title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=907 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Older age and diclofenac are associated with increased risk of upper gastrointestinal bleeding in gout patients link: https://peerj.com/articles/11468 last-modified: 2021-05-20 description: BackgroundGouty arthritis is a disease of global burden in which defective metabolism of uric acid causes arthritis. Gouty arthritis or medications used for its treatment may lead to uric acid-associated complications such as upper gastrointestinal bleeding (UGIB) and renal impairment.MethodsIn this cross-sectional study with retrospective record review, 403 established gouty arthritis patients were recruited to determine the incidence of UGIB and associated factors among gout patients who were on regular nonsteroidal anti-inflammatory drugs (NSAIDs).ResultsThe mean age of the 403 gouty arthritis patients was 55.7 years old and the majority (n = 359/403; 89.1%) were male. The incidence of UGIB among gouty arthritis patients who were on NSAIDs was 7.2% (n = 29/403). Older age (p < 0.001), diclofenac medication (p = 0.003), pantoprazole medication (p = 0.003), end-stage renal failure (ESRF) (p = 0.007), smoking (p = 0.035), hypertension (p = 0.042) and creatinine (p = 0.045) were significant risk factors for UGIB among the gouty arthritis patients in univariable analysis. Older age (p = 0.001) and diclofenac medication (p < 0.001) remained significant risk factors for UGIB among the gouty arthritis patients in multivariable analysis.ConclusionsAge and diclofenac were significantly associated with UGIB among patients with gouty arthritis on regular NSAIDs, indicating that these factors increased the risks of developing UGIB in gout patients. Hence, these high-risk groups of gouty arthritis patients should be routinely monitored to avoid the potential onset of UGIB. Our data also suggest that diclofenac should be prescribed for the shortest duration possible to minimize the risk of developing UGIB in gout patients. creator: Wan Syamimee Wan Ghazali creator: Wan Mohd Khairul Bin Wan Zainudin creator: Nurul Khaiza Yahya creator: Asmahan Mohamed Ismail creator: Kah Keng Wong uri: https://doi.org/10.7717/peerj.11468 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wan Ghazali et al. title: Molecular epidemiology of vancomycin-resistant Enterococcus faecium clinical isolates in a tertiary care hospital in southern Thailand: a retrospective study link: https://peerj.com/articles/11478 last-modified: 2021-05-20 description: ObjectiveVancomycin-resistant enterococci are nosocomial pathogens that are responsible for commonly causing healthcare-associated infections, and they exhibit increased resistance to many antimicrobials, particularly to vancomycin. The epidemiological data available on vancomycin-resistant enterococci (VRE) in Thailand are inadequate.MethodsUsing enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), this study investigated genes that encode antimicrobial resistance and genetic relatedness to further understand VRE prevalence. Ninety VRE isolates were collected between 2011 and 2019 from a tertiary care hospital in southern Thailand. Antimicrobial susceptibility was determined using the disk diffusion method and E-test methods. Multiplex PCR was performed to detect the van gene and virulence genes.ResultsThe study showed a high prevalence of diverse multidrug-resistant VRE strains. The prevalence of VRE infection was the highest in 2014 (28 isolates, 39.4%). VRE were mostly found in the urogenital tract (26 isolates, 28.9%), followed by the digestive tract (20%), body fluid, i.e., pancreatic cyst fluid, peritoneal dialysis fluid, Jackson–Pratt (JP) drain (20%), and blood specimens (10%). Patients in medical and surgical wards had 71.1% multi-drug-resistant and 28.9% extensively drug-resistant (XDR) VRE strains, respectively. The most prevalent antibiotic resistance was to ampicillin (74.4%). Susceptibility to gentamicin and meropenem were similar (7% and 10%, respectively). Four isolates (4.4%) were resistant to colistin. Only vanA was detected among the strains. The virulence gene test showed that the detection rates of enterococcal surface protein (esp) and hyaluronidase (hyl) genes were 91.1% and 5.6%, respectively. According to ERIC-PCR analysis, 51 of 90 strains had clonality, with a similarity rate of 95%.ConclusionsWe conclude that there is a need to implement infection control practices and active surveillance. Molecular techniques can effectively detect antibiotic-resistant genes, which would allow monitoring to control VRE infection in hospitals. creator: Phanvasri Saengsuwan creator: Kamonnut Singkhamanan creator: Siribhorn Madla creator: Natnicha Ingviya creator: Chonticha Romyasamit uri: https://doi.org/10.7717/peerj.11478 