title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=217 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections link: https://peerj.com/articles/18471 last-modified: 2024-11-08 description: BackgroundDetermining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses.MethodsIn this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology.ResultsA total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p < 0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively.ConclusionOur study demonstrates the high accuracy of probe capture sequencing technology compared to blood cultures in the identification of pathogenic microorganisms in BSI upon final clinical diagnosis. Among the different sample types, white blood cell samples had a lower clinical compliance rate compared to plasma samples, possibly due to the higher host rate in cell samples, which impairs the sensitivity of pathogen detection. creator: Xinyuan Liu creator: Zhitao Gan creator: Zengshun Lin creator: Xiaojun Lin creator: Jianying Yuan creator: Lili Rong creator: Jiachang Chen creator: Jun Liu creator: Yingzhen Li creator: Chaohui Hu uri: https://doi.org/10.7717/peerj.18471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: The impact of hsa-miR-1972 on the expression of von Willebrand factor in breast cancer progression regulation link: https://peerj.com/articles/18476 last-modified: 2024-11-08 description: BackgroundBreast cancer (BC) is one of most frequent female malignancies that poses multiple challenges in treatment and prevention. This study aimed to explore the role of miRNAs and their target genes during the BC progression.MethodsBased on the BC data (113 normal and 1,118 tumor samples) from the TCGA-BRCA dataset, a single-sample gene set enrichment analysis (ssGSEA) was applied to calculate the cancer migration scores, and weighted gene co-expression network analysis (WGCNA) were performed using the WGCNA R package, with a focus on the set of genes associated with cancer migration. Key modules and hub genes related to cell migration and signaling pathways were identified. Survival analysis of hub genes was conducted using the survminer R package, and prediction of regulatory miRNAs were performed to analyze their impact on BC prognosis. In addition, the BC cell lines MCF-7 and MDA-MB-231 were used to further explore the effect of hsa-miR-1972 mimics on the gene expression and angiogenic factor regulation.ResultsThe study classified important modules (MEblue, MEmagenta, MEpink, and MEfloralwhite) associated with cell migration and identified three hub genes, namely, MRPL20, COL4A1 and VWF. Survival analysis showed that certain hub genes with a low expression were related to a poor prognosis, whereas low-expressed COL4A1 and VWF were related to better survival outcomes. We also found that hsa-miR-1972 mimics significantly downregulated critical genes involved in BC metastasis and angiogenesis and effectively inhibited the proliferation of BC cell lines, showing a strong therapeutic potential. Manipulation of VWF expression in cells overexpressing hsa-miR-1972 had significant effects on the malignant markers and angiogenic factors, suggesting a novel therapeutic direction for BC treatment.ConclusionOur study highlighted the complex interplay of genetic factors in BC progression as well as the therapeutic potential of targeting specific miRNAs and their related hub genes. These findings provided novel insights into the pathogenesis of BC and suggested new direction for the therapeutic development for the cancer. creator: Changjiang Yu creator: Tao Zhang creator: Fan Chen creator: Zhenyang Yu uri: https://doi.org/10.7717/peerj.18476 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu et al. title: Spatiotemporal variations of atmospheric black carbon concentration and its correlation with meteorological and environmental factors in Xinjiang, China, from 2010 to 2022 link: https://peerj.com/articles/18187 last-modified: 2024-11-07 description: Black carbon (BC) is a pollutant produced by the combustion of fossil fuels and biomass fuels, which has a huge impact on regional climate, atmospheric environment, and human health. In this study, based on MERRA-2 reanalysis data and ground-based observation data, the Mann-Kendall (MK) test and random forest (RF) model were used to explore the spatiotemporal variation characteristics of atmospheric BC concentration in Xinjiang, China and its correlation with meteorological and environmental covariates in 2010–2022. The results showed that the use of MERRA-2 reanalysis data to explore the spatiotemporal variation characteristics of BC concentration in Xinjiang had high reliability (relative average deviation (RAD) = 0.65). From 