title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=204 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Risk factors and prediction models for recurrent acute ischemic stroke: a retrospective analysis link: https://peerj.com/articles/18605 last-modified: 2024-11-25 description: BackgroundIschemic stroke is one of the leading causes of disability and death worldwide, with a high risk of recurrence that severely impacts the quality of life of patients. Therefore, identifying and analyzing the risk factors for recurrent ischemic stroke is crucial for the prevention and management of this disease.MethodsA total of 114 cases of recurrent acute ischemic stroke patients admitted from July 2017 to March 2021 were selected as the observation group, and another 409 cases of initial ischemic stroke patients from the same period as the control group. The clinical data of the observation group and the control group were compared to analyze the risk factors associated with the readmission of ischemic stroke. A single-factor analysis (Model 1), Least Absolute Shrinkage and Selection Operator (LASSO) regression, and machine learning methods (Model 2) were used to screen important variables, and a multi-factor COX Proportional Hazards Model regression stroke recurrence risk prediction model was constructed. The predictive performance of the model was evaluated by the consistency index (C-index).ResultsMultivariate COX regression analysis revealed that history of hypertension (Hazard Ratio [HR] = 2.549; 95% Confidence Interval (CI) [1.503–4.321]; P = 0.001), history of cerebral infarction (HR = 1.709; 95% CI [1.066–2.738]; P = 0.026), cerebral artery stenosis (HR = 0.534; 95% CI [0.306–0.931]; P = 0.027), carotid arteriosclerosis (HR = 1.823; 95% CI [1.137–2.924]; P = 0.013), systolic blood pressure (HR = 0.981; 95% CI [0.971–0.991]; P < 0.0001), red cell distribution width-coefficient of variation (RDW-CV) (HR = 1.251; 95% CI [1.019–1.536]; P = 0.033), mean platelet volume (MPV) (HR = 1.506; 95% CI [1.148–1.976]; P = 0.003), uric acid (UA) (HR = 0.995; 95% CI [0.991–1.000]; P = 0.049) were found significantly associated with acute ischemic stroke. The C-index of the full COX model was 0.777 (0.732~0.821), showing a good discrimination between Model 1 and Model 2.ConclusionsHistory of hypertension, history of cerebral infarction, cerebral artery stenosis, carotid atherosclerosis, systolic blood pressure, UA, RDW-CV, and MPV were identified as risk factors for acute ischemic stroke recurrence. The model can be used to predict the recurrence of acute ischemic stroke. creator: Liuhua Ke creator: Hongyu Zhang creator: Kang Long creator: Zheng Peng creator: Yongjun Huang creator: Xingxuan Ma creator: Wanjun Wu uri: https://doi.org/10.7717/peerj.18605 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Ke et al. title: Effect of the diet level of whole-plant corn silage on the colonic microflora of Hezuo pigs link: https://peerj.com/articles/18630 last-modified: 2024-11-25 description: BackgroundWhole-plant corn silage (WPCS) is an important roughage source for livestock, and have critical influences on rumen or intestinal microbiota, thus affecting the growth performance and feed efficiency. Our previous studies showed that adding WPCS to the diet of Hezuo pigs could promote the growth and fiber digestibility. While the aim of this study is to understand the effect of dietary WPCS on the colonic microflora in Hezuo pigs, which is essential for improving the roughage exploitation of pigs.MethodsThirty-two Hezuo pigs with similar body weight (7.88 ± 0.81) kg were selected and randomly divided into four groups with eight pigs in each group. Pigs in the control group were fed a basal diet, pigs in the experimental groups (Groups I, II, and III) were fed basal diet supplemented with 5%, 10%, and 15% WPCS, respectively, under 120 d experimental period. Six pigs from each group were picked for collecting colonic contents samples. 16S rRNA sequencing was performed to analyze the colonic microbiota of experimental pigs.ResultsThe results showed that community richness indexes Chao1 and Observed_species in group III of Hezuo pig were significantly lower than that of the other three groups, community diversity indexes Shannon and Simpson were significantly higher in group I and II in comparison to the control group, and significantly lower in group III in comparison to the control group, group I and II. Adding WPCS to the diet of Hezuo pigs has no influence on the colonic dominant phylum, Clostridium sensu stricto 1 and Rikenellaceae RC9 gut group were most prevalent in the colon of Hezuo pig. When compared with the control group, the relative abundance of Streptococcus was significantly decreased in three experimental groups, while p-251-o5, Parabacteroides, Prevotellaceae UCG-003, Prevotellaceae UCG-001, and F082 exhibited significantly higher relative abundances in at least two experimental groups. Fibrobacter, Rikenellaceae RC9 gut group in group I, UCG-010 in group II, Bacteroides in group III exhibited increased relative