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Saengsuwan et al. title: Seminar-case learning model improves clinical teaching: a prospective randomized controlled trial link: https://peerj.com/articles/11487 last-modified: 2021-05-20 description: PurposeThe purpose of this research was to assess whether the efficacy of the seminar-case learning model is superior to the traditional lecture-based learning model in the gastroenterology curriculum for first-year graduate students.Materials & MethodsThis research was a prospective randomized controlled trial that enrolled 92 first-year postgraduate students with a rotation internship in the gastroenterology department. The students were randomly divided into 2 groups and then subjected to an identical version of the curriculum for 8 weeks. The experimental group (n = 50) used the seminar-case learning model, while the control group (n = 42) used the traditional lecture-based learning model. Examinations consisted of a theoretical test and a case analysis test, and anonymous questionnaires were used to assess teaching quality.ResultsAll participants completed the examinations and questionnaires. The average theoretical test score of the experimental group was no statistical significance with that of the control group (P = 0.17). The average case analysis test score of the experimental group was significantly higher than that of the control group (P < 0.05). The indicators of the experimental group’s feedback were better than those of the control group, such that there were significantly higher learning interest and motivation, a better understanding of diseases and knowledge, improvements in clinical thinking and summary ability, and an active classroom atmosphere in the experimental group (P < 0.05). However, students in the experimental group felt more burdensome.ConclusionCompared to the traditional method, the seminar-case learning model showed a higher efficacy. The seminar-case learning model effectively improved students’ outcomes and satisfaction, which helped students narrow the gap between theoretical knowledge and clinical practical application. creator: Peiyuan Li creator: Bin Zeng creator: Xuanmin Chen creator: Zhifeng Liu creator: Jing Yang uri: https://doi.org/10.7717/peerj.11487 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Efficacy of an improved method to screen semiochemicals of insect link: https://peerj.com/articles/11510 last-modified: 2021-05-20 description: BackgroundA combination of gas chromatography-electroantennographic detection (GC-EAD) and gas chromatography-mass spectrometry (GC-MS) is typically used to screen active compounds that play a role in the regulation of insect behavior. This method uses two kinds of gas chromatography (GC) equipment and needs to compare compounds between the two chromatograms, and it is tedious and costly. To improve detection efficiency, as well as reduce costs and the rate of missed detection, we designed a system connecting gas chromatography (GC), electroantennography (EAG), and mass spectrometry (MS), with MS used instead of the flame ionization detector (FID) as the GC-EAD detector. To verify the feasibility of the improved method, we compare two methods—GC-EAG-MS and GC-EAD—through a series of experiments. Some researchers made similar improvements, but these were not compared with GC-EAD, and their method needed to be improved in the synchronization and split ratio. Our method has been optimized and improved in these aspects.MethodsHelicoverpa armigera was the test organism; the improved method and conventional method were used to detect known and unknown compounds, as well as screen out active compounds that could generate responses in H. armigera antennae.ResultsScreening known single compounds using the two methods, the active compound benzaldehyde was detected in all seven concentrations of solution. By using the two methods, the five same active compounds of Helicoverpa armigera were detected in high concentration solution of the mixed compounds (100 mg L−1, 50 mg L−1); the four same active compounds were detected at 20 mg L−1 concentration; two identical same compounds were detected in low concentration solution (concentrations of 10 mg L−1 and below). By using the two methods, six identical active compounds of Helicoverpa armigera were detected in unknown compounds.ConclusionThe improved method was consistent with the conventional method in terms of accuracy and sensitivity. However, compared with the traditional methods, Gas chromatography-electroantennographic-mass spectrometry (GC-EAG-MS) saved the cost of GC and FID equipment, thereby greatly lowering the experimental cost. In the experiment, GC-EAG-MS combined the two experimental operations of screening active substances by GC-EAD and identifying active substances by GC-MS into one, which not only reduced the experimental