Osteomyelitis of the femur caused by Metamycoplasma orale in an immunocompromised patient using metagenomic next-generation sequencing: A case report.

Background: Metamycoplasma orale (M.orale), a symbiotic bacterium observed in the human oral cavity, is generally regarded as non-pathogenic to humans. Although infrequent, symptomatic infections caused by M.orale may occur in individuals with compromised humoral immunity. Accurate identification and early diagnosis of M.orale still present significant challenges due the limitations associated with conventional detection methods. Although metagenomic next-generation sequencing (mNGS) is currently widely utilized in clinical practices and exhibits a remarkable specificity and sensitivity for detecting various pathogens, its application in the diagnosis of M.orale-induced osteomyelitis remains largely unexplored. Case description: In this report, we present a case study of osteonecrosis caused by M.orale in a 20-year-old female patient with nephrotic syndrome and other comorbidities. She was administered long-term hormone therapy and immunosuppressants, leading to her admission to the hospital due to recurrent fever, hip abscess and left thigh pain. Imaging examination revealed bilateral mid-femoral lesions, with the extensive nature of the left femoral lesion suggesting a potential secondary infection. Although no pathogen was detected in pus culture, mNGS analysis identified M.orale in the sample. Following treatment with doxycycline and levofloxacin, the patient's symotoms improved and she was discharged with favorable outcomes. Conclusion: mNGS enables rapid identification of etiology in patients with osteomyelitis caused by the rare pathogen M.orale. This case accentuate the strength of mNGS for early detection and targeted clinical treatment of infectious diseases caused by uncommon pathogens.

Meta-analysis of effects of yoga exercise intervention on sleep quality in breast cancer patients.

Objective: This study seeks to systematically evaluate and test the effects of yoga exercise intervention programs on sleep quality in breast cancer patients in order to suggest more optimized exercise programs. Method: Computer searches of the PubMed, Embase, Cochrane Library, Web of Science and CINAHL databases are conducted from the date of their inception to June 8th, 2022 to collect randomized controlled trials on the effects of yoga exercise intervention on sleep quality in breast cancer patients. Two investigators independently carry out the inclusion and exclusion criteria literature screening, data extraction and methodological quality assessment of the included literature by applying the Cochrane risk of bias tool. Subgroup analysis is performed using RevMan 5.4.1 software, and the six moderating variables of intervention format, intervention type, weekly intervention frequency, total intervention duration, single intervention duration and intervention evaluation at different time points are set for the 782 subjects of the 12 included publications. Results: Twelve randomized controlled trials with a total sample size of 782 subjects are included, including 393 subjects in the experimental group and 389 subjects in the control group. The meta-analysis shows that yoga exercise intervention is effective in improving sleep quality in breast cancer patients [SMD = -0.40, 95% CI: (-0.71, -0.09), P = 0.01]; yoga exercise intervention focusing on positive meditation [SMD = -0.55, 95% CI: (-1.08, -0.03), P = 0.04] is effective in improving sleep; yoga exercise intervention two or three times a week is effective in improving sleep quality [SMD = -0.69, 95% CI: (-1.19, -0.19), P = 0.007]; yoga exercise intervention for 6-8 weeks significantly improves sleep quality [SMD = -0.86, 95% CI: (-1.65, -0.08), P =0.03]; and evaluation immediately after the end of intervention improves sleep outcomes [SMD = -0.17, 95% CI: (-0.33, 0.00), P = 0.05], while differences in sleep quality improvement are not statistically significant for the remaining subgroup outcomes (P > 0.05). Conclusion: The available evidence suggests that yoga exercise intervention has good effects on improving sleep quality in breast cancer patients. Positive meditation intervention type, intervention frequency of two or three times per week, total intervention duration of 6-8 weeks and evaluation immediately after the end of intervention are shown to be effective in improving sleep quality.

Evaluation of DNA adduct damage using G-quadruplex-based DNAzyme.

Toxicity assessment is a major problem in pharmaceutical candidates and industry chemicals development. However, due to the lack of practical analytical methods for DNA adduct analysis, the safety evaluation of drug and industry chemicals was severely limited. Here, we develop a DNAzyme-based method to detect DNA adduct damage for toxicity assessment of drugs and chemicals. Among 18 structural variants of G4 DNAzyme, EA2 DNAzyme exhibits an obvious DNA damaging effect of styrene oxide (SO) due to its unstable structure. The covalent binding of SO to DNAzyme disrupts the Hoogsteen hydrogen bonding sites of G-plane guanines and affects the formation of the G4 quadruplex. DNA damage chemicals reduce the peroxidase activity of the G4 DNAzyme to monitor the DNA adduct damage by disrupting the structural integrity of the G4 DNAzyme. Our method for genotoxic assessment of pharmaceutical candidates and industrial chemicals can elucidate the complex chemical pathways leading to toxicity, predict toxic effects of chemicals, and evaluate possible risks to human health.

