title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=445 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Standardization of in situ coral bleaching measurements highlights the variability in responses across genera, morphologies, and regions link: https://peerj.com/articles/16100 last-modified: 2023-10-02 description: Marine heatwaves and regional coral bleaching events have become more frequent and severe across the world’s oceans over the last several decades due to global climate change. Observational studies have documented spatiotemporal variation in the responses of reef-building corals to thermal stress within and among taxa across geographic scales. Although many tools exist for predicting, detecting, and quantifying coral bleaching, it remains difficult to compare bleaching severity (e.g., percent cover of bleached surface areas) among studies and across species or regions. For this review, we compiled over 2,100 in situ coral bleaching observations representing 87 reef-building coral genera and 250 species of common morphological groups from a total of 74 peer-reviewed scientific articles, encompassing three broad geographic regions (Atlantic, Indian, and Pacific Oceans). While bleaching severity was found to vary by region, genus, and morphology, we found that both genera and morphologies responded differently to thermal stress across regions. These patterns were complicated by (i) inconsistent methods and response metrics across studies; (ii) differing ecological scales of observations (i.e., individual colony-level vs. population or community-level); and (iii) temporal variability in surveys with respect to the onset of thermal stress and the chronology of bleaching episodes. To improve cross-study comparisons, we recommend that future surveys prioritize measuring bleaching in the same individual coral colonies over time and incorporate the severity and timing of warming into their analyses. By reevaluating and standardizing the ways in which coral bleaching is quantified, researchers will be able to track responses to marine heatwaves with increased rigor, precision, and accuracy. creator: Adi Khen creator: Christopher B. Wall creator: Jennifer E. Smith uri: https://doi.org/10.7717/peerj.16100 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Khen et al. title: Different patterns of foreground and background processing contribute to texture segregation in humans: an electrophysiological study link: https://peerj.com/articles/16139 last-modified: 2023-10-02 description: BackgroundFigure-ground segregation is a necessary process for accurate visual recognition. Previous neurophysiological and human brain imaging studies have suggested that foreground-background segregation relies on both enhanced foreground representation and suppressed background representation. However, in humans, it is not known when and how foreground and background processing play a role in texture segregation.MethodsTo answer this question, it is crucial to extract and dissociate the neural signals elicited by the foreground and background of a figure texture with high temporal resolution. Here, we combined an electroencephalogram (EEG) recording and a temporal response function (TRF) approach to specifically track the neural responses to the foreground and background of a figure texture from the overall EEG recordings in the luminance-tracking TRF. A uniform texture was included as a neutral condition. The texture segregation visual evoked potential (tsVEP) was calculated by subtracting the uniform TRF from the foreground and background TRFs, respectively, to index the specific segregation activity.ResultsWe found that the foreground and background of a figure texture were processed differently during texture segregation. In the posterior region of the brain, we found a negative component for the foreground tsVEP in the early stage of foreground-background segregation, and two negative components for the background tsVEP in the early and late stages. In the anterior region, we found a positive component for the foreground tsVEP in the late stage, and two positive components for the background tsVEP in the early and late stages of texture processing.DiscussionIn this study we investigated the temporal profile of foreground and background processing during texture segregation in human participants at a high time resolution. The results demonstrated that the foreground and background jointly contribute to figure-ground segregation in both the early and late phases of texture processing. Our findings provide novel evidence for the neural correlates of foreground-background modulation during figure-ground segregation in humans. creator: Baoqiang Zhang creator: Saisai Hu creator: Tingkang Zhang creator: Min Hai creator: Yongchun Wang creator: Ya Li creator: Yonghui Wang uri: https://doi.org/10.7717/peerj.16139 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Long non-coding RNA NMRAL2P promotes glycolysis and reduces ROS in head and neck tumors by interacting with the ENO1 protein and