steps, but also avoided the false positive caused by the comparison of the two chromatograms, and it greatly reduced the difficulty level of the overall experimental analysis. GC-EAG-MS is more convenient, efficient, economical, and practical, and could confidently replace traditional methods. With further optimization, it could be widely applied in the study of plant and insect chemical ecology. creator: Chongyang Li creator: Jianmin Cao creator: Xiufang Wang creator: Pengjun Xu creator: Xinwei Wang creator: Guangwei Ren uri: https://doi.org/10.7717/peerj.11510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: High fructose exposure modifies the amount of adipocyte-secreted microRNAs into extracellular vesicles in supernatants and plasma link: https://peerj.com/articles/11305 last-modified: 2021-05-19 description: BackgroundHigh fructose exposure induces metabolic and endocrine responses in adipose tissue. Recent evidence suggests that microRNAs in extracellular vesicles are endocrine signals secreted by adipocytes. Fructose exposure on the secretion of microRNA by tissues and cells is poorly studied. Thus, the aim of this study was to evaluate the effect of fructose exposure on the secretion of selected microRNAs in extracellular vesicles from 3T3-L1 cells and plasma from Wistar rats.Methods3T3-L1 cells were exposed to 550 µM of fructose or standard media for four days, microRNAs levels were determined in extracellular vesicles of supernatants and cells by RT-qPCR. Wistar rats were exposed to either 20% fructose drink or tap water for eight weeks, microRNAs levels were determined in extracellular vesicles of plasma and adipose tissue by RT-qPCR.ResultsThis study showed that fructose exposure increased the total number of extracellular vesicles released by 3T3-L1 cells (p = 0.0001). The levels of miR-143-5p were increased in extracellular vesicles of 3T3-L1 cells exposed to fructose (p = 0.0286), whereas miR-223-3p levels were reduced (p = 0.0286). Moreover, in plasma-derived extracellular vesicles, miR-143-5p was higher in fructose-fed rats (p = 0.001), whereas miR-223-3p (p = 0.022), miR-342-3p (p = 0.0011), miR-140-5p (p = 0.0129) and miR-146b-5p (p = 0.0245) were lower.ConclusionFructose exposure modifies the levels of microRNAs in extracellular vesicles in vitro and in vivo. In particular, fructose exposure increases miR-143-5p, while decreases miR-223-3p and miR-342-3p. creator: Adrián Hernández-Díazcouder creator: Javier González-Ramírez creator: Abraham Giacoman-Martínez creator: Guillermo Cardoso-Saldaña creator: Eduardo Martínez-Martínez creator: Horacio Osorio-Alonso creator: Ricardo Márquez-Velasco creator: José L. Sánchez-Gloria creator: Yaneli Juárez-Vicuña creator: Guillermo Gonzaga creator: Laura Gabriela Sánchez-Lozada creator: Julio César Almanza-Pérez creator: Fausto Sánchez-Muñoz uri: https://doi.org/10.7717/peerj.11305 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hernández-Díazcouder et al. title: Changes in anti-nutrient, phytochemical, and micronutrient contents of different processed rubber (Hevea brasiliensis) seed meals link: https://peerj.com/articles/11327 last-modified: 2021-05-19 description: Rubber (Hevea brasiliensis) is a perennial plant crop grown in many parts of Africa, South East Asia, and South America, especially within the hot and humid climatic regions. Rubber seed, either as feed or food, is a useful raw material to produce edible oil and protein. Despite the huge quantity of rubber seeds produced in Nigeria and its potential as a protein source, rubber seeds still appear neglected and under-utilised as feed/food given its perception as inedible and toxic due to the high concentration of cyanogenic glycoside. Therefore, the quest for effective processing technique(s) that would enhance its food use application is very fitting. This current study was directed to determine the changes in anti-nutrient, phytochemical, and micronutrient contents of different processed rubber seed meals. Specifically, the rubber seeds underwent processing, which employed boiling and the combined action of boiling and fermentation methods that brought about three seed meal flour groups, i.e., raw (RRSM), boiled (BRSM), and fermented (FRSM) seed meals. These were subsequently analysed for anti-nutrient/phytochemical (oxalate, phytate, tannin, phenols, saponin, hydrogen cyanide (HCN), alkaloids, flavonoids, and trypsin inhibitors), and micronutrient (which involved minerals (magnesium, phosphorus, calcium, iron, zinc, potassium, sodium, manganese, lead, and selenium) and vitamin (vitamin B1, B2, B3, C, E, and beta carotene)) contents. The results showed that the processing methods used to achieve the RRSM, BRSM, and FRSM, reduced the anti-nutrients (phytate, tannin, and oxalate) below the acceptable limits, and the HCN below the toxic levels. Importantly, the