes insulin resistance, late-stage autophagy inhibition, ER stress, and apoptosis in adipose tissue. Autophagy suppression may not affect insulin signaling transduction via phosphatase expression but indirectly causes insulin resistance through ER stress or apoptosis. creator: Yovita Permata Budi creator: Yi-Hsuan Li creator: Chien Huang creator: Mu-En Wang creator: Yi-Chun Lin creator: De-Shien Jong creator: Chih-Hsien Chiu creator: Yi-Fan Jiang uri: https://doi.org/10.7717/peerj.13867 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Budi et al. title: Increased mental stress among undergraduate medical students in south-western Saudi Arabia during the COVID-19 pandemic link: https://peerj.com/articles/13900 last-modified: 2022-08-15 description: BackgroundThe COVID-19 pandemic has disrupted the daily life and academic trajectory of many students. The objectives of this study were to evaluate the effect of the pandemic on perceived stress levels among medical students.MethodsComparative pre-pandemic and pandemic surveys were conducted among samples of undergraduate medical students. Students responded to a questionnaire including personal and academic data, and Cohen’s Perceived Stress Scale (PSS).ResultsOverall, the prevalence of high perceived stress during the pandemic (20.6%) was significantly higher (p = 0.001) than pre-pandemic (11.6%). A multivariable analysis revealed that the independent factors associated with high perceived stress were: participation in the study during the pandemic (aOR = 1.79, 95% CI: 1.22–2.63), female sex (aOR = 1.74, 95% CI: 1.23–2.47), younger age (aOR = 1.62, 95% CI: 1.04–2.55) and lower family income (aOR = 1.50, 95% CI: 1.12–2.03). PSS score was negatively correlated with increasing age, family income, and academic level. PSS score was positively correlated with: worries about the possible disruption of education or exams, excessive news exposure, worries about the possibility of COVID-19 infection, and the effects of mandatory isolation and social distancing.ConclusionThe COVID-19 pandemic increased the level of stress among medical students. Female students, younger students, and those in lower academic grades are the most at risk of having high stress. Worries about possible academic disruptions due to the pandemic are significant stressors. The implementation of online stress management programs is recommended. creator: Nabil J. Awadalla creator: Abdullah A. Alsabaani creator: Mohammed A. Alsaleem creator: Safar A. Alsaleem creator: Ayoub A. Alshaikh creator: Suliman H. Al-Fifi creator: Ahmed A. Mahfouz uri: https://doi.org/10.7717/peerj.13900 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Awadalla et al. title: Flotillin-1 promotes EMT of gastric cancer via stabilizing Snail link: https://peerj.com/articles/13901 last-modified: 2022-08-15 description: Gastric cancer is one of the most common malignancies worldwide and has been identified as the third leading cause of cancer-related mortality. Flotillin-1 is a lipid raft-associated scaffolding protein and plays an important role in the progression and development of several malignant carcinomas. Flotillin-1 is involved in epithelial-mesenchymal transition (EMT) process of several solid tumors to promote metastasis. However, the detailed characteristics and mechanisms of Flotillin-1 in gastric cancer have rarely been investigated. In this study, we found Flotillin-1 upregulated in gastric cancer, and the high expression of Flotillin-1 correlated with a worse prognosis. The migration and invasion ability of gastric cancer cells was upregulated by overexpressing Flotillin-1. Knockdown of Flotillin-1 inhibits gastric cancer cells metastasis. Flotillin-1 is a key regulator of EMT process and promotes gastric cancer cells metastasis through inducing EMT. Flotillin-1 may interact with a deubiquitinase to inhibit the ubiquitination of Snail in gastric cancer cells to promote EMT process. Our study provides a rationale and potential target for the treatment of gastric cancer. creator: Ying Huang creator: Yun Guo creator: Yi Xu creator: Fei Liu creator: Suli Dai uri: https://doi.org/10.7717/peerj.13901 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Huang et al. title: Does shrub encroachment reduce foraging grass abundance through plant-plant competition in Lesotho mountain rangelands? link: https://peerj.com/articles/13597 last-modified: 2022-08-12 description: Shrub encroachment is understood to be an important problem facing rangeland ecosystems globally. The phenomenon is still poorly understood both in regard to its impacts (e.g., on diversity, productivity, and soil properties) and its causes. We study the impacts and causes of dwarf shrub encroachment in the highlands of Lesotho. There, shrubs have been described as indicators