promoting GPX2 transcription link: https://peerj.com/articles/16140 last-modified: 2023-10-02 description: BackgroundMetabolic reprogramming is a key marker in the occurrence and development of tumors. This process generates more reactive oxygen species (ROS), promoting the development of oxidative stress. To prevent ROS from harming tumor cells, tumor cells can increase the production of reducing agents to counteract excessive ROS. NMRAL2P has been shown to promote the production of reductive mRNA and plays an important role in the process of oxidative stress.MethodsIn this study, the clinical data and RNA sequencing of head and neck tumors were obtained from The Cancer Genome Atlas data set. The long non-coding RNA (LncRNA) related to oxidative stress were then identified using differential and correlation analyses. The differential expression and prognosis of the identified lncRNA were then verified using samples from the library of the Second Hospital of Hebei Medical University. Only NMRAL2P was substantially expressed in cancer tissues and predicted a poor prognosis. The tumor-promoting impact of NMRAL2P was then confirmed using in vitro functional assays. The data set was then split into high- and low-expression subgroups based on the median gene expression of NMRAL2P to obtain the mRNA that had a large difference between the two groups, and examine the mechanism of NMRAL2P on GPX2 using quantitative real-time PCR, RNA binding protein immunoprecipitation assay, and chromatin immunoprecipitation. Mass spectrometry was used to identify NMRAL2P-binding proteins and western blotting was used to investigate probable mechanisms.ResultsThe lncRNA NMRAL2P is associated with oxidative stress in head and neck tumors. In vitro functional assays showed that the gene has a cancer-promoting effect, increasing lactic acid and superoxide dismutase production, and reducing the production of ROS and malondialdehyde. NMRAL2P promotes the transcription of GPX2 by binding to transcription factor Nrf2. The gene also inhibits the degradation of ENO1, a crucial enzyme in glycolysis, by binding to protein ENO1.ConclusionsThis study shows that NMRAL2P can promote glycolysis and reduce the harm to tumor cells caused by ROS. The gene can also be used as a possible target for the treatment of head and neck tumors. creator: Qian Nie creator: Huan Cao creator: JianWang Yang creator: Tao Liu creator: BaoShan Wang uri: https://doi.org/10.7717/peerj.16140 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nie et al. title: Anti-methicillin-resistant Staphylococcus aureus and antibiofilm activity of new peptides produced by a Brevibacillus strain link: https://peerj.com/articles/16143 last-modified: 2023-10-02 description: BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) is listed as a highly prioritized pathogen by the World Health Organization (WHO) to search for effective antimicrobial agents. Previously, we isolated a soil Brevibacillus sp. strain SPR19 from a botanical garden, which showed anti-MRSA activity. However, the active substances were still unknown.MethodsThe cell-free supernatant of this bacterium was subjected to salt precipitation, cation exchange, and reversed-phase chromatography. The antimicrobial activity of pure substances was determined by broth microdilution assay. The peptide sequences and secondary structures were characterized by tandem mass spectroscopy and circular dichroism (CD), respectively. The most active anti-MRSA peptide underwent a stability study, and its mechanism was determined through scanning electron microscopy, cell permeability assay, time-killing kinetics, and biofilm inhibition and eradication. Hemolysis was used to evaluate the peptide toxicity.ResultsThe pure substances (BrSPR19-P1 to BrSPR19-P5) were identified as new peptides. Their minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) against S. aureus and MRSA isolates ranged from 2.00 to 32.00 and 2.00 to 64.00 µg/mL, respectively. The sequence analysis of anti-MRSA peptides revealed a length ranging from 12 to 16 residues accompanied by an amphipathic structure. The physicochemical properties of peptides were predicted such as pI (4.25 to 10.18), net charge at pH 7.4 (−3 to +4), and hydrophobicity (0.12 to 0.96). The CD spectra revealed that all peptides in the water mainly contained random coil structures. The increased proportion of α-helix structure was observed in P2−P5 when incubated with SDS. P2 (NH2-MFLVVKVLKYVV-COOH) showed the highest antimicrobial activity and high stability under stressed conditions such as temperatures up to 100 °C, solution of pH 3 to 10, and proteolytic enzymes. P2 disrupted the cell membrane and caused bacteriolysis, in which its action was dependent on the incubation time and peptide concentration. Antibiofilm activity of P2 was determined by which the half-maximal inhibition of biofilm formation was observed at 2.92 and 4.84 µg/mL for S. aureus TISTR 517 and MRSA isolate 2468, respectively. Biofilm eradication of tested pathogens was found at the P2 concentration of 