abundance as compared with the control group. PICRUSt functional annotation indicated that the functions of cellular process and signaling were significantly increased in all WPCS-rationed groups, cancers, nervous system, immune system and environmental adaptation were all differed from groups I and II; three predominant pathways of translation, nucleotide metabolism and signal were only differed from the group II.ConclusionsFeeding with 5% and 10% WPCS for Hezuo pigs could improve their colonic microflora diversity, and increase the relative abundance of fiber-digesting bacteria, which may potentially help to improve the fibre digestibility of Hezuo pigs by regulating the microbial function of cellular process and signaling, nucleotide metabolism, translation. creator: Qiaoli Yang creator: Longlong Wang creator: Pengfei Wang creator: Zunqiang Yan creator: Qiong Chen creator: Pengxia Zhang creator: Jie Li creator: Rui Jia creator: Yao Li creator: Xitong Yin creator: Shuangbao Gun uri: https://doi.org/10.7717/peerj.18630 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Climate change effect on the widely distributed Palearctic plant bug species (Insecta: Heteroptera: Miridae) link: https://peerj.com/articles/18377 last-modified: 2024-11-22 description: Insects are poikilothermic organisms and temperature increase usually accelerates their development rates, population and distribution area growth. Therefore, it is assumed that global warming can be beneficial for the pests and other widespread species at least in the relatively cool temperate zones. However, climate change’s effect on the widespread species in the Palearctic remains poorly studied. This work was performed on three plant bug species (Insecta: Heteroptera: Miridae), at present inhabiting Europe and Asia. Liocoris tripustulatus is known from the Western Palearctic, Lygocoris pabulinus occupies the territories from Western Europe to South Asia, Lygus punctatus is distributed from Northern Europe to the Far East. In this paper, it is tested whether temperature rise is positively connected with the area of preferred climatic conditions for those species, and explores the particular climatic variables which can be limiting for the distribution of those species. Maxent software was used for the environmental niche modeling and to find the variables with significant contribution to the climatic models for the studied species. Based on those models, areas with preferred climatic conditions over different periods were calculated in QGIS. Principal component analysis and logistic regression were performed to find the variables highly contributing to the differences between the species. The results contradict the assumption that temperature growth alone can be a predictor for the widespread species and pest distribution range change. All species differ in suitable climatic conditions and their area dynamics in time, and the temperature affects each species differently. Only Liocoris tripustulatus might significantly expand its distribution area by 2070 due to the climate change. The areas in Asia and above the polar circle will be more suitable by that time for all three species than now. However, conditions in Europe might be less suitable for Lygocoris pabulinus and Lygus punctatus in the future. Both, temperature and precipitation variables, can be important for shaping distribution of Liocoris tripustulatus and Lygocoris pabulinus. Mean annual temperature and temperature in winter, most probably, limit the distribution of at least Liocoris tripsutulatus and Lygus punctatus, but changes in this variable affect those two species differently. creator: Anna A. Namyatova creator: Polina A. Dzhelali creator: Veronica D. Tyts creator: Alexander A. Popkov uri: https://doi.org/10.7717/peerj.18377 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Namyatova et al. title: Fluctuations of continuous soil moisture evaporation under different rainfall conditions during the growing period of the non-monsoon season, the eastern Loess Plateau link: https://peerj.com/articles/18514 last-modified: 2024-11-22 description: Soil moisture is an important link between material and energy exchange between the land and atmosphere, and its evaporation loss is crucial to sustainable development of agriculture. Based on observations of long-term stable isotopes of soil moisture in the eastern Loess Plateau (ECLP) during the non-rainy season growing period, this study systematically explored soil water evaporation loss at different soil depths using the Craig–Gordon model and revealed the internal relationship between soil evaporation loss and environmental elements. Main findings included: (1) The soil moisture content showed a gradual decreasing trend, with a weak soil moisture δ18O fluctuation appearing in April, whereas a stronger fluctuation was observed in June. (2) A significant vertical spatial heterogeneity was observed in soil moisture δ18O of each soil layer. Enriched soil moisture δ18O values appeared in the 0–20 cm soil layer, and the minimum value appeared in