Gut microbial interactions based on network construction and bacterial pairwise cultivation.

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.

Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.

Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.

Potential causal associations between leisure sedentary behaviors, physical activity, sleep traits, and myopia: a Mendelian randomization study.

BACKGROUND: Myopia is the most prevalent refractive error and a growing global health concern that significantly affects visual function. Researchers have recently emphasized considerably on the influence of lifestyle on myopia incidence and development. This study investigates the relationship between leisure sedentary behaviors (LSB)/physical activity (PA)/sleep traits and myopia. METHODS: LSB, PA, and sleep trait-associated genetic variants were used as instrument variables in a Mendelian randomization (MR) study to examine their causal effects on myopia. Summary genome-wide association studies (GWASs) statistical data for LSB and PA were obtained from UK Biobank, and the data of sleep traits was obtained from UK Biobank, UK Biobank and 23andMe, and FinnGen. We used summary statistics data for myopia from MRC IEU. The MR analyses was performed using the inverse variance-weighted (IVW), MR-Egger, weighted median, and MR Pleiotropy RESidual Sum and Outlier methods. RESULTS: Computer use was genetically predicted to increase the myopia risk [IVW odds ratio (OR) = 1.057; 95% confidence interval (CI), 1.038-1.078; P = 7.04 × 10- 9]. The self-reported moderate-to-vigorous physical activity (MVPA) (IVW OR = 0.962; 95% CI, 0.932-0.993; P = 1.57 × 10- 2) and television watching (IVW OR = 0.973; 95% CI, 0.961-0.985, P = 1.93 × 10- 5) were significantly associated with a lower myopia risk. However, genetically predicted sleep traits or accelerometer-measured physical activity had no significant associations with myopia. CONCLUSION: Our results indicated that computer use is a risk factor for myopia, whereas television watching and MVPA may protect against myopia. These findings shed new light on possible strategies for reducing the prevalence of myopia.

A spider mating plug functions to protect sperm.

Mating plugs in animals are ubiquitous and are commonly interpreted to be products of mating strategies. In spiders, however, mating plugs may also take on functions beyond female remating prevention. Due to the vagaries of female genital (spermathecal) anatomy, most spiders face the problem of having to secure additional, non-anatomical, protection for transferred sperm. Here, we test the hypothesis that mating plugs, rather than (or in addition to) being adaptations for mating strategies, may serve as sperm protection mechanism. Based on a comparative study on 411 epigyna sampled from 36 families, 187 genera, 330 species of entelegyne spiders, our results confirm the necessity of a sperm protection mechanism. We divided the entelegyne spermathecae into four types: SEG, SED, SCG and SCD. We also studied detailed morphology of epigynal tracts in the spider Diphya wulingensis having the SEG type spermathecae, using 3D-reconstruction based on semi thin histological series section. In this species, we hypothesize that two distinct types of mating plug, the sperm plug and the secretion plug, serve different functions. Morphological details support this: sperm plugs are formed on a modified spermathecal wall by the spilled sperm, and function as a temporary protection mechanism to prevent sperm from leaking and desiccating, while secretion plugs function in postcopulation both as a permanent protection mechanism, and to prevent additional mating. Furthermore, with the modified spermathecal wall of S2 stalk, the problem of shunt of sperm input and output, and the possibility of female multiple mating have been resolved. Variation in spermathecal morphology also suggests that the problem of sperm protection might be resolved in different ways in spiders. Considering mating plugs of varying shapes and origins in the vast morphospace of spiders, we conclude that mating plugs might serve different purposes that relate both to mating strategies, as well as to sperm protection.

Christensenella minuta interacts with multiple gut bacteria.

Introduction: Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored. Methods: In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners. Results: Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network. Conclusions: C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health.

Endovascular Therapy for Basilar Artery Occlusion in Sudden Onset to Maximal Deficit Ischemic Events.

BACKGROUND: The presence of sudden onset to maximal deficit (SOTMD) in patients with acute basilar artery occlusion often results in more severe outcomes. However, the effect of endovascular therapy on SOTMD and whether the outcome is affected by onset-to-puncture time remain unclear. METHODS AND RESULTS: This retrospective analysis was conducted using data from the prospective BASILAR (Endovascular Treatment for Acute Basilar Artery Occlusion Study Registry). Consecutive patients with basilar artery occlusion receiving endovascular therapy were dichotomized into SOTMD and non-SOTMD cohorts. The primary outcomes included a favorable outcome (modified Rankin scale 0-3), recanalization, and mortality at 90 days. The outcomes of patients with SOTMD were analyzed using multivariable logistic regression. In the multivariate analysis, a favorable outcome was similar between the two cohorts (odds ratio [OR], 0.88 [95% CI, 0.58-1.34]; P=0.5), although the mortality of patients with SOTMD was higher than that of patients with non-SOTMD (OR, 1.67 [95% CI, 1.14-2.44]; P=0.008). The probability of mortality increased from 40.0% at 1 hour to 70.0% at 6 hours in the SOTMD cohort, and favorable outcomes of patients with non-SOTMD declined from 38.0% at 1 hour to 18.0% at 8 hours. CONCLUSIONS: No significant difference was observed in favorable outcomes between the SOTMD and non-SOTMD groups, although mortality was higher in the SOTMD cohort. The patients with SOTMD had a stronger time dependence for endovascular therapy in terms of mortality, while the time dependency regarding favorable outcome in the NSOTMD group was even higher. REGISTRATION: URL: https://www.chictr.org.cn; Unique identifier: ChiCTR1800014759.