processing methods herein have not yet succeeded in removing HCN in the (processed) rubber seed meals, but can be seen to be heading toward the right direction. The FRSM obtained significantly lower (p < 0.05) anti-nutrient/phytochemical, but significantly higher (p < 0.05) mineral contents, compared with the other groups (RRSM and BRSM), except for flavonoids that obtained a 30% increase over the BRSM. Some mineral and vitamin contents could be lost in the BRSM compared to the others (RRSM and FRSM) in this study. Additionally, the FRSM obtained higher vitamin contents, after those of RRSM. Overall, the combined action of boiling and fermentation should be recommended for the proper utilisation of rubber seed as food/feed. creator: Chidinma M. Agbai creator: Ijeoma A. Olawuni creator: Chigozie E. Ofoedu creator: Chidi J. Ibeabuchi creator: Charles Odilichukwu R. Okpala creator: Ivan Shorstkii creator: Małgorzata Korzeniowska uri: https://doi.org/10.7717/peerj.11327 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Agbai et al. title: Local-scale impact of wind energy farms on rare, endemic, and threatened plant species link: https://peerj.com/articles/11390 last-modified: 2021-05-19 description: BackgroundWind energy farms have become a popular solution to produce green energy worldwide. Their development within protected areas has increased dramatically in the past decade, and the effects on the rare, endemic and threatened plant species (i.e., protected plant species), essential for habitat conservation and management, are little known. Only a few studies directly quantify the impacts of wind energy farms on them. Our study analyzes the impact of wind energy farms on rare, endemic, and threatened plant species in steppic habitats and their recovery potential over a ten-year period on a wind energy farm within the Dealurile Agighiolului Natura 2000 site (Dobrogea Region, SE Romania).MethodsWe surveyed the rare, endemic, and threatened plant species within a radius of approximately 50 m around each of the 17 wind towers during the wind farm operational phase. We selected 34 plots to allow the investigation of two types of areas: (1) a disturbed area overlapping the technological platform, where the vegetation was removed before construction, and (2) an adjacent undisturbed area. To understand the effects of the wind energy farm on the rare, endemic, and threatened plant species diversity and the differences between the disturbed and undisturbed areas, we calculated under both conditions: (1) plant species richness; (2) sample-size-based rarefaction and extrapolation with Hill numbers parameterized by species richness; (3) non-metric multidimensional scaling of Jaccard dissimilarity index; (4) functional diversity; (5) beta-diversity (including replacement and nestedness of species).ResultsAs a result of the disturbances caused by the wind energy farm’s development, we identified a sharp contrast between the diversity of rare, endemic, and threatened plants inhabiting disturbed and undisturbed areas near the wind towers. Our research showed that less than 40% of the total inventoried rare, endemic, and threatened species colonized the disturbed sites. Species turnover within undisturbed plots was higher than disturbed plots, implying that the plant community’s heterogeneity was high. However, a higher richness in rare, endemic, and threatened plant species was found in the plots around the wind towers in grasslands of primary type. Sample-size-based rarefaction and extrapolation with Hill numbers by observed species richness indicated an accurate estimation of species richness in disturbed habitats, demonstrating that recovery after wind energy farm construction was incomplete after ten years of low-intensity plant restoration and conservation activities. Thus, we consider that operating activities must be reconfigured to allow the complete recovery of the communities with rare, endemic, and threatened plant species. creator: Mihaela Urziceanu creator: Paulina Anastasiu creator: Laurentiu Rozylowicz creator: Tatiana Eugenia Sesan uri: https://doi.org/10.7717/peerj.11390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Urziceanu et al. title: SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method link: https://peerj.com/articles/11426 last-modified: 2021-05-19 description: Long non-coding RNA (lncRNA)–microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs. Accordingly, predicting lncRNA–miRNA interactions provides an important basis for understanding the mechanisms of action of ncRNAs. However, the accuracy of the established prediction methods is still limited. In this study, we used structural consistency to measure the predictability of interactive links based on a bilayer network by integrating information for known lncRNA–miRNA interactions, an