2010 to 2022, the annual average concentration of atmospheric BC in Xinjiang was 195.40 ± 15.55 ng/m3, and the multi-year average change rate was −0.05%. The winter season had the highest atmospheric BC concentration (145.52 ± 39.31 ng/m3), followed by autumn (124.95 ± 28.82 ng/m3), spring (74.05 ± 9.96 ng/m3), and summer (73.41 ± 5.69 ng/m3). The atmospheric BC concentration had a significant spatial variation, showing two high-BC-concentration areas on the northern slope of the Tianshan Mountains (centered on Urumqi-Changji-Shihezi region) and the urban agglomeration around the Tarim Basin (centered on Kashgar). The RF model analysis showed that meteorological factors including snow depth, surface temperature, and humidity as well as environmental factors including NO2, PM10, and SO2 were the main factors affecting the BC concentration. This work is of great significance for clarifying the accumulation and spatial distribution characteristics of atmospheric BC in northwest China and the factors influencing the atmospheric BC concentration, and helps to raise public attention to the increasingly serious climate change and public health problems caused by BC. creator: Xiang Xie creator: Zhujun Zhao creator: Shuting Li creator: Zhongqi Lu creator: Lijuan Chen creator: Jiangjiang Cai uri: https://doi.org/10.7717/peerj.18187 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xie et al. title: High variability in the attractiveness of municipally-planted decorative plants to insects link: https://peerj.com/articles/17762 last-modified: 2024-11-06 description: Insect populations are declining globally. A major driver of this decline is land use change, including urbanisation. However, urban environments can also offer a wide range of floral resources to pollinators, through ornamental plantings, but these can vary widely in their attractiveness to insects. Often, the largest single planter of ornamental plants in an urban area is the municipality. Here we evaluated the decorative plantings carried out by the city municipality of Regensburg, Germany, by systematically surveying insect visitations on different plant types in late summer, when forage is often limited for pollinators. We found a 130-fold difference from the least to the most attractive plants, and high variation in which insect groups were attracted to which plants. While honey bees, which are not a conservation concern, were the most common insect visitors, some decorative plants attracted a very large proportion of wild bees, flies, and wasps. Our results demonstrate that there is great scope for increasing the supply of urban forage to pollinators in general, and specific groups in particular, without requiring new decorative plant types to be sourced or planted. We argue that providing local evidence-based guidance to municipalities offers a quick and potentially cost-neutral method for supporting urban insect populations. creator: Tomer J. Czaczkes creator: Carsten Breuss creator: Christoph Kurze uri: https://doi.org/10.7717/peerj.17762 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Czaczkes et al. title: Reliability and utility of blood glucose levels in the periodontal pockets of patients with type 2 diabetes mellitus: a cross-sectional study link: https://peerj.com/articles/18239 last-modified: 2024-11-06 description: BackgroundSeveral studies have measured gingival blood glucose (GBG) levels, but few have confirmed systematic bias using Bland–Altman analysis. This study compared the effectiveness of GBG levels with that of fingertip blood glucose (FTBG) levels using Bland–Altman and receiver operating characteristic (ROC) analyses.MethodsA total of 15 healthy volunteers and 15 patients with type 2 diabetes were selected according to inclusion and exclusion criteria. Each group comprised eight male and seven female participants. The GBG and FTBG levels were measured using a self-monitoring blood glucose device after periodontal examination. Pearson’s product‒moment correlation and simple linear regression analyses were performed. In addition, Bland‒Altman analysis was also performed to assess the degree of agreement between the two methods. ROC analysis was conducted to determine the sensitivity, specificity, and cutoff values for patients with diabetes. The area under the ROC curve (AUC) was used to identify significant differences.ResultsThe mean GBG and FTBG levels were 120 ± 44.8 mg/dL and 137 ± 45.1, respectively, for the whole sample. The mean GBG and FTBG levels were 145 ± 47.2 mg/dL and 163 ± 49.1, respectively, in the diabetes group. The mean GBG and FTBG levels in the nondiabetes group were 95.3 ± 25.2 and 111 ± 18.8, respectively. Patients with diabetes were more likely to