128 µg/mL. Furthermore, P2 hemolytic activity was less than 10% at concentrations up to 64 µg/mL, which reflected the hemolysis index thresholds of 32.ConclusionFive novel anti-MRSA peptides were identified from SPR19. P2 was the most active peptide and was demonstrated to cause membrane disruption and cell lysis. The P2 activity was dependent on the peptide concentration and exposure time. This peptide had antibiofilm activity against tested pathogens and was compatible with human erythrocytes, supporting its potential use as an anti-MRSA agent in this post-antibiotic era. creator: Abiodun Ogunsile creator: Nuttapon Songnaka creator: Somchai Sawatdee creator: Monthon Lertcanawanichakul creator: Sucheewin Krobthong creator: Yodying Yingchutrakul creator: Jumpei Uchiyama creator: Apichart Atipairin uri: https://doi.org/10.7717/peerj.16143 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ogunsile et al. title: Inter-rater and test-retest reliabilities of lumbar stiffness measurement in the postero-anterior direction using a portable algometer and the Kinovea program link: https://peerj.com/articles/16148 last-modified: 2023-10-02 description: BackgroundBack pain negatively impacts a person’s quality of life and can cause major disability or even death. The measurement of spinal stiffness can be utilized as a promising tool to guide therapeutic decisions regarding physical therapy that result in effective back pain management. This study aimed to determine the reliability of instrumented postero-anterior (PA) stiffness assessment of the lumbar spine in asymptomatic participants by novice assessors using a portable algometer and the Kinovea program.MethodsThirty asymptomatic participants aged 18–25 years were enrolled in this study. Two novice assessors examined the participants for lumbar spinal stiffness at L1–L5 for two consecutive days. The algometer was applied to measure the PA force that applied to each lumbar. The stiffness assessment of each lumbar region was recorded as a video. The 600 data sets of assessment videos were imported into the Kinovea program to perform displacement measurements of each lumbar level. Spinal displacement values at 15 N were defined by graph plotting between force and displacement. The spinal stiffness values were defined by slope calculation. Both variables were analyzed for inter-rater and test-retest reliabilities using intra-class correlation coefficients (ICCs) and standard error of measurement (SEM). Bland-Altman analysis was applied to assess the inter-rater and test-retest systematical bias and limits of agreement of measuring displacement and stiffness.ResultsThe inter-rater reliability of measuring the displacement and the stiffness of L1–L5 was moderate to good (displacement ICCs: 0.67–0.83, stiffness ICCs: 0.60–0.83). The test-retest reliability of measuring the displacement and stiffness of L1–L5 were moderate to good, ICCs: 0.57–0.86 and ICCs: 0.51–0.88, respectively. The inter-rater analysis’s Bland-Altman plot showed that the systematic bias was 0.83 when measuring displacement and 0.20 when measuring stiffness and the bias of both parameters were in both directions. While the test-retest systematically biased measurements of displacement and stiffness were −0.26 mm and 0.22 N/mm, respectively, and the bias of both parameters were in both directions.ConclusionsThe moderate-to-good inter-rater and test-retest reliabilities of the portable instrumented spinal stiffness assessment using a digital algometer and the Kinovea program by novice assessors were demonstrated in this study. Bland-Altman analysis showed that measuring stiffness was more stable and had less systematic bias than measuring displacement. To figure out how reliable the device is in general, more comprehensive studies should be comparatively conducted in the future on subgroups of patients with normal vertebra, hypomobile or hypermobile conditions. creator: Wantanee Yodchaisarn creator: Sunthorn Rungruangbaiyok creator: Maria de Lourdes Pereira creator: Chadapa Rungruangbaiyok uri: https://doi.org/10.7717/peerj.16148 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yodchaisarn et al. title: Genome-wide identification and characterization of ABA receptor pyrabactin resistance 1-like protein (PYL) family in oat link: https://peerj.com/articles/16181 last-modified: 2023-10-02 description: Abscisic acid (ABA) is a phytohormone that plays an important role in plant growth and development. Meanwhile, ABA also plays a key role in the plant response to abiotic stressors such as drought and high salinity. The pyrabactin resistance 1-like (PYR/PYL) protein family of ABA receptors is involved in the initial step of ABA signal transduction. However, no systematic studies of the PYL family in “Avena sativa, a genus Avena in the grass family Poaceae,” have been conducted to date. Thus, in this study, we performed a genome-wide screening to identify PYL genes in oat and characterized their responses to drought stress. A total of 12 AsPYL genes distributed on nine chromosomes were