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Bioinformatic methodologies play a crucial role in the assessment of gut microbiota, offering advanced tools for analyzing complex microbial communities. These methodologies involve high-throughput sequencing technologies, such as 16S rRNA gene sequencing and metagenomics, which generate vast amounts of data on microbial diversity and functional potential, as well as whole-genome sequencing, which, while being more costly, has a more expansive potential. Bioinformatics tools and algorithms process these data to identify microbial taxa and quantify and elucidate their roles within the microbiome. Advanced statistical and computational models further enable the identification of microbiota patterns associated with various diseases and health conditions. Overall, bioinformatic approaches are essential for deciphering the complexities of gut microbiota so that, in the future, we may be able to discover treatments and technologies aimed at restoring or optimizing the microbiome. The goal of this review is to describe the differences in methodology and utilization of 16S versus whole-genome sequencing to address the increased understanding of the role that the gut microbiome plays in human physiology and pathology.

Objective To evaluate co-prescribing of sedatives hypnotics and opioids.Design Retrospective study evaluating the association of patient characteristics and comorbidities with coprescribing.Setting and participants Using the national Merative MarketScan Database between 2005 and 2018, we identified patients who received an incident sedative prescription with or without subsequent, incident opioid prescriptions within a year of the sedative prescription in the USA.Outcome measures Coprescription of sedative-hypnotics and opioids.Results A total of 2 632 622 patients (mean (SD) age, 43.2 (12.34) years; 1 297 356 (62.5%) female) received incident prescriptions for sedatives over the course of the study period. The largest proportion of sedative prescribing included benzodiazepines (71.1%); however, z-drugs (19.9%) and barbiturates (9%) were also common. About 557 845 (21.2%) patients with incident sedatives also received incident opioid prescriptions. About 59.2% of these coprescribed patients received opioids coprescription on the same day. Multivariate logistic regression findings showed that individuals with a comorbidity index score of 1, 2 or ≥3 (aOR 1.19 (95% CI 1.17 to 1.21), 1.17 (95% C 1.14 to 1.19) and 1.25 (95% C 1.2 to 1.31)) and substance use disorder (1.21 (95% C 1.19 to 1.23)) were more likely to be coprescribed opioids and sedatives. The likelihood of receiving both opioid and sedative prescriptions was lower for female patients (aOR 0.93; 95% CI 0.92 to 0.94), and those receiving a barbiturate (aOR 0.3; 95% CI 0.29 to 0.31) or z-drugs (aOR 0.67; 95% CI 0.66 to 0.68) prescriptions at the index date.Conclusions Coprescription of sedatives with opioids was associated with the presence of comorbidities and substance use disorder, gender and types of sedatives prescribed at the index date. Additionally, more than half of the coprescribing occurred on the same day which warrants further evaluation of current prescribing and dispensing best practice guidelines.

The vascular endothelium is vital for cardio-pulmonary homeostasis and, thus, plays a crucial role in preventing life-threatening lung diseases. The transcription factor GATA2 is essential for hematopoiesis and maintaining vascular integrity. Heterozygous mutations in GATA2 can lead to a primary immunodeficiency syndrome with pulmonary manifestations. Some GATA2 haploinsufficient patients develop pulmonary hypertension (PH), characterized by vascular remodeling and occlusion of small pulmonary arteries. However, the mechanism underlying pulmonary vascular remodeling in GATA2 haploinsufficient patients remain unclear. To understand how GATA2 deficiency affects pulmonary artery homeostasis, we applied a chronic hypoxia-mediated PH model using inducible systemic Gata2 conditionally deficient (G2-CKO) mice. The G2-CKO mice exhibited augmented pulmonary vascular remodeling, with enhanced α-smooth muscle actin accumulation and increased apoptotic cells in the vascular wall upon chronic hypoxia. Transcript analysis and chromatin immunoprecipitation assays using mouse pulmonary vascular endothelial cells revealed that GATA2 directly regulates the expression of G6pdx (a crucial cytoprotective enzyme) and Bmp4 (a growth factor that mediates vascular homeostasis). These results suggest that GATA2-deficient lungs are vulnerable to the hypoxic stress due to a diminished cellular protective response, making G2-CKO mice more prone to vascular remodeling upon chronic hypoxia. These findings provide insights into the mechanisms underlying GATA2-haploinsufficiency-related pulmonary hypertension.

