Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review
Background Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. Methodology A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms “vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”. Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. Results Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. Conclusion Considerable differences in study design and data formatting methods may contribute to underrepresentation of GBS, and other known pathogens, in existing vaginal microbiome literature. Previous studies have identified considerable variation in methodology across vaginal microbiome studies. This study adds to this body of work because in addition to laboratory or statistical methods, how results and data are shared (e.g., only analyzing genus level data or 20 most abundant microbes), may hinder reproducibility and limit our understanding of the influence of less abundant microbes. Sharing detailed methods, analysis code, and raw data may improve reproducibility and ability to more accurately compare microbial communities across studies.
Lim et al. (2021) Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review. PeerJ 9:e11437 https://doi.org/10.7717/peerj.11437
Machine learning in dental, oral and craniofacial imaging: a review of recent progress
Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study.
Ren et al. (2021) Machine learning in dental, oral and craniofacial imaging: a review of recent progress. PeerJ 9:e11451 https://doi.org/10.7717/peerj.11451
The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study
Background The outbreak of the novel Corona Virus Infectious Disease 2019 (COVID-19) has spread rapidly to many countries leading to thousands of deaths globally. The burden of this pandemic has affected the physical and mental health of the frontline health care workers (HCWs) who are exposed to high risk of infection and psychological stressors. Aims The aim is to measure the level of depression among healthcare workers in Saudi Arabia during COVID-19 pandemic to establish interventional strategies. Method A descriptive cross-sectional study was used to conduct the current study. The data of this study was recruited between 15 June and 15 July 2020 from healthcare providers who work in both public and private healthcare sectors in Riyadh and Eastern province in Saudi Arabia utilizing a self-administered questionnaire. The study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-2). Data were collected by using The Zung Self-Rating Depression Scale SDS. A total of 900 healthcare providers working in the healthcare setting during COVID-19 pandemic were invited to participate in the study. A total of 650 healthcare providers participated in the study by completing and submitting the survey. Results Almost 30% suffered from depression which can be divided into three categories; mild depression (26.2%), moderate/major (2.5%) and severe/extreme (0.8%). The finding shows that the level of depression among respondents at the age range of 31–40 years old was significantly higher than the level of depression among respondents with the age above 50 years old. Non-Saudi healthcare workers experienced more depression than Saudi workers. It also shows how nurses suffered from depression compared to their physician colleagues. Those who did not suffer from sleeping disorder perceived more depression as compared to those who are having sleeping disorder. Conclusion It is recommended that health care facilities should implement strategies to reduce the prevalence of mental health problems among healthcare providers and eventually it will improve their performance in provision of safe and high-quality care for patients.
Al Mutair et al. (2021) The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study. PeerJ 9:e11469 https://doi.org/10.7717/peerj.11469
Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study
Background To verify the association between weekly leisure walking time and positive self-rated health in the Brazilian adult and elderly population. Methods This cross-sectional study used information collected in 2019 across all regions of Brazil. This study included 25,785 people aged ≥ 18 years (mean = 51.6; standard deviation = 18.0) from all capitals of the Brazilian states who reported practicing walking as physical activity during leisure time. Self-rated health was the dependent variable (positive or negative). The leisure walking time/week was the main exposure and it was categorized in “150 minutes/week”, “150–299 minutes/week” and “≥ 300 minutes/week”. We used binary logistic regression to estimate odds ratio (OR) and 95% confidence intervals (95% CI) that was adjusted for relevant covariates. Results We found that individuals who reported leisure walking for a period from 150 to 299 minutes/week and those who reported walking for a period ≥ 300 minutes/week were respectively 28% (OR = 1.28. 95% CI [1.10–1.48]) and 52% (OR = 1.52. 95% CI [1.27–1.82]) more likely of perceiving their health positively compared to those who reported walking for a period < 150 minutes/week. Individuals who reported leisure walking time <150 minutes/week had 72.3% (95% CI [70.4–74.1]) probability of perceiving their health positively. Individuals who reported leisure walking time from 150 to 299 minutes/week had 76.6% (95% CI [75.0 –78.3) probability of perceiving their health positively. On the other hand, individuals who reported leisure walking time ≥ 300 minutes/week had 79.2% probability (95% CI [77.1–81.4]) of perceiving their health positively. Conclusion Longer leisure walking time was associated with positive self-rated health among adults and older adults in Brazil.