the 40–60 cm soil layer. (3) A significant spatial and temporal heterogeneity was observed in the soil moisture evaporation loss fraction (f) (0–23.35%), with weaker values at the beginning of the study period and larger values between mid-late May and mid-June. The largest soil evaporation loss was observed in the 0–20 cm soil layer (average value of 8.97%), a fluctuating decreasing trend appeared with increasing soil depth. (4) Regional soil moisture evaporation loss was positively correlated with regional air temperature (T) and potential evapotranspiration (ET0) and negatively correlated with soil water content (SWC) and relative humidity (RH). The correlation between soil moisture evaporation loss and environmental elements gradually weakened with increasing soil depth. (5) The environmentally driven model of continuous evaporation of soil moisture was suitable for larger amounts, especially for the surface soil layers. The results of this study have important implications for water resource management, ecosystem stability, and sustainable regional agriculture in the ECLP. creator: Congjian Sun creator: Sitong Meng creator: Wei Chen uri: https://doi.org/10.7717/peerj.18514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sun et al. title: Targeting squalene epoxidase in the treatment of metabolic-related diseases: current research and future directions link: https://peerj.com/articles/18522 last-modified: 2024-11-22 description: Metabolic-related diseases are chronic diseases caused by multiple factors, such as genetics and the environment. These diseases are difficult to cure and seriously affect human health. Squalene epoxidase (SQLE), the second rate-limiting enzyme in cholesterol synthesis, plays an important role in cholesterol synthesis and alters the gut microbiota and tumor immunity. Research has shown that SQLE is expressed in many tissues and organs and is involved in the occurrence and development of various metabolic-related diseases, such as cancer, nonalcoholic fatty liver disease, diabetes mellitus, and obesity. SQLE inhibitors, such as terbinafine, NB598, natural compounds, and their derivatives, can effectively ameliorate fungal infections, nonalcoholic fatty liver disease, and cancer. In this review, we provide an overview of recent research progress on the role of SQLE in metabolic-related diseases. Further research on the regulation of SQLE expression is highly important for developing drugs for the treatment of metabolic-related diseases with good pharmacological activity. creator: Mingzhu Chen creator: Yongqi Yang creator: Shiting Chen creator: Zhigang He creator: Lian Du uri: https://doi.org/10.7717/peerj.18522 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses link: https://peerj.com/articles/18543 last-modified: 2024-11-22 description: BackgroundAutophagy plays a key role in the development of carotid atherosclerosis (CAS). This study aimed to identify key autophagy-related genes (ATGs) related with CAS using bioinformatics analysis, in vivo AS mouse model, and in vitro experiments.MethodsThe GSE100927 and GSE28829 datasets were downloaded from the Gene Expression Omnibus (GEO) database. An integrated bioinformatics analyses of differentially expressed ATGs (DE-ATGs) was conducted. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify the biological processes and pathways associated with DE-ATGs. Protein-protein interaction (PPI) network was constructed with the DE-ATGs to identify the key CAS-related DE-ATGs. Receiver operating characteristic (ROC) curve analysis was used to determine the diagnostic value of the key CAS-related DE-ATGs. CIBERSORT analysis was performed to determine the infiltration status of 22 immune cell types and their correlation with the expression levels of the key CAS-related DE-ATGs. Hematoxylin and eosin (HE) staining was used to estimate the plaque histology in the AS mouse model. Western blotting, quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) were performed to validate the protein and mRNA expression levels of the key CAS-related DE-ATGs in the in vitro and in vivo models.ResultsWe compared transcriptome profiles of 12 early CAS plaques and 29 advanced CAS plaques in the GSE100927 dataset and identified 41 DE-ATGs (33 up-regulated and eight down-regulated). Functional enrichment analysis showed that the DE-ATGs were closely related with apoptosis, autophagy, and immune activation. ROC curve analysis showed that the area under the curve (AUC) values for the three key CAS-related DE-ATGs (CCL2, LAMP2, and CTSB) were 0.707, 0.977, and 0.951, respectively. CIBERSORT analyses showed close association between the three key CAS-related DE-ATGs and the infiltration of immune cell types in the plaques. Finally, the western blot, qRT-PCR, and IHC staining confirmed that CCL2, LAMP2, and CTSB were highly expressed in the plaques of the AS model mice or ox-LDL-treated human umbilical vein endothelial cells (HUVECs) and human aorta vascular smooth muscle cells (HAoSMCs).ConclusionWe identified and validated three key CAS-associated