have a probing pocket depth (PPD) of ≥4 mm at the sampled site. Pearson’s product‒moment correlation and simple linear regression analyses revealed a significant correlation between the GBG and FTBG measurements. Bland–Altman analysis revealed that GBG and FTBG measurements differed significantly among all participants; however, no significant differences were observed among the patients with diabetes (mean difference (MD) ± standard deviation (SD) = −18.1 ± 34.2, 95% confidence interval (CI) [−37.0 to 0.88]) or among the participants with a PPD of ≥4 mm (MD ± SD = −15.2 ± 30.4, 95% CI [−30.8 to 0.43]). The sensitivity, specificity, and cutoff values of the GBG measurements for detecting diabetes were 80%, 93%, and 123.5 mg/dL, respectively. The sensitivity, specificity, and cutoff values of the FTBG measurements for detecting diabetes were 73%, 87%, and 134.0 mg/dL, respectively. No significant differences were observed between the AUCs (0.078, 95% CI [−0.006 to 0.161]).ConclusionsThe GBG measurements aligned with the FTBG measurements in the patients with diabetes and among the participants with a PPD of ≥4 mm. Patients with diabetes were more likely to have a PPD of ≥4 mm at the sampled site, GBG levels can be used to screen for type 2 diabetes in dental clinics. creator: Yutaka Terada creator: Hiroyuki Watanabe creator: Mari Mori creator: Kotoko Tomino creator: Masaya Yamamoto creator: Mitsuru Moriya creator: Masahiro Tsuji creator: Yasushi Furuichi creator: Tomofumi Kawakami creator: Toshiyuki Nagasawa uri: https://doi.org/10.7717/peerj.18239 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Terada et al. title: Prevalence of oral submucous fibrosis across diverse populations: a systematic review and meta-analysis link: https://peerj.com/articles/18385 last-modified: 2024-11-06 description: PurposeThe aim is to offer a comprehensive overview of oral submucous fibrosis (OSF) prevalence and explore its epidemiological characteristics across various demographic groups and geographical locations, thereby helping the formulation of public health management policies.MethodsStudies reporting OSF prevalence were identified from electronic databases including the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE via PubMed, EMBASE via OVID, and Web of Science. Pooled prevalence and quality assessment using the New-Ottawa Scale were conducted. Two reviewers screened and selected records, assessed quality, and independently extracted data. This systematic review and meta-analysis followed the PRISMA guidelines and was registered on PROSPERO (CRD42024532975).ResultsSixty-three studies, encompassing 11,434 cases in a total population of 769,860, reported OSF prevalence. The majority of studies (forty-one) were from India. The pooled prevalence of OSF across all populations was 3.0% (95% CI [2.8–3.2]%). In non-risk populations, risk populations, and consecutive dental patients, the pooled prevalence stood at 2.4% (95% CI [2.1–2.6]%), 4.5% (95% CI 3.5-5.6%), and 5.6% (95% CI [3.8–7.5]%), respectively. Subgroup analysis by age, sex, and geographical region revealed higher prevalence rates among those aged 50 and above (4.2%, 95% CI [3.0–5.4]%), males (3.3%, 95% CI [2.9–3.7]%), and in India (4.0%, 95% CI [3.7–4.3]%). As the exposure to risk factors exceeded 50% in the surveyed population, the prevalence of OSF notably increased. Most studies met satisfactory quality standards.ConclusionsOur research findings reveal a comprehensive prevalence of OSF across all populations at 3.0% (95% CI [2.8–3.2]%). And, existing evidence indicates a relatively low prevalence of OSF associated with tobacco, alcohol, and Areca (betel) nut use. However, further large-scale studies are recommended to validate these findings. Understanding the prevalence and distribution patterns of OSF may assist in healthcare intervention planning and alleviate the oral cancer burden associated with OSF. creator: Mengqi Wang creator: Chengchen Duan creator: Yuzi Wei creator: Xiaoping Xu uri: https://doi.org/10.7717/peerj.18385 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Long-term changes in soil biological activity and other properties of raised beds in Longan orchards link: https://peerj.com/articles/18396 last-modified: 2024-11-06 description: IntroductionThe Longan fruit tree of the Vietnam Mekong Delta is grown in raised beds to improve water drainage during the rainy season and can live as long as 100 years.ObjectiveThis research explores the extent to which the soil microorganisms as well as soil physical and chemical properties of these raised beds degrade over a period of 60 years under traditional management practices.Materials and MethodsRaised bed topsoil samples at depths of 