Simultaneous detection of acetaminophen, catechol and hydroquinone using a graphene-assisted electrochemical sensor.

Simple, rapid and sensitive analysis of drug-derived pollutants is critically valuable for environmental monitoring. Here, taking acetaminophen, hydroquinone and catechol as a study example, a sensor based on an ITO/APTES/r-GO@Au electrode was developed for separate and simultaneous determination of phenolic pollutants. ITO electrodes that are modified with 3-aminopropyltriethoxysilane (APTES), graphene (GO) and Au nanoparticles (Au NPs) can significantly enhance the electronic transport of phenolic pollutants at the electrode surface. The redox mechanisms of phenolic pollutants include the electron transfer with the enhancement of r-GO@Au. The modified ITO electrode exhibits excellent electrical properties to phenolic pollutants and a good linear relationship between ECL intensity and the concentration of phenolic pollutants, with a limit of detection of 0.82, 1.41 and 1.95 µM, respectively. The separate and simultaneous determination of AP, CC and HQ is feasible with the ITO/APTES/r-GO@Au electrode. The sensor shows great promise as a low-lost, sensitive, and rapid method for simultaneous determination of drug-derived pollutants.

NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata.

Data management is a critical challenge required to improve the rigor and reproducibility of large projects. Adhering to Findable, Accessible, Interoperable, and Reusable (FAIR) standards provides a baseline for meeting these requirements. Although many existing repositories handle data in a FAIR-compliant manner, there are limited tools in the public domain to handle the metadata burden required to connect data from multi-omic projects that span multiple institutions and are deposited in diverse repositories. One promising approach is the SEEK platform, which allows for diverse metadata and provides an established repository. SEEK is challenged by the assumption of single deposition events where a sample is immutable once entered in the database. This is structured for published data but presents a limitation for ongoing studies where multiple sequential events may occur in a single sample at different sites. To address this issue, we have created a modified wrapper around the SEEK platform that allows for active data management by establishing more discrete sample types that are mutable to permit the expansion of the types of metadata, allowing researchers to track additional information. The use of discrete nodes also converts assays from nodes to edges, creating a network model of the study and more accurately representing the experimental process. With these changes to SEEK, users are able to collect and organize the information that researchers need to improve reusability and reproducibility as well as make data and metadata available to the scientific community through public repositories.

Long-term effect of epigenetic modification in plant-microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process.

BACKGROUND: Soil microbiomes are considered a cornerstone of the next green revolution, and plant growth-promoting bacteria (PGPB) are critical for microbiome engineering. However, taking plant-beneficial microorganisms from discovery to agricultural application remains challenging, as the mechanisms underlying the interactions between beneficial strains and plants in native soils are still largely unknown. Increasing numbers of studies have indicated that strains introduced to manipulate microbiomes are usually eliminated in soils, while others have reported that application of PGPB as inocula significantly improves plant growth. This contradiction suggests the need for a deeper understanding of the mechanisms underlying microbe-induced growth promotion. RESULTS: We showed PGPB-induced long-term plant growth promotion after elimination of the PGPB inoculum in soils and explored the three-way interactions among the exogenous inoculum, indigenous microbiome, and plant, which were key elements of the plant growth-promoting process. We found the rhizosphere microbiome assembly was mainly driven by plant development and root recruitments greatly attenuated the influence of inocula on the rhizosphere microbiome. Neither changes in the rhizosphere microbiome nor colonization of inocula in roots was necessary for plant growth promotion. In roots, modification of DNA methylation in response to inoculation affects gene expression related to PGPB-induced growth promotion, and disruptions of the inoculation-induced DNA methylation patterns greatly weakened the plant growth promotion. Together, our results showed PGPB-induced DNA methylation modifications in roots mediated the promotion process and these modifications remained functional after elimination of the inoculum from the microbiome. CONCLUSION: This study suggests a new mechanism in which PGPB affect DNA methylation in roots to promote plant growth, which provides important insights into microbiome-plant interactions and offers new strategies for plant microbiome engineering beyond the perspective of maintaining inoculum persistence in soils. Video abstract.

Comparative Genomic Analysis of Pseudoxanthomonas sp. X-1, a Bromoxynil Octanoate-Degrading Bacterium, and Its Related Type Strains.

Most Pseudoxanthomonas species described have been derived from water, plants, or contaminated soils. Here, a strain Pseudoxanthomonas sp. X-1 isolated from bromoxynil octanoate (BO)-contaminated soil is presented. Strain X-1 could degrade BO and produce bromoxynil. The optimal conditions for degradation of BO by strain X-1 were an initial BO concentration of 0.1 mM, 30 °C, pH 7, and Mn2+ concentration of 1.0 mM. The bacterial morphological, physiological, and biochemical characteristics of strain X-1 were described, which showed differences comparing with other related type strains. The genome of strain X-1 was sequenced, and a comparative genomic analysis of X-1 and other Pseudoxanthomonas species was conducted to explore the mechanisms underlying the differences among these strains. The genome of strain X-1 encodes 4160 genes, 4078 of which are protein-coding genes and 68 are RNA coding genes. Specifically, strain X-1 encodes enzymes belonging to 778 Enzyme Commission (EC) numbers, much more than those of other related strains, and 62 of them are unique. Eight genes coding esterase are detected in strain X-1 which leads to the ability of BO degradation. This study provides strain, enzyme, and genome resources for the microbial remediation of environments polluted by herbicide BO.