identified. The phylogenetic analysis divided these AsPYLs into three subfamilies, based on structural and functional similarities. Gene and motif structure analysis of AsPYLs revealed that members of each subfamily share similar gene and motif structure. Segmental duplication appears to be the driving force for the expansion of PYLs, Furthermore, stress-responsive AsPYLs were detected through RNA-seq analysis. The qRT-PCR analysis of 10 AsPYL genes under drought, salt, and ABA stress revealed that AsPYL genes play an important role in stress response. These data provide a reference for further studies on the oat PYL gene family and its function. creator: Wenbo Mi creator: Kaiqiang Liu creator: Guoling Liang creator: Zhifeng Jia creator: Xiang Ma creator: Zeliang Ju creator: Wenhui Liu uri: https://doi.org/10.7717/peerj.16181 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mi et al. title: Serotypes, virulence factors and multilocus sequence typing of Glaesserella parasuis from diseased pigs in Taiwan link: https://peerj.com/articles/15823 last-modified: 2023-09-29 description: BackgroundGlaesserella parasuis (G. parasuis) belongs to the normal microbiota of the upper respiratory tract in the swine, but virulent strains can cause systemic infections commonly known as Glässer’s disease that leads to significant economic loss in the swine industry. Fifteen serotypes of G. parasuis have been classified by gel immunodiffusion test while the molecular serotyping based on variation within the capsule loci have further improved the serotype determination of unidentified field strains. Serovar has been commonly used as an indicator of virulence; however, virulence can be significantly differ in the field isolates with the same serotype. To date, investigations of G. parasuis isolated in Taiwan regarding antimicrobial resistance, serotypes, genotypes and virulence factors remain unclear.MethodsA total of 276 G.parasuis field isolates were collected from 263 diseased pigs at the Animal Disease Diagnostic Center of National Chiayi University in Taiwan from January 2013 to July 2021. Putative virulence factors and serotypes of the isolates were identified by polymerase chain reaction (PCR) and antimicrobial susceptibility testing was performed by microbroth dilution assay. Additionally, the epidemiology of G. parasuis was characterized by multilocus sequence typing (MLST).ResultsSerotype 4 (33.3%) and 5 (21.4%) were the most prevalent, followed by nontypable isolates (15.9%), serotype 13 (9.4%), 12 (6.5%), 14 (6.2%), 7 (3.3%), 1 (1.8%), 9 (1.1%), 11 (0.7%) and 6 (0.4%). Nine out of 10 putative virulence factors showed high positive rates, including group 1 vtaA (100%), fhuA (80.4%), hhdA (98.6%), hhdB (96.0%), sclB7 (99.6%), sclB11 (94.9%), nhaC (98.2%), HAPS_0254 (85.9%), and cirA (99.3%). According to the results of antimicrobial susceptibility testing, ceftiofur and florfenicol were highly susceptible (>90%). Notably, 68.8% isolates showed multidrug resistance. MLST revealed 16 new alleles and 67 new sequence types (STs). STs of these isolated G. parasuis strains were classified into three clonal complexes and 45 singletons by Based Upon Related Sequence Types (BURST) analysis. All the G. parasuis strains in PubMLST database, including strains from the diseased pigs in the study, were defined into two main clusters by Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Most isolates in this study and virulent isolates from the database were mainly located in cluster 2, while cluster 1 included a high percentage of nasal isolates from asymptomatic carriers. In conclusion, this study provides current prevalence and antimicrobial susceptibility of G. parasuis in Taiwan, which can be used in clinical diagnosis and treatment of Glässer’s disease. creator: Ching-Fen Wu creator: Chia-Yu Hsu creator: Chi-Chung Chou creator: Chao-Min Wang creator: Szu-Wei Huang creator: Hung-Chih Kuo uri: https://doi.org/10.7717/peerj.15823 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wu et al. title: Genome-wide identification and analysis of Lateral Organ Boundaries Domain (LBD) transcription factor gene family in melon (Cucumis melo L.) link: https://peerj.com/articles/16020 last-modified: 2023-09-29 description: BackgroundLateral Organ Boundaries Domain (LBD) transcription factor (TF) gene family members play very critical roles in several biological processes like plant-spesific development and growth process, tissue regeneration, different biotic and abiotic stress responses in plant tissues and organs. The LBD genes have been analyzed in various species. Melon (Cucumis melo L.), a member of the Cucurbitaceae family, is economically important and contains important molecules for nutrition and human health such as vitamins A and C, β-carotenes, phenolic acids, phenolic acids, minerals and folic acid. However, no studies have been reported so far about LBD genes in melon hence this is the first study for LBD genes in this plant.ResultsIn this study, 40 melon CmLBD TF genes were identified, which were