lncRNA similarity network, and an miRNA similarity network. In particular, by using the structural perturbation method, we proposed a framework called SPMLMI to predict potential lncRNA–miRNA interactions based on the bilayer network. We found that the structural consistency of the bilayer network was higher than that of any single network, supporting the utility of bilayer network construction for the prediction of lncRNA–miRNA interactions. Applying SPMLMI to three real datasets, we obtained areas under the curves of 0.9512 ± 0.0034, 0.8767 ± 0.0033, and 0.8653 ± 0.0021 based on 5-fold cross-validation, suggesting good model performance. In addition, the generalizability of SPMLMI was better than that of the previously established methods. Case studies of two lncRNAs (i.e., SNHG14 and MALAT1) further demonstrated the feasibility and effectiveness of the method. Therefore, SPMLMI is a feasible approach to identify novel lncRNA–miRNA interactions underlying complex biological processes. creator: Mingmin Xu creator: Yuanyuan Chen creator: Wei Lu creator: Lingpeng Kong creator: Jingya Fang creator: Zutan Li creator: Liangyun Zhang creator: Cong Pian uri: https://doi.org/10.7717/peerj.11426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: MicroRNA panel in serum reveals novel diagnostic biomarkers for prostate cancer link: https://peerj.com/articles/11441 last-modified: 2021-05-19 description: PurposeMicroRNAs (miRNAs), which could be stably preserved and detected in serum or plasma, could act as biomarkers in cancer diagnosis. Prostate cancer is the second cancer in males for incidence. This study aimed to establish a miRNA panel in peripheral serum which could act as a non-invasive biomarker helping diagnosing PC.MethodsA total of 86 PC patients and 86 normal control serum samples were analyzed through a four-stage experimental process using quantitative real-time polymerase chain reaction. Logistic regression method was used to construct a diagnostic model based on the differentially expressed miRNAs in serum. Receiver operating characteristic curves were constructed to evaluate the diagnostic accuracy. We also compared the 3-miRNA panel with previously reported biomarkers and verified in four public datasets. In addition, the expression characteristics of the identified miRNAs were further explored in tissue and serum exosomes samples.ResultsWe identified a 3-miRNA signature including up-regulated miR-146a-5p, miR-24-3p and miR-93-5p for PC detection. Areas under the receiver operating characteristic curve of the 3-miRNA panel for the training, testing and external validation phase were 0.819, 0.831 and 0.814, respectively. The identified signature has a very stable diagnostic performance in the large cohorts of four public datasets. Compared with previously identified miRNA biomarkers, the 3-miRNA signature in this study has superior performance in diagnosing PC. What’s more, the expression level of miR-93-5p was also elevated in exosomes from PC samples. However, in PC tissues, none of the three miRNAs showed significantly dysregulated expression.ConclusionsWe established a three-miRNA panel (miR-146a-5p, miR-24-3p and miR-93-5p) in peripheral serum which could act as a non-invasive biomarker helping diagnosing PC. creator: Shiyu Zhang creator: Cheng Liu creator: Xuan Zou creator: Xiangnan Geng creator: Xin Zhou creator: XingChen Fan creator: Danxia Zhu creator: Huo Zhang creator: Wei Zhu uri: https://doi.org/10.7717/peerj.11441 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes link: https://peerj.com/articles/11456 last-modified: 2021-05-19 description: Every day more plant genomes are available in public databases and additional massive sequencing projects (i.e., that aim to sequence thousands of individuals) are formulated and released. Nevertheless, there are not enough automatic tools to analyze this large amount of genomic information. LTR retrotransposons are the most frequent repetitive sequences in plant genomes; however, their detection and classification are commonly performed using semi-automatic and time-consuming programs. Despite the availability of several bioinformatic tools that follow different approaches to detect and classify them, none of these tools can individually obtain accurate results. Here, we used Machine Learning algorithms based on k-mer counts to classify LTR retrotransposons from other genomic sequences and into lineages/families with an F1-Score of 95%, contributing to develop a free-alignment and automatic method to analyze these sequences. creator: Simon Orozco-Arias creator: Mariana S. Candamil-Cortés creator: Paula A. Jaimes creator: Johan S. Piña creator: Reinel Tabares-Soto creator: Romain Guyot creator: Gustavo Isaza uri: https://doi.org/10.7717/peerj.11456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Orozco-Arias et al.