Global value chains participation and carbon emissions embodied in exports of China: Perspective of firm heterogeneity.

This paper studies the impact of global value chains (GVCs) participation on carbon emissions embodied in exports (EEE) of China during 2005-2016, and analyses firm heterogeneity from the perspective of firm ownership and trade patterns; Then, industries are classified based on factor intensity and technology level, and the industrial heterogeneity of different firms is analyzed; Finally, through counterfactual analysis, this paper evaluates EEE under four anti-globalization scenarios. The empirical study shows that with the increase of GVCs position, EEE first increases and then decreases, showing an inverted U-shaped distribution. From the perspective of firm ownership, the relationship between GVCs position of domestic firms and EEE is inverted U-shaped distribution, while GVCs position of multinational enterprises (MNEs) is positively correlated with EEE. The relationship of capital-intensive and technology-intensive domestic firms, high-tech and medium-tech manufacturing domestic firms are also inverted U-shaped distribution. The positive correlation of MNEs is reflected in the low-tech manufacturing industries. From the perspective of trade patterns, with the increase of GVCs position, EEE of processing trade firms presents an inverted U-shaped distribution, while it is not significant for general trade firms. The inverted U-shaped relationship between GVCs position in capital-intensive industries and EEE are confirmed in all firms. Under anti-globalization scenarios of 50% backflow, EEE would increase. Under scenarios of 100% backflow, EEE would reduce. The results above provide useful references to achieve carbon emission reduction targets.

Viewing RNA-seq data on the entire human genome.

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI's Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated by NCBI at Brandeis University. The backend data pipeline was developed and deployed on a shared AWS EC2 instance. Source code is available at https://github.com/NCBI-Hackathons/rnaseqview.

Loss of Dab2 expression in breast cancer cells impairs their ability to deplete TGF-ß and induce Tregs development via TGF-ß.

Dab2 is a multifunctional adapter protein which is frequently under-expressed in a variety of cancers. It is implicated in many critical functions, including several signaling pathways, cell arrangement, differentiation of stem cells, and receptor endocytosis. Transforming growth factor-ß (TGF-ß) is a secreted multifunctional protein that controls several developmental processes and pathogenesis of many diseases. It has been documented that Dab2 played an important role in TGF-ß receptors endocytosis. Here, we present evidence that re-expression of Dab2 in SK-BR-3 cell partially restored its ability to deplete TGF-ß in surrounding medium by normalizing the trafficking of TGF-ß receptors. We also demonstrate that the difference in TGF-ß depletions produced by Dab2 expression was sufficient to impact on the conversion of naive CD4+ T cells to regulatory T cells (Tregs), and thus inhibited the proliferation of T cells. This work revealed a critical result that breast cancer cell was deficient in Dab2 expression and related receptor endocytosis-mediated TGF-ß depletion, which may contribute to the accumulation of TGF-ß in tumor microenvironment and the induction of immune tolerance.

Diagnostic accuracy of high-resolution MRI using a microscopy coil for patients with presumed DCIS following mammography screening.

PURPOSE: To prospectively evaluate the accuracy of high-resolution (HR)-MRI as a secondary examination in women with abnormal calcifications detected on mammography. MATERIALS AND METHODS: We used a 4.7-cm microscopy coil to acquire HR-MRI signal data. We examined 52 women with breast lesions preoperatively using HR-MRI and vacuum-assisted core needle biopsy. The lesions were suspicious of malignancy, classified as category 3-5 on mammography (Breast Imaging Reporting and Data System [BI-RADS]), and without a palpable mass. All visualized suspicious lesions were correlated with histological findings. We compared the HR-MRI and pathological findings and calculated the sensitivity, specificity, and accuracy. RESULTS: We compared the breast HR-MRI results with the gold standard of pathological results for studies of malignancy (DCIS and invasive cancer), and found a sensitivity of 88.5%, specificity of 92.3%, and accuracy of 90.4%. The positive predictive value (PPV) was 92%, and the negative predictive value (NPV) was 88.9%. When breast MRI was compared with pathological results for studies that diagnosed DCIS only, the results revealed a sensitivity of 88.6%, specificity of 88.2%, accuracy of 88.5%, PPV of 93.9%, and NPV of 78.9%. CONCLUSION: HR-MRI using a microscopy coil is a useful, reliable, safe, and minimally invasive procedure that is a good choice for secondary assessment of abnormal calcification in the breast.