title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=421 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Progress in the mechanism of autophagy and traditional Chinese medicine herb involved in alcohol-related liver disease link: https://peerj.com/articles/15977 last-modified: 2023-09-15 description: Alcohol-related liver disease (ALD) is chronic liver damage caused by long-term heavy drinking with, extremely complicated pathogenesis. The current studies speculated that excessive alcohol and its metabolites are the major causes of liver cell toxicity. Autophagy is evolutionarily conserved in eukaryotes and aggravates alcoholic liver damage, through various mechanisms, such as cellular oxidative stress, inflammation, mitochondrial damage and lipid metabolism disorders. Therefore, autophagy plays an critical role in the occurrence and development of ALD. Some studies have shown that traditional Chinese medicine extracts improve the histological characteristics of ALD, as reflected in the improvement of oxidative stress and lipid droplet clearance, which might be achieved by inducing autophagy. This article reviews the mechanisms of quercetin, baicalin, glycycoumarin, salvianolic acid A, resveratrol, ginsenoside rg1, and dihydromyricetin inducing autophagy and their participation in the inhibition of ALD. The regulation of autophagy in ALD by these traditional Chinese medicine extracts provides novel ideas for the treatment of the disease; however, its molecular mechanism needs to be elucidated further. creator: Wenwen Han creator: Haiyu Li creator: Hanqi Jiang creator: Hang Xu creator: Yifeng Lin creator: Jiahuan Chen creator: Chenchen Bi creator: Zheng Liu uri: https://doi.org/10.7717/peerj.15977 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Han et al. title: The morphoanatomy of Serjania erecta Radlk (Sapindaceae) provides evidence of biotrophic interactions by endophytic fungi within leaves link: https://peerj.com/articles/15980 last-modified: 2023-09-15 description: BackgroundThe leaves of Serjania erecta Radlk (Sapindaceae) are renowned in ethnobotany for their medicinal properties and are significant as a medicinal resource for traditional Brazilian communities. As necrotic spots are common on these leaves, indicating interaction with phytopathogenic fungi, it was hypothesized that biotrophic fungal species colonize the leaf tissues of S. erecta.MethodsTo test this hypothesis, we employed standard techniques in plant anatomy, which enabled us to investigate the interaction of fungal structures with plant tissues and describe the morphoanatomical and histochemical characteristics of the epidermis and limbus of S. erecta.ResultsThe anatomical analysis showed the existence of leaf teeth on the leaf tips. Additionally, hyphae, conidiospores, and spores of Bipolaris/Curvularia species were detected on the adaxial epidermis. Moreover, melanized microsclerotia were found in glandular areas of the leaf teeth and the phloem, providing evidence of biotrophic behavior. The hypothesis that biotrophic phytopathogenic fungi interact with S. erecta leaf tissues was confirmed, despite the presence of many bioactive compounds (such as flavonoids, alkaloids, and essential oils), as evidenced by histochemical analyses. The presence of tector, glandular, and scabiform trichomes on the leaf teeth and epidermis was also revealed. This study presents, for the first time, the synthesis of essential oils and alkaloids in the leaves of S. erecta. Additionally, it investigates previously unexplained aspects of the anatomy and histochemistry of the species, as well as its interaction with resident microorganisms. Therefore, it is recommended that future research focus on extracting and characterizing the oils and alkaloids of S. erecta, as well as exploring other aspects related to its microbiome and its relationship. creator: Samylla Tássia Ferreira de Freitas creator: Giselle Faria creator: Fabiano Guimarães Silva creator: Marco Aurélio Batista creator: Damiana Souza Santos Augusto creator: Fábio Henrique Dyszy creator: Luciana Cristina Vitorino uri: https://doi.org/10.7717/peerj.15980 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Freitas et al. title: Divergent recovery trajectories of intertidal and subtidal coral communities highlight habitat-specific recovery dynamics following bleaching in an extreme macrotidal reef environment link: https://peerj.com/articles/15987 last-modified: 2023-09-15 description: Coral reefs face an uncertain future punctuated by recurring climate-induced disturbances. Understanding