ATGs, namely, CCL2, LAMP2, and CTSB with high diagnostic value. These three key CAS-associated ATGs are promising diagnostic markers and therapeutic targets for patients with CAS. creator: Tiegen Huang creator: Chen Su creator: Quanli Su creator: Yali Nie creator: Zhenni Xiao creator: Yao Tang creator: Jiahao Wang creator: Xiaotian Luo creator: Yixin Tang uri: https://doi.org/10.7717/peerj.18543 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Huang et al. title: Different sound exposures causes alterations in stress-related serum indicators, behaviors, and cecal microbiota of green-shell egg-laying chickens under different stocking densities link: https://peerj.com/articles/18544 last-modified: 2024-11-22 description: Sound and stocking density are two common factors which influence the performance and welfare of layers. Accumulated studies have been conducted on the impacts of the two factors on production performance, while knowledge regarding the impacts of the two factors and their interactions on stress-related serum indicators, behaviors, and cecal bacterial communities in laying hens is still limited. A 3 × 3 factorial design with three sound sources (natural sound (NS), instrumental music (IMS), or mixed road noise (MRS)) and three stocking densities (low density (LD), medium density (MD), and high density (HD)) was used in this 24-day experiment, in which 378 30-week-old Xiandao green-shell layers were randomly distributed into nine treatments with six replicates per treatment. At the 3rd, 12th, and 24th experimental day, we evaluated the serum levels of adrenocorticotropic hormone (ACTH) and corticosterone (CORT) and recorded stress-related animal behaviors. At the end of the experiment, 16S rRNA gene amplicon sequencing of the cecal bacterial communities was performed. Our results confirmed that MRS and HD induced significantly elevated serum ACTH and CORT levels, and were correlated with significantly increased feather pecking behavior. IMS and LD were associated with enhanced preening behavior and reduced feather pecking behavior. LD significantly increased the Firmicutes/Bacteriodetes ratio and IMS significantly enriched the beneficial Lactobacillus population. Based on the obtained results we proposed that music exposure and reduced stocking density were helpful in reducing stress and improving cecal bacterial profile, which were beneficial for improving layers’ health status and welfare. creator: Shiwen Cao creator: Manhong Ye creator: Wanhong Wei creator: Fengping Yang uri: https://doi.org/10.7717/peerj.18544 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cao et al. title: Tilianin content and morphological characterization of colchicine-induced autotetraploids in Agastache mexicana link: https://peerj.com/articles/18545 last-modified: 2024-11-22 description: BackgroundAgastache mexicana Linton & Epling subsp. mexicana (Lamiaceae) is an aromatic medicinal plant, characterized by a high concentration of tilianin, a flavonoid with therapeutic potential in cardiovascular diseases. In this study, we have explored the use of colchicine to obtain autotetraploid lines of A. mexicana and analyze their morphological characteristics. In addition, we aimed to identify polyploid plants with a high content of tilianin.MethodsIn vitro seedlings at the stage of cotyledon emergence were dipped in colchicine solution at 0.0%, 0.1%, 0.3%, and 0.5% (w/v) for 6, 12, and 24 h. Seedlings were cultured on half-strength basal Murashige and Skoog medium supplemented with 20 g/L sucrose. After 2 months, the shoots from surviving seedlings were excised and grown individually in the same medium to obtain plantlets. The ploidy level of all materials was verified through flow cytometry and chromosome counting before acclimatization and transfer to the greenhouse. The investigated characteristics included length, density and stomatal index, leaf area, chlorophyll content, flower size and color, and tilianin content measured by high-performance liquid chromatography.ResultsThe most efficient production of tetraploid in terms of percentage was achieved with 0.1% colchicine for 6 h resulting in no generation of mixoploids. Tetraploid plants had twice the number of chromosomes (2n = 4x = 36) and nearly twice the total DNA content (2.660 ± 0.236 pg) of diploids. Most tetraploid A. mexicana plants showed variations in flower and leaf characteristics compared to the diploid controls. High-performance liquid chromatography analysis showed that tetraploid plants with small leaves produced the greatest amount of tilianin; up to 32.964 ± 0.004 mg/g dry weight (DW), compared to diploid plants with 6.388 ± 0.005 mg/g DW.ConclusionIn vitro polyploidization using colchicine demonstrates potential for enhancing bioactive constituents of A. mexicana. This approach has proven effective in generating elite tetraploid lines with increased tilianin production. creator: Angélica Martínez-Aguilar creator: Evert Villanueva Sánchez creator: Susana Valencia-Díaz creator: Samuel E. Estrada-Soto creator: Selene Napsucialy-Mendivil creator: Rodrigo Barba-Gonzalez creator: Iran Alia-Tejacal creator: José de Jesús Arellano-García creator: Oscar Gabriel Villegas Torres creator: Karla Catalina Cruz Torres creator: Irene Perea-Arango uri: https://doi.org/10.7717/peerj.18545 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Martínez-Aguilar et al. title: Exploring quadriceps activity variations in women: the role of seated posture during stair climbing link: https://peerj.com/articles/18547 last-modified: 2024-11-22 description: BackgroundAdults in modern society spend most of their time in a sitting position. However, sitting for long periods of time can affect the length and sensation of the quadriceps muscle and negatively affect the performance of functional tasks required in daily life. In addition, it may have different characteristics according to sitting postures.AimThe aim of this study is to investigate the differences in quadriceps muscle activity during stair climbing and descending based on various sitting postures.MethodsThirty healthy adult women were classified into sitting upright (SU), sitting with legs crossed (SLC), and sitting with ankles crossed over knees (SAC). The muscle activities of the vastus medialis (VM), vastus lateral (VL), and rectus femoris (RF) were collected during climbing and descending the stairs three times each. After which a sitting posture was maintained for 15 min, the post-measurement was performed in the same way as the pre-measurement. One-way analysis of variance or Kruskal-Walli’s test was used to check homogeneity between each group, least significant difference (LSD) was used for post-hoc testing. Paired-sample t-test or Wilcoxon signed-rank test was used to check before-and-after differences within the group. Repeated measures analysis of variance was used to determine between-group and within-group interactions.ResultsVM muscles were significantly decreased after maintaining a sitting posture during descending stairs of SAC group (p = 0.047). In conclusion, this study indicates that maintaining a SAC sitting posture for a certain period causes a temporary decrease in muscle activity of the VM muscle during descending stairs. This provides important implications for early treatment to manage knee pain and strengthen quadriceps muscles in women. Future studies should focus on groups with patellofemoral pain syndrome or knee pain to better understand the impact of sitting posture on quadriceps activity. creator: SaBin Chun creator: JongChul Park uri: https://doi.org/10.7717/peerj.18547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chun and Park title: Tae-miR396b regulates TaGRFs in spikes of three wheat spike mutants link: https://peerj.com/articles/18550 last-modified: 2024-11-22 description: Tillering and spike differentiation are key agronomic traits for wheat (Triticum aestivum L.) production. Numerous studies have shown that miR396 and growth-regulating factor genes (GRFs) are involved in growth and development of different plant organs. Previously, we have reported that wheat miR396b (tae-miR396b) and their targets TaGRFs (T. aestivum GRFs) play important roles in regulating wheat tillering. This study was to investigate the regulatory roles of tae-miR396b and TaGRFs played during wheat spike development. Wheat cultivar Guomai 301 (wild type, WT) and its three sipke mutants dwarf round spike mutant (drs), apical spikelet sterility mutant (ass) and prematurely terminated spike differentiation mutant (ptsd1) were studied. Three homeologous genes of tae-miR396b on the long arms of chromosomes 6A, 6B, and 6D were identified, and they encoded the same mature miRNA. Complementary sequences of mature tae-miR396b were identified in 23 TaGRFs, indicating they were the target genes of tae-miR396b. Tae-miR396b had different regulatory effects on TaGRFs between Guomai 301 and its mutants. TaGRF2-7A was confirmed to be the target gene of tae-miR396b by molecular interaction assay. The expression levels of tae-miR396b and TaGRFs were different between WT and mutants drs, ass and ptsd1 at the floret primordium visible (S1), the two awns/spikelet reaching apical meristem of the spikelet (S2), and the green anther stage (S3). The expression level of tae-miR396b in WT was significantly higher than that in mutants drs and ass. The most TaGRFs were negatively regulated by tae-miR396b. The abnormal expressions of TaGRF1 (6A, 6D), TaGRF2 (7A, 7B, 7D), TaGRF4 (6A, 6B), TaGRF5 (4A, 7A, 7D), and TaGRF10 (6A, 6B, 6D) were important causes for abnormal spike development in the three mutants. This study laid foundation for further elucidating functions of tae-miR396b and TaGRFs underlying wheat spike development. Regulating tae-miR396b and TaGRFs will be a new approach for wheat high yield breeding. creator: Ziping Yao creator: Qi Wang creator: Ying Xue creator: Zhiheng Liang creator: Yongjing Ni creator: Yumei Jiang creator: Peipei Zhang creator: Ting Wang creator: Qiaoyun Li creator: Lei Li creator: Jishan Niu uri: https://doi.org/10.7717/peerj.18550 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yao et al.