0–20 cm were obtained from four different Longan orchards raised bed age groups: group 1) 15–25 years (L1–L5); group 2) 26–37 years (L6–L10); group 3) 38–45 years (L11–L15); and group 4) 46–60 years. Soil biological properties were tested for nitrogen-fixing bacteria, phosphorus solubilizing bacteria, potassium solubilizing bacteria, calcium solubilizing bacteria and silicate solubilizing bacteria, β-glucosidase, urease, phosphomonoesterase, and phytase. Soil samples were also tested for moisture content, soil texture, soil porosity, and bulk density as well as soil chemical properties including pH, electrical conductivity (EC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (NH4+, NO3−), available phosphorus (AP), exchangeable potassium (K+), exchangeable calcium (Ca2 +), available silicate (SiO2), available copper (Cu), zinc (Zn), boron (B) and manganese (Mn). Key findings: The results showed that soil moisture, soil porosity, sand content, SOM, TP, TK, available P, exchangeable Ca2 +, available Si, nitrogen fixing bacteria number, β-glucosidase, urease, phosphomonoesterase, and phytase gradually and significantly decreased in the raised bed soil as the Longan orchard increased in age. Pearson correlation analysis between the ages of Longan orchards and soil properties revealed that raised bed ages were positively correlated with soil bulk density, but negatively correlated with soil moisture content, soil porosity, SOM, TN, β-glucosidase, urease, phosphomonoesterase, and phytase. Principal component analysis (PCA) showed Longan yields had a positive correlation with available NO3− but negative correlation with NFB, exchangeable Ca2 +, pH, and available B. These findings reveal that traditional long-term management of Longan trees in raised beds significantly reduce soil organic matter, moisture content, porosity, and soil fertility with impacts on soil microbial numbers and activity within raised bed soils.Future DirectionsThis suggests that more sustainable management practices, such as mulch and cover crops that decrease soil compaction and increase soil organic matter, improve soil porosity, total N, and feed soil microorganisms that are critical to nutrient cycling are needed to improve raised bed soil quality. creator: Nghia Khoi Nguyen creator: Phuong Minh Nguyen creator: Anh Thy Thi Chau creator: Luan Thanh Do creator: Thu Ha Thi Nguyen creator: Duong Hai Vo Tran creator: Xa Thi Le creator: Javad Robatjazi creator: Hendra Gonsalve W. Lasar creator: Lois Wright Morton creator: M. Scott Demyan creator: Huu-Tuan Tran creator: Hüseyin Barış Tecimen uri: https://doi.org/10.7717/peerj.18396 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Nguyen et al. title: Construction of a high-density genetic map using specific-locus amplified fragment sequencing and quantitative trait loci analysis for tillering related traits in Psathyrostachys juncea perennial grass link: https://peerj.com/articles/18409 last-modified: 2024-11-06 description: BackgroundRussian wildrye (RWR, Psathyrostachys juncea) is an outcrossing perennial grass that plays a crucial role in foragaing and rangeland restoration due to its tiller producing capabilities, nevertheless, a genetic map has yet to be constructed due to a shortage of efficient and reliable molecular markers. This also limits the identification, localization, and cloning of economically important traits related to tiller density during breeding.MethodsTherefore, this study aimed to create a F1 mapping population with 147 individual lines and their two parents, which were selected based on varying tiller densities. We then used this mapping population to conduct specific-locus amplified fragment sequencing (SLAF-seq) to generate SLAF markers and discover single nucleotide polymorphisms (SNPs).ResultsInitially, we generated a total of 1,438.38 million pair-end reads with an average sequencing depth of 84.92 in the maternal line, 79.34 in the parental line, and 27.05 in each F1 individual line, respectively. Following the filtering of low-depth SLAF tags, a total of 558,344 high-quality SLAFs were identified. A total of 1,519,903 SNP markers were obtained, and 62,424 polymorphic SNPs were discovered. From these, 4,644 polymorphic SNPs were selected and used for the construction of a genetic map encompassing seven linkage groups. The genetic map spanned 1,416.60 cM with an average distance of 0.31 cM between adjacent markers. Comparative analysis between the seven linkage groups of RWR SLAF tag and the whole-genome sequences in barley (Hordeum vulgare L.) revealed homology values ranging from 17.5% to 34.6%, and the collinearity between the RWR linkage groups and the barley homology groups ranged from 0.6787 to 0.9234, with