Therapeutic Drug Monitoring in Patients with Systemic Lupus Erythematosus: Utility and Gaps.

Despite advances in the treatment of patients with systemic lupus erythematous (SLE), outcomes have remained suboptimal. Persistent disease activity, patient comorbidities and drug toxicities contribute to the accrual of progressive irreversible damage and high rates of morbidity and mortality. Currently, similar drug doses and regimens are promulgated in the treatment guidelines for all SLE patients, despite the vast differences in patient and environmental factors that affect the drugs' metabolism and blood concentrations. This causes a disconnect between drug dosing and drug blood concentrations, which can then result in unpredictability in drug toxicities and therapeutic effects. In this review, we discuss commonly used oral immunosuppressive medications in SLE, their pharmacogenomics, and factors affecting their metabolism and blood concentrations. Further, we highlight the role of therapeutic drug monitoring in SLE, which is the first accessible step to individualising therapy.

Ketamine in the Management of Acute Pain: A Comprehensive Meta-Analysis.

This review was conducted to find the effectiveness and safety of ketamine in managing acute or sudden pain in the emergency scenarios. The research was carried out using databases such as PubMed, MEDLINE, Cochrane trial registries, and EMBASE from inception up to July 2022. The meta-analysis employed using the random-effects model and presented results as pooled standardised mean difference (SMD) and risk ratio (RR) alongside their 95% confidence intervals (CIs). The pooled SMD for pain assessment within 15 minutes stood at -0.72 (95% CI: -1.55 to 0.12). At 30 minutes, SMD was -0.27 (95% CI: -0.48 to -0.05), and by 45 minutes, it was -0.04 (95% CI: -0.26 to 0.18). Between the 45-minute and 60-minute mark, the SMD was -0.03 (95% CI: -0.22 to 0.17), and after the 60-minute interval, it was registered at 0.11 (95% CI: -0.10 to 0.22). Pooled RR reflecting the requirement for supplementary analgaesics was 0.96 (95% CI: 0.65-1.41). The study found that ketamine's efficacy and safety were comparable or even superior to opioids in addressing sudden pain in the emergency contexts. Key Words: Ketamine, Meta-analysis, Opioids, Acute pain, Emergency.

A systematic review of qualitative research on the self-management experience of breast cancer patients.

OBJECTIVE: To integrate the qualitative research on the self-management experience of breast cancer patients and conduct a systematic review of their self-management experience. METHODS: Using a computer to search a series of databases such as CNKI, Wanfang, VIP, and China Biomedical Database, systematically collect and integrate qualitative research on the self-management experience of breast cancer patients, and the search time is limited to January 2010 to December 2022. The qualitative research quality evaluation standard of the Joanna Briggs Institute Centre for Evidence-Based Health Care in Australia was used as the evaluation standard of this project to complete the accurate evaluation of the literature; Meta-analysis was used to complete the effective integration of the results. RESULTS: 17 pieces of literature were included in this project, and 37 research results with strong integrity were extracted accordingly. On this basis, 7 different categories were summarised, and three integrated results were obtained: the experience of maintaining self-management, symptom recognition, and self-management. CONCLUSION: In the different stages of self-management of breast cancer patients, medical staff should give targeted guidance to help patients obtain a good prognosis.

Epidemiological survey of elderly patients diagnosed with COVID-19 at mobile field hospitals.