separated into seven groups through phylogenetic analysis. Cis-acting elements showed that these genes were associated with plant growth and development, phytohormone and abiotic stress responses. Gene Ontology (GO) analysis revealed that of CmLBD genes especially function in regulation and developmental processes. The in silico and qRT-PCR expression patterns demonstrated that CmLBD01 and CmLBD18 are highly expressed in root and leaf tissues, CmLBD03 and CmLBD14 displayed a high expression in male-female flower and ovary tissues.ConclusionsThese results may provide important contributions for future research on the functional characterization of the melon LBD gene family and the outputs of this study can provide information about the evolution and characteristics of melon LBD gene family for next studies. creator: Ebru Derelli Tufekci uri: https://doi.org/10.7717/peerj.16020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Derelli Tufekci title: Poor sleep quality and suicidal ideation among pregnant women during COVID-19 in Ethiopia: systematic review and meta-analysis link: https://peerj.com/articles/16038 last-modified: 2023-09-29 description: IntroductionCOVID-19 has profoundly impacted the mental health and well-being of pregnant women worldwide. In Ethiopia, the poor sleep quality and suicidal ideation among pregnant women has increased due to the COVID-19 pandemic. This study aimed to provide comprehensive evidence on the prevalence and associated factors of poor sleep quality and suicidal ideation among pregnant women during COVID-19 in Ethiopia.Materials and MethodsThis study is based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendation. Data were searched from PubMed, Google Scholar, and African Journals Online from the occurrence of the COVID-19 pandemic to February 2023. Two researchers extracted the data and performed the methodological quality assessment independently. Random-effect model was used to estimate the pooled effect size and I2was used to check heterogeneity. Stata 14.0 (StataCorp, Collage Station, Texas, USA) was used for statistical analysis.ResultsFrom six studies the pooled prevalence of poor sleep quality was 55% (95% CI [0.42–0.69], I2 = 98.1%, p < 0.001). Age ≥ 30 years pooled AOR = 1.95, 95% CI (0.85, 3.06), 3rd trimester pooled AOR = 3.20, 95% CI (1.82, 4.58), substance use pooled AOR = 2.51, 95% CI (0.99, 4.04), depression pooled AOR = 2.97, 95% CI (0.92, 5.02) and stress pooled AOR 2.14, 95% CI (0.24, 4.03) were associated factors of poor sleep quality. Three studies reported about suicidal ideation and pooled prevalence was 11% (95% CI: 0.09, 0.13, I2 = 48.2%, p = 0.145). Depression pooled AOR = 3.19, 95% CI (1.68, 4.71) was the only associated factor of suicidal ideation.ConclusionDue to COVID-19 pregnant women in Ethiopia were affected by poor sleep quality and suicidal ideation. Thus, suitable and well designed programs proposing awareness of COVID-19, mental health counseling and involvement should be designed to improve the general mental health of pregnant women.Trial registrationPROSPERO registration number CRD42023389896. creator: Aragaw Asfaw Hasen creator: Abubeker Alebachew Seid creator: Ahmed Adem Mohammed uri: https://doi.org/10.7717/peerj.16038 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hasen et al. title: Analysis of cerebral Interleukin-6 and tumor necrosis factor alpha patterns following different ventilation strategies during cardiac arrest in pigs link: https://peerj.com/articles/16062 last-modified: 2023-09-29 description: Hypoxia-induced neuroinflammation after cardiac arrest has been shown to be mitigated by different ventilation methods. In this prospective randomized animal trial, 35 landrace pigs were randomly divided into four groups: intermittent positive pressure ventilation (IPPV), synchronized ventilation 20 mbar (SV 20 mbar), chest compression synchronized ventilation 40 mbar (CCSV 40 mbar) and a control group (Sham). After inducing ventricular fibrillation, basic life support (BLS) and advanced life support (ALS) were performed, followed by post-resuscitation monitoring. After 6 hours, the animals were euthanized, and direct postmortem brain tissue samples were taken from the hippocampus (HC) and cortex (Cor) for molecular biological investigation of cytokine mRNA levels of Interleukin-6 (IL-6) and tumor necrosis factor alpha (TNFα). The data analysis showed that CCSV 40 mbar displayed low TNFα mRNA-levels, especially in the HC, while the highest TNFα mRNA-levels were detected in SV 20 mbar. The results indicate that chest compression synchronized ventilation may have a potential positive impact on the cytokine expression levels post-resuscitation. Further studies are needed to derive potential therapeutic algorithms from these findings. creator: Miriam Renz creator: Lea Müller creator: Manuel Herbst creator: Julian Riedel creator: Katja Mohnke creator: Alexander Ziebart creator: Robert Ruemmler uri: https://doi.org/10.7717/peerj.16062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Renz et al.