of generalized land degradation and soil erosion. Surprisingly, our findings show that grass abundance is not reduced by shrub abundance, but that forb abundance does decrease with shrub abundance. We suggest that not enough research has been done to examine the role of forbs in livestock diets, nor in assessing its role in plant-plant competition in grass-shrub systems. Equating shrub presence with declines in available forage may be hasty, as according to our results, grasses were not decreased by shrub expansion in this context; however, forbs are critical components of livestock diets. We propose that the role of forbs in this system should be further studied, focusing on the role that high-nutrient or N-fixing forbs could play in returning nutrients to the soil and affecting livestock grazing patterns, both of which could reduce shrub abundances and favor the establishment of a richer forb community. creator: Meredith Root-Bernstein creator: Colin Hoag uri: https://doi.org/10.7717/peerj.13597 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Root-Bernstein and Hoag title: Integrase deficient lentiviral vector: prospects for safe clinical applications link: https://peerj.com/articles/13704 last-modified: 2022-08-12 description: HIV-1 derived lentiviral vector is an efficient transporter for delivering desired genetic materials into the targeted cells among many viral vectors. Genetic material transduced by lentiviral vector is integrated into the cell genome to introduce new functions, repair defective cell metabolism, and stimulate certain cell functions. Various measures have been administered in different generations of lentiviral vector systems to reduce the vector’s replicating capabilities. Despite numerous demonstrations of an excellent safety profile of integrative lentiviral vectors, the precautionary approach has prompted the development of integrase-deficient versions of these vectors. The generation of integrase-deficient lentiviral vectors by abrogating integrase activity in lentiviral vector systems reduces the rate of transgenes integration into host genomes. With this feature, the integrase-deficient lentiviral vector is advantageous for therapeutic implementation and widens its clinical applications. This short review delineates the biology of HIV-1-erived lentiviral vector, generation of integrase-deficient lentiviral vector, recent studies involving integrase-deficient lentiviral vectors, limitations, and prospects for neoteric clinical use. creator: Chee-Hong Takahiro Yew creator: Narmatha Gurumoorthy creator: Fazlina Nordin creator: Gee Jun Tye creator: Wan Safwani Wan Kamarul Zaman creator: Jun Jie Tan creator: Min Hwei Ng uri: https://doi.org/10.7717/peerj.13704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yew et al. title: A retrospective study of risk factors for early-onset neonatal sepsis with intrapartum maternal fever link: https://peerj.com/articles/13834 last-modified: 2022-08-12 description: BackgroundIntrapartum fever is a well-known risk factor for adverse perinatal outcomes. In this study, we evaluated the clinical features for intrapartum maternal fever and investigated the risk factors for neonatal early-onset sepsis (EOS) with intrapartum maternal fever.MethodsThis retrospective cohort study involved a total of 568 neonates born to mothers with intrapartum maternal fever (temperature peak ≥38 degree Celsius) in Hangzhou Women’s Hospital from January 1st to December 31st, 2019. Neonates were assigned to the EOS and non-sepsis groups based on the diagnostic criteria for early-onset neonatal sepsis,. Demographic data, clinical information and laboratory test results were evaluated to assess the risk factors for EOS.ResultsA total of 568 neonates were included in this study, 84 of whom were diagnosed with EOS. The EOS group was significantly different from the non-sepsis group in 11 items including the both white blood cell (WBC) count and C-reactive protein (CRP) level of the mother before delivery (p < 0.05). A logistic regression analysis revealed that a high maternal WBC count before delivery (OR = 3.261, p = 0.019) and a maternal histological chorioamnionitis (HCA) diagnosis (OR = 5.608, p = 0.002) were independent risk factors for EOS. The optimal cut-off value for WBC (before delivery) was 16.75 × 10*9/L for EOS, according to receiver operating characteristic analysis (area under curve was 0.821).ConclusionsElevated prenatal maternal WBC counts and maternal HCA diagnosis are both independently associated with EOS. Prenatal maternal WBC counts can be used as a sensitive indicator to predict EOS early. creator: Hongmin An creator: Wei Zheng creator: Qinghua Zhu creator: Yun Chai uri: https://doi.org/10.7717/peerj.13834 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 An et al.