BACKGROUND: During the COVID-19 pandemic, the mobile field hospital, a rapidly deployable healthcare facility for emergency care, was effective in ensuring rapid diagnosis and treatment of patients with mild or asymptomatic SARS-CoV2 infections, effectively preventing the spread of COVID-19. OBJECTIVE: We conducted a survey to gain a thorough understanding of the epidemiological traits among the elderly who contracted the Omicron variant of the SARS-CoV-2 virus at a mobile field hospital set up at the National Exhibition and Convention Center (Shanghai). METHODS: A cross-sectional study approach was employed to examine various factors such as demographic characteristics, clinical features, vaccination status, and nucleic acid testing. We utilized the DezhenTech Integrated Electronic Medical Record Platform (Municipal Isolation Hospital) to collect data and focused on elderly individuals infected with COVID-19 in the fifth isolation zone of the mobile field hospital set up at the National Exhibition and Convention Center (Shanghai). The patients were categorized into different age groups for analysis. RESULTS: Among the 3,183 elderly patients, 54.7% were males and 45.3% were females, with an average age of 65.32 ± 4.41 years. Among them, 47.8% (1523/3183) were 60-64 years old, 34.0% (1082/3183) were 65-69 years old, 14.0% (444/3183) were 70-74 years old, 3.2% (103/3183) were 75-79 years old, and 1.0% (31/3183) were ⩾ 80 years old. The majority (95.7%) of the elderly patients with chronic conditions had hypertension, diabetes, and coronary heart disease. The first viral nucleic acid screening showed a higher positive rate in the community and hospital fever clinics. The cumulative positive rate of the nucleic acid test in the mobile field hospital was 38.7%. The average CT value of the COVID-19 ORF1ab gene was 34.56 ± 5.98, while the average CT value of the N gene was 33.10 ± 6.50. The patients took an average of 3.40 ± 0.45 days to test negative, with a positive rate of 15.4% and an average hospital stay of 7.45 ± 0.53 days. The overall rate of COVID-19 vaccine coverage was 68.0%, with an enhanced coverage rate of 40% and a non-coverage rate of 29.3%. CONCLUSIONS: The overall prognosis for elderly patients who experienced a mild or asymptomatic SARS-CoV-2 Omicron infection at the mobile field hospital was favorable, although the vaccination rate in general was not high. By effectively managing underlying health conditions, the duration of their hospital stay in the mobile field hospital was reduced.

Linc-ROR inhibits NK cell-killing activity by promoting RXRA ubiquitination and reducing MICB expression in gastric cancer patients.

Linc-ROR plays an important role in gastric cancer (GC) development and progression. This study sought to determine how the aberrant expression of Linc-ROR impacts GC progression and immune evasion, and to identify new targets for GC therapy. GC cells overexpressing Linc-ROR and GSAGS cells were cocultured with NK-92 cells, respectively, and Linc-ROR expression was determined using reverse transcription polymerase chain reaction. Linc-ROR overexpression experiments were used to measure the expression of MICB, a tumor protein that is recognized by natural killer (NK) cells. Bioinformatics analysis identified retinoid X receptor α (RXRA) and YY1 as MICB-specific transcription factors. Cotransfection and ubiquitinated drug experiments found that Linc-ROR promoted the ubiquitination and degradation of RXRA. Linc-ROR was upregulated in GC tissue and high expression was associated with tumor escape from NK-92 cell-mediated immunity. Linc-ROR overexpression inhibited the expression of MICB on the cell surface by degrading RXRA. These findings indicate that Linc-ROR promotes the binding of RXRA and E3 ligase UBE4B, reducing RXRA and MICB expression, and limiting NK cell-killing activity. Linc-ROR is a critical long noncoding RNA with a tumor-promoting function in GC and thus may serve as a potential therapeutic target.

A Study to Analyse the Feasibility and Effectiveness of Left Bundle Branch Area Pacing Used in Young Children.

This study aimed to investigate the feasibility and effectiveness of left bundle branch area pacing (LBBaP) in young children. From September 2020 to May 2021, a total of 31 children (≤ 7 years) with complete atrioventricular block were included. All patients were scheduled to undergo LBBaP. Pacing parameters, and cardiac function and synchrony were evaluated during follow-up. LBBaP succeeded in 21 children (3.3 ± 2.1 years old), with a success rate of 70.9%. LBBaP failed in nine children, who eventually received right ventricular septal pacing (RVSP). The average postoperative QRS duration in patients of LBBaP group was narrower than that of RVSP group: 100.9 ± 9.1 versus 114.2 ± 11.9 ms (P = 0.002). The median follow-up duration was 12 [interquartile range (IQR) 6-15] months. At last time of follow-up, the capture threshold of ventricular electrode in patients of LBBaP group were significantly lower than that of RVSP group (0.70 ± 0.25 versus 1.39 ± 0.94 V, P = 0.011). The echo-left ventricular ejection fraction (LVEF) in patients in the LBBaP group was better than that in the RVSP group (66.1 ± 3.3 versus 63.1 ± 2.2%, P = 0.025). LBBaP can be safely and effectively administered in young children. Satisfactory pacing parameters, and narrow QRS durations were obtained.

Baicalin attenuates pulmonary vascular remodeling by inhibiting calpain-1 mediated endothelial-to-mesenchymal transition.