Silva (2021) Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study. PeerJ 9:e11471 https://doi.org/10.7717/peerj.11471
Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years
Context Yunnan Province is an important ecological security barrier in China. This study investigated the temporal and spatial changes to landscape ecology and is of great significance for guiding landscape protection and future socio-economic development. Objectives To analyze the temporal and spatial changes of the landscape patterns at the county, river basin, and provincial levels, and clarify and describe the temporal and spatial differentiation characteristics of the landscape patterns in Yunnan Province. Methods Based on landscape ecology, GIS spatial analysis, and spatio-temporal change analysis, nine landscape pattern indices, and spatial autocorrelation for different years, were calculated. Results The landscape of Yunnan Province has evolved as a whole toward isolation. The indices of separation and fragmentation changed significantly from 2010 to 2015. From 2015 to 2018 the rate of fragmentation decreased. Fragmentation in the Nu Jiang and Irrawaddy River basins was less than in other basins. The landscape patterns of the Jinsha and Pearl River basins were relatively fragmented due to human activity, socioeconomic development, and utilization. The differences between the Lancang and Red River Basins were relatively small and at an intermediate level. Conclusions Spatial autocorrelation analysis indicated that there are three areas with typical clusters, namely the Hengduan Mountains where the degree of fragmentation of the landscape was low, while landscape connectivity and aggregation were high. The subtropical region of Southern Yunnan displayed high landscape heterogeneity, a complex shape index, and high connectivity and sprawl. Central Yunnan exhibited a fragmented landscape with poor connectivity and aggregation. These three regions correspond with “the three screens and two belts” in the Main Functional Planning Area of Yunnan Province.
Spatial and Geographic Information Science
Liu et al. (2021) Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years. PeerJ 9:e10923 https://doi.org/10.7717/peerj.10923
Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes
This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mixture at a lower supplemental level (20 g/day) to increase milk fat (%) and unsaturated fatty acid content in buffalo.
Hassan et al. (2021) Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes. PeerJ 9:e11241 https://doi.org/10.7717/peerj.11241
The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper
Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.
Environmental Contamination and Remediation
Clavero-León et al. (2021) The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper. PeerJ 9:e11373 https://doi.org/10.7717/peerj.11373
DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway
Background Hepatic fibrosis is a common response to chronic liver injury. Recently, the role of DZNep (a histone methyltransferase EZH2 inhibitor) in repressing pulmonary and renal fibrosis was verified. However, the potential effect of DZNep on hepatic fibrosis has not been elucidated. Methods The hepatic fibrosis model was established in rats treated with CCl4 and in hepatic stellate cells (HSCs) treated with TGF-β1. The liver tissues were stained with H&E and Masson’s trichrome. The expression of EZH2, SOCS7, collagen I, αSMA mRNA and miR-199-5p was assessed using qPCR, immunohistochemical or western blot analysis. A dual-luciferase reporter assay was carried out to validate the regulatory relationship of miR-199a-5p with SOCS7. Results The EZH2 level was increased in CCl4-treated rats and in TGF-β1-treated HSCs, whereas DZNep treatment significantly inhibited EZH2 expression. DZNep repressed hepatic fibrosis in vivo and in vitro, as evidenced by the decrease of hepatic fibrosis markers (α-SMA and Collagen I). Moreover, miR-199a-5p expression was repressed by DZNep in TGF-β1-activated HSCs. Notably, downregulation of miR-199a-5p decreased TGF-β1-induced expression of fibrosis markers. SOCS7 was identified as a direct target of miR-199a-5p. The expression of SOCS7 was decreased in TGF-β1-activated HSCs, but DZNep treatment restore d SOCS7 expression. More importantly, SOCS7 knockdown decreased the effect of DZNep on collagen I and α SMA expression in TGF-β1-activated HSCs. Conclusions DZNep suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 axis, suggesting that DZNep may represent a novel treatment for fibrosis.