: Objectives: To study COVID?19 (Delta Variant) cases and close contacts co?located within households. Focusing on epidemiology of transmission of COVID?19, quarantine duration and utilisation of infection control behaviours under a telehealth model of care in an elimination setting. Methods: A retrospective cohort analysis examined household spread of infection, duration of quarantine and change in PCR CT value during illness. A survey explored infection control behaviours used by household members during isolation and quarantine. Results: The cohort was 141 individuals in 35 households. Thirty?seven were index cases, and 48 became positive during quarantine, most within 10 days. Whole?household infection occurred in 12 households with multiple members. Behaviours focused on fomite transmission reduction rather than preventing aerosol transmission. The median duration of close contact household quarantine was 25 days. The majority of COVID?19 cases were de?isolated after 14 days with no evidence of further community transmission. Conclusion: Intrahousehold transmission was not universal and, if it occurred, usually occurred quickly. Behaviours utilised focused on fomites, suggesting a need for improved education regarding the potential utilisation of strategies to prevention the transmission of aerosols. Households experienced long durations of home?based quarantine. Implications for public health: The impact of long quarantine durations must be considered, particularly where most community benefit from quarantine is achieved within 10 days from exposure in the setting of the Delta Variant. Education of households regarding aerosol risk reduction is a potential strategy in the household setting of individuals at risk of disease progression., The incursion of SARS?CoV?2 into the Australian community from returning travellers and subsequent community transmission has required a significant public health response since the commencement of the pandemic. In the [...]

Abstract Ribosomal protein dysfunction causes diverse human diseases, including Diamond–Blackfan anemia (DBA). Despite the universal need for ribosomes in all cell types, the mechanisms underlying ribosomopathies, which are characterized by tissue-specific defects, are still poorly understood. In the present study, we analyzed the transcriptomes of single purified erythroid progenitors isolated from the bone marrow of DBA patients. These patients were categorized into untreated, glucocorticoid (GC)-responsive and GC-non-responsive groups. We found that erythroid progenitors from untreated DBA patients entered S-phase of the cell cycle under considerable duress, resulting in replication stress and the activation of P53 signaling. In contrast, cell cycle progression was inhibited through induction of the type 1 interferon pathway in treated, GC-responsive patients, but not in GC-non-responsive patients. Notably, a low dose of interferon alpha treatment stimulated the production of erythrocytes derived from DBA patients. By linking the innately shorter cell cycle of erythroid progenitors to DBA pathogenesis, we demonstrated that interferon-mediated cell cycle control underlies the clinical efficacy of glucocorticoids. Our study suggests that interferon administration may constitute a new alternative therapeutic strategy for the treatment of DBA. The trial was registered at www.chictr.org.cn as ChiCTR2000038510.

Abstract Background Hypoxia is a hallmark of the tumor microenvironment (TME) and in addition to altering metabolism in cancer cells, it transforms tumor-associated stromal cells. Within the tumor stromal cell compartment, tumor-associated macrophages (TAMs) provide potent pro-tumoral support. However, TAMs can also be harnessed to destroy tumor cells by monoclonal antibody (mAb) immunotherapy, through antibody dependent cellular phagocytosis (ADCP). This is mediated via antibody-binding activating Fc gamma receptors (FcγR) and impaired by the single inhibitory FcγR, FcγRIIb. Methods We applied a multi-OMIC approach coupled with in vitro functional assays and murine tumor models to assess the effects of hypoxia inducible factor (HIF) activation on mAb mediated depletion of human and murine cancer cells. For mechanistic assessments, siRNA-mediated gene silencing, Western blotting and chromatin immune precipitation were utilized to assess the impact of identified regulators on FCGR2B gene transcription. Results We report that TAMs are FcγRIIbbright relative to healthy tissue counterparts and under hypoxic conditions, mononuclear phagocytes markedly upregulate FcγRIIb. This enhanced FcγRIIb expression is transcriptionally driven through HIFs and Activator protein 1 (AP-1). Importantly, this phenotype reduces the ability of macrophages to eliminate anti-CD20 monoclonal antibody (mAb) opsonized human chronic lymphocytic leukemia cells in vitro and EL4 lymphoma cells in vivo in human FcγRIIb+/+ transgenic mice. Furthermore, post-HIF activation, mAb mediated blockade of FcγRIIb can partially restore phagocytic function in human monocytes. Conclusion Our findings provide a detailed molecular and cellular basis for hypoxia driven resistance to antitumor mAb immunotherapy, unveiling a hitherto unexplored aspect of the TME. These findings provide a mechanistic rationale for the modulation of FcγRIIb expression or its blockade as a promising strategy to enhance approved and novel mAb immunotherapies.

The vascular endothelium is vital for cardio-pulmonary homeostasis and, thus, plays a crucial role in preventing life-threatening lung diseases. The transcription factor GATA2 is essential for hematopoiesis and maintaining vascular integrity. Heterozygous mutations in GATA2 can lead to a primary immunodeficiency syndrome with pulmonary manifestations. Some GATA2 haploinsufficient patients develop pulmonary hypertension (PH), characterized by vascular remodeling and occlusion of small pulmonary arteries. However, the mechanism underlying pulmonary vascular remodeling in GATA2 haploinsufficient patients remain unclear. To understand how GATA2 deficiency affects pulmonary artery homeostasis, we applied a chronic hypoxia-mediated PH model using inducible systemic Gata2 conditionally deficient (G2-CKO) mice. The G2-CKO mice exhibited augmented pulmonary vascular remodeling, with enhanced α-smooth muscle actin accumulation and increased apoptotic cells in the vascular wall upon chronic hypoxia. Transcript analysis and chromatin immunoprecipitation assays using mouse pulmonary vascular endothelial cells revealed that GATA2 directly regulates the expression of G6pdx (a crucial cytoprotective enzyme) and Bmp4 (a growth factor that mediates vascular homeostasis). These results suggest that GATA2-deficient lungs are vulnerable to the hypoxic stress due to a diminished cellular protective response, making G2-CKO mice more prone to vascular remodeling upon chronic hypoxia. These findings provide insights into the mechanisms underlying GATA2-haploinsufficiency-related pulmonary hypertension. [ABSTRACT FROM AUTHOR]