Background: Previous studies have demonstrated the beneficial effect of baicalin on pulmonary arterial hypertension (PAH), but the mechanism is unclear. Aim: The aim of the present study was to evaluate the effect of baicalin on pulmonary vascular remodeling (PVR) with a focus on calpain-1-mediated endothelial-to-mesenchymal transition (EndMT). Methods: PAH was induced by intraperitoneal injection of monocrotaline (MCT) in rats and hypoxia in calpain-1 gene knockout (Capn1-/-) and wild-type C57BL/6 mice. An in vitro PVR model was established in PASMCs and HPAECs. Results: The data showed that baicalin treatment and calpain-1 inhibition alleviated MCT and hypoxia-induced increases in right ventricular systolic pressure (RVSP), prevented right ventricle hypertrophy and PVR, and attenuated cardiopulmonary fibrosis. Moreover, baicalin ameliorated PAH-induced EndMT, as evidenced by the suppressed expression of mesenchymal markers vimentin, and α-SMA and restored expression of endothelial markers CD31, and VE-cadherin. In vitro studies showed that baicalin treatment blocked TGF-ß1-induced EndMT in HPAECs and abolished hypoxia-induced PASMC proliferation and migration. All the beneficial effects of baicalin on PVR in vitro and in vivo were accompanied by suppressed calpain-1 expression. Further study demonstrated that baicalin treatment and calpain-1 inhibition inhibited the enhanced expression of PI3K and p-AKT both in vitro and in vivo. Conclusions: In conclusion, baicalin treatment attenuates PVR by inhibiting calpain-1 and PI3K/Akt-mediated EndMT.

Influence of tumor mycobiome on cancer pathogenesis (Review).

Cancer tissues harbor a large microbiome. There is growing evidence that the tumor microbiome is significantly correlated with the prognosis of cancer patients, but the exact underlying mechanisms have remained elusive. Although the tumor mycobiome is less abundant than the biome of bacteria, it is prevalent in most cancers in humans. The present review describes in detail the impact of the tumor mycobiome on cancer pathogenesis. The tumor mycobiome promotes tumor progression and metastasis by affecting the human immune system, maintaining a pro-inflammatory environment, producing aflatoxins, attenuating cell adhesion mechanisms and fungal-bacterial interactions. Furthermore, the tumor mycobiome likewise has great potential for cancer prevention, diagnosis and treatment.

Impact of HIV/HCV Co-Infection on Mortality and Attrition in Antiretroviral Therapy Among People with HIV - Guangxi Zhuang Autonomous Region, China, 2003-2022.

What is already known about this topic?: The effects of concurrent human immunodeficiency virus (HIV)/hepatitis C virus (HCV) infection on mortality and patient attrition in those undergoing antiretroviral therapy continue to be a contested area of research. What is added by this report?: According to the propensity score-matched cohort, individuals with HIV/HCV co-infection exhibit an elevated risk of all-cause mortality [adjusted hazard ratio: 2.048, 95% confidence interval (CI): 1.526-2.749] and attrition (adjusted incidence rate ratio: 1.659, 95% CI: 1.4.8-1.961) compared to their counterparts who are mono-infected with HIV. What are the implications for public health practice?: The pressing need for tailored testing and follow-up protocols for individuals co-infected with HIV/HCV cannot be overstated.

Function of Cytochrome P450s and Gut Microbiome in Biopesticide Adaptation of Grapholita molesta on Different Host Diets.

Insects that feed on various host plants possess diverse xenobiotic adaptations; however, the underlying mechanisms are poorly understood. In the present study, we used Grapholita molesta, which shifts feeding sites from peach shoots to apple fruits, as a model to explore the effects of shifts in host plant diet on the profiles of cytochrome P450s and the gut bacteria microbiome, as well as their effects on biopesticide adaptation. We found that the sensitivity of the fruit-feeding G. molesta to emamectin benzoate biopesticide was significantly lower than that of the shoot-feeding larvae. We also found that the P450 enzyme activity and the expression of nine cytochrome P450s were enhanced in G. molesta fed on Fuji apples compared to those fed on peach shoots. The survival rates of G. molesta exposed to emamectin benzoate significantly decreased as each of three of four emamectin benzoate-inducted cytochrome P450 genes were silenced. Furthermore, we discovered the gut bacteria dynamics of G. molesta changed with the host shift and the structure of the gut bacteria microbiome was determined by the final diet ingested; additionally, the dysbiosis of the gut microbiota induced by antibiotics could significantly increase the sensitivity to emamectin benzoate. Taken together, our results suggest that the expression of P450s and the composition of the gut bacteria microbiome promote adaptation to emamectin benzoate in G. molesta, providing new insights into the molecular mechanisms underlying xenobiotic adaptation in this notorious pest.

Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling.

Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory 'ground truth'. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.