how reefs can recover from and reassemble after mass bleaching events is therefore important to predict their responses and persistence in a rapidly changing ocean. On naturally extreme reefs characterized by strong daily temperature variability, coral heat tolerance can vary significantly over small spatial gradients but it remains poorly understood how this impacts bleaching resilience and recovery dynamics, despite their importance as resilience hotspots and potential refugia. In the macrotidal Kimberley region in NW Australia, the 2016 global mass bleaching event had a strong habitat-specific impact on intertidal and subtidal coral communities at our study site: corals in the thermally variable intertidal bleached less severely and recovered within six months, while 68% of corals in the moderately variable subtidal died. We therefore conducted benthic surveys 3.5 years after the bleaching event to determine potential changes in benthic cover and coral community composition. In the subtidal, we documented substantial increases in algal cover and live coral cover had not fully recovered to pre-bleaching levels. Furthermore, the subtidal coral community shifted from being dominated by branching Acropora corals with a competitive life history strategy to opportunistic, weedy Pocillopora corals which likely has implications for the functioning and stress resilience of this novel coral community. In contrast, no shifts in algal and live coral cover or coral community composition occurred in the intertidal. These findings demonstrate that differences in coral heat tolerance across small spatial scales can have large consequences for bleaching resilience and that spatial patchiness in recovery trajectories and community reassembly after bleaching might be a common feature on thermally variable reefs. Our findings further confirm that reefs adapted to high daily temperature variability play a key role as resilience hotspots under current climate conditions, but their ability to do so may be limited under intensifying ocean warming. creator: P. Elias Speelman creator: Michael Parger creator: Verena Schoepf uri: https://doi.org/10.7717/peerj.15987 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Speelman et al. title: Examination of distraction and discomfort caused by using glare monitors: a simultaneous electroencephalography and eye-tracking study link: https://peerj.com/articles/15992 last-modified: 2023-09-15 description: BackgroundSince the COVID-19 pandemic started, remote work and education and digital display use have become more prevalent. However, compared with printed material, digital displays cause more eye fatigue and may decrease task performance. For instance, the reflections on the monitor can cause discomfort or distraction, particularly when glare monitors are used with black backgrounds.MethodsThis study simultaneously uses electroencephalography (EEG) and an eye-tracker to measure the possible negative effects of using a glare monitor on the illegibility of sentences.ResultsThe experiment results showed no difference in reading time and subjective illegibility rating between glare and non-glare monitors. However, with glare monitors, eye fixation when reading lasted longer. Further, EEG beta (15–20 Hz) power variations suggested that the participants were less engaged in the reading task when a glare monitor was used with a black background.ConclusionsThese results indicate that the negative effects of using a glare monitor are subtle but certainly present. They also show that physiological measures such as EEG and eye tracking can assess the subtle effects in an objective manner, even if behavioral measures such as subjective illegibility ratings or reading time may not show the differences. creator: Yoritaka Akimoto creator: Keito Miyake uri: https://doi.org/10.7717/peerj.15992 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Akimoto and Miyake title: Predictive value of abdominal wall scar score for pelvic floor function rehabilitation, vaginal microecology and complications after cesarean section link: https://peerj.com/articles/16012 last-modified: 2023-09-15 description: ObjectiveTo explore the predictive value of the abdominal wall scar score for pelvic floor function rehabilitation, vaginal microecology and complications after cesarean section.MethodsA total of 120 pregnant women who underwent cesarean section in our hospital from January to December 2022 were selected. The patients were divided into observation group (score ≥ 60, n = 52) and control group (score < 60, n = 68) according to the preoperative score of abdominal wall scar and whether the score exceeded 60. The pelvic floor function rehabilitation, vaginal microecology and complications were compared between the two groups, and the score of abdominal wall scar was evaluated by receiver operating characteristic (ROC) curve. The predictive value of pelvic floor function rehabilitation, vaginal microecology and complications after cesarean section was evaluated.ResultsThere were significant differences between the two groups in postpartum class I and class II muscle fiber strength and pelvic floor muscle potential (P < 0.05). ROC curve showed that the AUC of abdominal scar score in predicting pelvic floor function rehabilitation was 0.806 (95% CI [0.684–0.927]), the specificity was 80.17%, and the sensitivity was 79.76%. There was significant difference in the abnormal rate of leukocte estrase (LE) and Acetylaminoglucosidase (NAG) between the two groups (P < 0.05). ROC curve showed that the AUC of abdominal scar score in predicting vaginal microecology was 0.871 (95% CI [0.776–0.966]), the specificity was 85.09%, and the sensitivity was 82.36%. There was significant difference in the incidence of postpartum complications between the two groups (P < 0.05). ROC curve showed that the AUC of abdominal scar score in predicting complications was 0.844 (95% CI [0.735–0.953]), the specificity was 82.27%, and the sensitivity was 81.15%.ConclusionThe abdominal scar score has a certain effect on predicting the recovery of pelvic floor function, vaginal microecology and complications after cesarean section. Therefore, it can help the medical staff to adjust the treatment measures in time, which can be used as a means of preoperative auxiliary examination. creator: Yanhong Yang creator: Hailan Yang creator: Jingru Ji creator: Ye Zhao creator: Yinfang He creator: Junyan Wu uri: https://doi.org/10.7717/peerj.16012 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yang et al. title: DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing link: https://peerj.com/articles/16026 last-modified: 2023-09-15 description: The discovery of low-coverage (i.e. uncovered) regions containing clinically significant variants, especially when they are related to the patient’s clinical phenotype, is critical for whole-exome sequencing (WES) based clinical diagnosis. Therefore, it is essential to develop tools to identify the existence of clinically important variants in low-coverage regions. Here, we introduce a desktop application, namely DEVOUR (DEleterious Variants On Uncovered Regions), that analyzes read alignments for WES experiments, identifies genomic regions with no or low-coverage (read depth < 5) and then annotates known variants in the low-coverage regions using clinical variant annotation databases. As a proof of concept, DEVOUR was used to analyze a total of 28 samples from a publicly available Hirschsprung disease-related WES project (NCBI Bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19327), revealing the potential existence of 98 disease-associated variants in low-coverage regions. DEVOUR is available from https://github.com/projectDevour/DEVOUR under the MIT license. creator: Erdem Türk creator: Akif Ayaz creator: Ayhan Yüksek creator: Barış E. Süzek uri: https://doi.org/10.7717/peerj.16026 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Türk et al. title: Simulation of hearing loss can induce pitch shifts for complex tones link: https://peerj.com/articles/16053 last-modified: 2023-09-15 description: BackgroundMost studies on pitch shift provoked by hearing loss have been conducted using pure tones. However, many sounds encountered in everyday life are harmonic complex tones. In the present study, psychoacoustic experiments using complex tones were performed on healthy participants, and the possible mechanisms that cause pitch shift due to hearing loss are discussed.MethodsTwo experiments were performed in this study. In experiment 1, two tones were presented, and the participants were asked to select the tone that was higher in pitch. Partials with frequencies less than 250, 500, 750, or 1,000 Hz were eliminated from the harmonic complex tones and used as test tones to simulate low-tone hearing loss. Each tone pair was constructed such that the tone with a lower fundamental frequency (F0) was higher in terms of the frequency of the lowest partial. Furthermore, partials whose frequencies were greater than 1,300 or 1,600 Hz were also eliminated from these test tones to simulate high-tone hearing loss or modified