an average value of 0.8158. Additionally, 143 significant quantitative trait locus (QTLs) with Logarithm of Odds (LOD) value greater than 2.5 for five tiller related traits were detected using three consecutive years of phenotypic trait data from the F1 population, further verifying the map’s reliability. creator: Yingmei Ma creator: Yudong Chang creator: Zhen Li creator: Zhiqi Gao creator: Feng Han creator: Yong Wang creator: Lan Yun uri: https://doi.org/10.7717/peerj.18409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ma et al. title: Identification of Meloidogyne panyuensis (Nematoda: Meloidogynidae) infecting Orah (Citrus reticulata Blanco) and its impact on rhizosphere microbial dynamics: Guangxi, China link: https://peerj.com/articles/18495 last-modified: 2024-11-06 description: Root-knot nematode disease severely affects the yield and quality of the mandarin variety Citrus reticulata Blanco “Orah” in Guangxi, China. Nevertheless, the pathogen and the effects of this disease on microbial communities remain inadequately understood. This study identified the root-knot nematode Meloidogyne panyuensis in the rhizosphere of infected Orah using morphological and molecular biological methods. Soil chemical properties indicated that organic matter, total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), total potassium (TK), and available potassium (AK) were significantly higher in the rhizosphere soil of M. panyuensis-infected Orah than in that of healthy plants. The relative abundance of the bacteria Bacillus, Sphingomonas, and Burkholderia-Caballeronia-Paraburkholderia, as well as the fungi Lycoperdon, Fusarium, Neocosmospora, Talaromyces, and Tetragoniomyces, was elevated in the rhizosphere soil of M. panyuensis-infected plants. Furthermore, organic matter, TN, available nitrogen (AN), TP, AP, TK, and AK exhibited positive correlationswith these bacteria and fungi in the rhizosphere soil of M. panyuensis-infected Orah. Potential biocontrol strains, such as Burkholderia spp., were identified by comparing the differences in rhizosphere microbial composition between healthy Orah and M. panyuensis-infected Orah. Our findings provide a foundation for the early warning and prevention of root-knot nematode disease in Orah. creator: Xiaoxiao Zhang creator: Wei Zhao creator: Yuming Lin creator: Bin Shan creator: Shanshan Yang uri: https://doi.org/10.7717/peerj.18495 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: MiR-301b-3p promotes breast cancer development through inhibiting the expression of transforming growth factor-beta receptor 2 link: https://peerj.com/articles/18324 last-modified: 2024-11-05 description: BackgroundBreast cancer (BC) is a serious health threat to the patients. The present work explored the mechanism of miR-301b-3p and transforming growth factor-beta receptor 2 (TGFBR2 ) in affecting BC progression.MethodsThe miR-301b-3p-inhibitor and si-TGFBR2 solution were added to the DEME/F12 medium to culture the BC and normal breast epithelial cell lines to prepare negative control, miR-301b-3p-IN and miR-301b-3p-IN+si-TGFBR2 in the two types of cell lines. The relative expression of target genes and the interference effect were analyzed by quantitative real-time PCR (qRT- PCR). Cell viability was detected applying cell counting kit-8 (CCK-8) assay. Transwell and wound healing assay were conducted to evaluate the invasion and migration of BC cells after miR-301b-3p inhibition. Additionally, cell apoptosis and the expression STAT protein were measured by flow cytometry and Western blot, respectivelyResultsThe qRT-PCR results showed that miR-301b-3p were high-expressed but the level of TGFBR2 was significantly inhibited in BC cells. The miR-301b-3p-inhibitor significantly downregulated the expression of miR-301b-3p and upregulated that of TGFBR2. Meanwhile, inhibition of miR-301b-3p suppressed the cell viability, invasion, and migration of BC cells, which, however, were restored by the inhibition of TGFBR2. MiR-301b-3p conferred anti-apoptosis ability to BC cells, while TGFBR2 promoted apoptosis of BC cells through producing an antagonistic effect with miR-301b-3p. We found that miR-301b-3p played a crucial role in the phosphorylation of STAT1 and STAT3 to promote BC progression.ConclusionThe present findings demonstrated that miR-301b-3p played a crucial role in promoting BC cell growth, invasion and migration and anti-apoptosis, and that targeting TGFBR2 could inhibit the tumor-promoting effect of miR-301b-3p. creator: Jian Lou creator: Xueni Liu creator: Yanru Xie creator: Minhua Wu creator: Weibo Mao creator: Xiaozhen Ying uri: https://doi.org/10.7717/peerj.18324 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lou et al.