Ding et al. (2021) DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway. PeerJ 9:e11374 https://doi.org/10.7717/peerj.11374
Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells
Background. Multiple studies have indicated crucial roles of NAD+ deficiency in several neurological diseases and aging. It is critical to discover the mechanisms underlying the NAD+ deficiency. A decreased level of Nicotinamide phosphoribosyltransferase (Nampt)—an important enzyme in the salvage pathway of NAD+ synthesis—has been found under certain pathological conditions, while the mechanisms underlying the Nampt decrease are unclear. The purpose of this study is to test the hypothesis that oxidative stress can produce decreased Nampt, and to investigate the biological effects of Nampt on NAD+ synthesis and cell survival under both basal and oxidative stress conditions. Methods. We used differentiated PC12 cells as a cellular model to investigate the effects of oxidative stress on the levels of Nampt. Multiple assays, including flow cytometry-based cell death assays and NAD+ assays were conducted. Results. First, oxidative stress can decrease the levels of Nampt mRNA and Nampt protein; second, Nampt plays significant roles in NAD+ synthesis under both basal conditions and oxidative stress conditions; third, Nampt plays critical roles in cell survival under both basal conditions and oxidative stress conditions; and fourth, oxidative stress produced decreased NAD+ levels and cell survival partially by decreasing Nampt. Collectively, our study has indicated that oxidative stress is a pathological factor leading to decreased Nampt, which plays important roles in oxidative stress-produced decreases in NAD+ levels and cell survival. Our findings have indicated major roles of Nampt in maintaining NAD+ levels and cell survival under both basal and oxidative stress conditions.
Zhou et al. (2021) Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells. PeerJ 9:e11401 https://doi.org/10.7717/peerj.11401
The relationship between PLOD1 expression level and glioma prognosis investigated using public databases
Background Glioma is the most common type of intracranial tumor with high malignancy and poor prognosis despite the use of various aggressive treatments. Targeted therapy and immunotherapy are not effective and new biomarkers need to be explored. Some Procollagen-lysine 2-oxyglutarate 5-dioxygenase (PLOD) family members have been found to be involved in the metastasis and progression of tumors. Both PLOD2 and PLOD3 had been reported to be highly expressed in gliomas, while the prognostic value of PLOD1 remains to be further illustrated, so we want to investigate the PLOD1 expression in glioma and its clinical implication. Methods We collected gene expression and corresponding clinical data of glioma from the Chinese Glioma Genome Atlas (CGGA) database, The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. First, we analyzed the expression and mutation of PLOD1 in gliomas and its relationship with clinicopathologic characteristics. Then, we conducted survival analysis, prognostic analysis and nomogram construction of the PLOD1 gene. Finally, we conducted gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) to explore possible mechanisms and gene co-expression analysis was also be performed. Results The results showed that the expression level of PLOD1 was higher in gliomas than normal tissues, and high expression of PLOD1 was related to poor survival which can serve as an oncogenic factor and an independent prognostic indicator for glioma patients. Both the GO and GSEA analysis showed high expression of PLOD1 were enriched in Extracellular matrix (ECM) related pathways, the co-expression analysis revealed that PLOD1 was positively related to HSPG2, COL6A2, COL4A2, FN1, COL1A1, COL4A1, CD44, COL3A1, COL1A2 and SPP1, and high expression of these genes were also correlated to poor prognosis of glioma. Conclusions The results showed that high expression of PLOD1 leads to poor prognosis, and PLOD1 is an independent prognostic factor and a novel biomarker for the treatment of glioma. Furthermore, targeting PLOD1 is most likely a potential therapeutic strategy for glioma patients.
Tian et al. (2021) The relationship between PLOD1 expression level and glioma prognosis investigated using public databases. PeerJ 9:e11422 https://doi.org/10.7717/peerj.11422