sounds that patients may hear in everyday life. When a tone with a lower F0 was perceived as higher in pitch, it was considered a pitch shift from the expected tone. In experiment 2, tonal sequences were constructed to create a passage of the song “Lightly Row.” Similar to experiment 1, partials of harmonic complex tones were eliminated from the tones. After listening to these tonal sequences, the participants were asked if the sequences sounded correct based on the melody or off-key.ResultsThe results showed that pitch shifts and the melody sound off-key when lower partials are eliminated from complex tones, especially when a greater number of high-frequency components are eliminated.ConclusionConsidering that these experiments were performed on healthy participants, the results suggest that the pitch shifts from the expected tone when patients with hearing loss hear certain complex tones, regardless of the underlying etiology of the hearing loss. creator: Issei Ichimiya creator: Hiroko Ichimiya uri: https://doi.org/10.7717/peerj.16053 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ichimiya and Ichimiya title: Correlation analysis of lipid accumulation index, triglyceride-glucose index and H-type hypertension and coronary artery disease link: https://peerj.com/articles/16069 last-modified: 2023-09-15 description: ObjectiveThe current research was designed to explore the relationship between the lipid accumulation index (LAP), coronary artery disease (CAD), and the triglyceride-glucose (TyG) index in patient with H-type hypertension.MethodsFrom June 2021 to January 2022, our hospital’s information management system collected data on 186 patients with essential hypertension. The participants were categorized into two groups (H-type hypertension (n = 113) and non-H-type hypertension (n = 73)) based on their homocysteine levels. Both groups’ general condition, lipid accumulation index, triglyceride-glucose index, and Gensini score were compared to determine the factors influencing the severity of CAD in H-type hypertension patients.ResultsThere were statistically significant differences (P < 0.05) in homocysteine (Hcy, GLP-1 and SAA) level, LAP, and TyG indexes, but not in body mass index (BMI), smoking, sex, age, total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), fasting plasma glucose (FPG), diastolic blood pressure, and systolic blood pressure. Additionally, there were substantial variations between the two groups regarding the number of lesion branches, degree of stenosis, and Gensini score (P > 0.05). patient with grade III to IV lesions had substantially higher LAP and TyG indices than those with stage I to II (P < 0.05). TyG (OR = 2.687) and TyG-LAP (OR = 4.512) were the factors determining the incidence of coronary artery disease in H-type hypertension, according to multivariate logistic regression analysis. The lesion number, stenosis degree, and Gensini score (P < 0.05) varied among both groups. LAP and TyG indexes were substantially greater in patients with double and triple vessel lesions than in those without lesions or with single vessel lesions (P < 0.05); similarly, these two indexes were considerably higher in individuals with grade III to IV lesions than in patients with grade I to II lesions (P < 0.05). As per the Pearson correlation analysis, the LAP, TyG indices and SAAlevel were adversely connected to the Gensini score (r = 0.254, 0.262, 0.299, P < 0.05), the GLP-1 level was negatively correlated to the Gensini score (r = −0.291, P < 0.05). TyG (OR = 2.687) and TyG-LAP (OR = 4.512) were the factors determining the frequency of coronary artery disease in H-type hypertension, according to multivariate logistic regression analysis.ConclusionIn conclusion, the LAP and TyG indexes were observed to be closely related to the degree of CAD in H-type individuals with hypertension, which can better understand the pathogenesis of coronary artery disease in patients with H-type hypertension and is of great significance for guiding clinical doctors to carry out personalized treatment and management. creator: Wenwen Yuan creator: Yan Shao creator: Dong Zhao creator: Bin Zhang uri: https://doi.org/10.7717/peerj.16069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yuan et al. title: Mycorrhizal inoculation enhanced tillering in field grown wheat, nutritional enrichment and soil properties link: https://peerj.com/articles/15686 last-modified: 2023-09-13 description: To meet food security, commercial fertilizers are available to boost wheat yield, but there are serious ill effects associated with these fertilizers. Amongst various organic alternatives, inoculating crop fields with mycorrhizal species is the most promising option. Although, mycorrhizae are known to enhance wheat yield, but how the mycorrhizae influence different yield and quality parameters of wheat, is not clear. Therefore, this study was undertaken to investigate the influence of indigenous mycorrhizal species on the growth of wheat, its nutritional status and soil properties, in repeated set of field experiments. In total 11 species of mycorrhizae were isolated from the experimental sites with Claroideoglomus, being the most dominant one. Five different treatments were employed during the present study, keeping plot size for each replicate as 6 × 2 m. Introduction of consortia of mycorrhizae displayed a significant increase in number of tillers/plant (49.5%), dry biomass (17.4%), grain yield (21.2%) and hay weight (16.7%). However, there was non-significant effect of mycorrhizal inoculation on 1,000 grains weight. Moreover, protein contents were increased to 24.2%. Zinc, iron, phosphorus and potassium concentrations were also increased to 24%, 21%, 30.9% and 14.8%, respectively, in wheat grains. Enhancement effects were also noted on soil fertility such as soil organic carbon % age, available phosphorus and potassium were increased up to 64.7%, 35.8% and 23.9%, respectively. Herein, we concluded that mycorrhizal introduction in wheat fields significantly increased tillering in wheat and this increased tillering resulted in overall increase in wheat biomass/yield. Mycorrhizae also enhanced nutritional attributes of wheat grains as well as soil fertility. The use of mycorrhizae will help to reduce our dependance on synthetic fertilizers in sustainable agriculture. creator: Muhammad Akbar creator: Safeer A. Chohan creator: Nasim A. Yasin creator: Aqeel Ahmad creator: Waheed Akram creator: Abdul Nazir uri: https://doi.org/10.7717/peerj.15686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Akbar et al. title: Maintenance of xylem hydraulic function during winter in the woody bamboo Phyllostachys propinqua McClure link: https://peerj.com/articles/15979 last-modified: 2023-09-13 description: BackgroundFrost is a common environmental stress for temperate plants. Xylem embolism occurs in many overwintering plants due to freeze-thaw cycles, so coping with freeze-thaw-induced embolisms is essential for the survival of temperate plants.MethodsThis study was conducted on Phyllostachys propinqua McClure, a woody bamboo species that was grown under natural frost conditions to explore its responses to winter embolisms. From autumn to the following spring, the following measurements were recorded: predawn branch and leaf embolism, branch and leaf relative water content (RWC), root pressure and soil temperature, xylem sap osmotic potential, branch and leaf electrolyte leakage (EL), branch nonstructural carbohydrate (NSC) content and leaf net photosynthetic rate.ResultsP. propinqua had a mean vessel diameter of 68.95 ±1.27 µm but did not suffer severe winter embolism, peaking around  60% in winter (January), with a distinct reduction in March when root pressure returned. Leaves had a more severe winter embolism, up to 90%. Leaf RWC was much lower in winter, and leaf EL was significantly higher than branch EL in all seasons. Root pressure remained until November when soil temperature reached 9 °C, then appeared again in March when soil temperatures increased from −6 °C (January) to 11 °C. Xylem sap osmotic potential decreased from autumn to winter, reaching a minimum in March, and then increasing again. Soluble sugar (SS) concentration increased throughout the winter, peaked in March, and then decreased.ConclusionsThese results suggest that (1) there is a hydraulic segmentation between the stem and leaf, which could prevent stem water loss and further embolization in winter; (2) maintenance of root pressure in early winter played an important role in reducing the effect of freeze-thaw cycles on the winter embolism; (3) the physiological process that resulted in a decrease in xylem sap osmotic potential and tissue water content, and an accumulation of SS associated with cold acclimation also aided in reducing the extent of freeze-thaw-induced embolism. All these strategies could be helpful for the maintenance of xylem hydraulic function of this bamboo species during winter. creator: Yongxin Dai creator: Lin Wang creator: Xianchong Wan uri: https://doi.org/10.7717/peerj.15979 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dai et al.