Bioinformatic methodologies play a crucial role in the assessment of gut microbiota, offering advanced tools for analyzing complex microbial communities. These methodologies involve high-throughput sequencing technologies, such as 16S rRNA gene sequencing and metagenomics, which generate vast amounts of data on microbial diversity and functional potential, as well as whole-genome sequencing, which, while being more costly, has a more expansive potential. Bioinformatics tools and algorithms process these data to identify microbial taxa and quantify and elucidate their roles within the microbiome. Advanced statistical and computational models further enable the identification of microbiota patterns associated with various diseases and health conditions. Overall, bioinformatic approaches are essential for deciphering the complexities of gut microbiota so that, in the future, we may be able to discover treatments and technologies aimed at restoring or optimizing the microbiome. The goal of this review is to describe the differences in methodology and utilization of 16S versus whole-genome sequencing to address the increased understanding of the role that the gut microbiome plays in human physiology and pathology. [ABSTRACT FROM AUTHOR]

Contemporary media industry and production studies takes a nuanced view of the relative independence and autonomy available to media producers. In this article, I apply this frame to the Australian independent screen production firm Kennedy Miller Mitchell. But rather than examining the firm through its commercial partnerships, I analyze its independence in respect of its historical relationship with Australian government agencies. I contend that it possesses negotiated dependencies with these government bodies, a term describing the nuances of a complex reciprocal relationship. While the firm’s activities have been shaped and constrained by government policy, I argue also that the firm has maintained agency through negotiations with the state. My analysis of Kennedy Miller Mitchell’s negotiated dependencies qualifies our understanding of this reputedly iconoclastic firm and treats the company as a significant case study of the limits of independence and autonomy in an industry underwritten by government intervention.

Innovative game-based training methods that leverage the ubiquity of cellphones and familiarity with phone-based interfaces have the potential to transform the training of public health practitioners in low-income countries such as Liberia. This article describes the design, development, and testing of a prototype of the Figure It Out mobile game. The prototype game uses a disease outbreak scenario to promote evidence-based decision-making in determining the causative agent and prescribing intervention measures to minimize epidemiological and logistical burdens in resource-limited settings. An initial prototype of the game developed by the US team was playtested and evaluated by focus groups with 20 University of Liberia Masters of Public Health (UL MPH) students. Results demonstrate that the learning objectives—improving search skills for identifying scientific evidence and considering evidence before decision-making during a public health emergency—were considered relevant and important in a setting that has repeatedly and recently experienced severe threats to public health. However, some of the game mechanics that were thought to enhance engagement such as trial-and-error and choose-your-own-path gameplay, were perceived by the target audience as distracting or too time-consuming, particularly in the context of a realistic emergency scenario. Gameplay metrics that mimicked real-world situations around lives lost, money spent, and time constraints during public health outbreaks were identified as relatable and necessary considerations. Our findings reflect cultural differences between the game development team and end users that have emphasized the need for end users to have an integral part of the design team; this formative evaluation has critically informed next steps in the iterative development process. Our multidisciplinary, cross-cultural and cross-national design team will be guided by Liberia-based public health students and faculty, as well as community members who represent our end user population in terms of experience and needs. These stakeholders will make key decisions regarding game objectives and mechanics, to be vetted and implemented by game design experts, epidemiologists, and software developers.

Abstract Background Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease, and gene expression profiling has identified several molecular subtypes with distinct biological and clinicopathological characteristics. While MIBC subtyping has primarily been based on messenger RNA (mRNA), long non-coding RNAs (lncRNAs) may provide additional resolution. Methods LncRNA expression was quantified from microarray data of a MIBC cohort treated with neoadjuvant chemotherapy (NAC) and radical cystectomy (RC) (n = 223). Unsupervised consensus clustering of highly variant lncRNAs identified a four-cluster solution, which was characterized using a panel of MIBC biomarkers, regulon activity profiles, gene signatures, and survival analysis. The four-cluster solution was confirmed in The Cancer Genome Atlas (TCGA) cohort (n = 405). A single-sample genomic classifier (GC) was trained using ridge-penalized logistic regression and validated in two independent cohorts (n = 255 and n = 94). Results NAC and TCGA cohorts both contained an lncRNA cluster (LC3) with favorable prognosis that was enriched with tumors of the luminal-papillary (LP) subtype. In both cohorts, patients with LP tumors in LC3 (LPL-C3) were younger and had organ-confined, node-negative disease. The LPL-C3 tumors had enhanced FGFR3, SHH, and wild-type p53 pathway activity. In the TCGA cohort, LPL-C3 tumors were enriched for FGFR3 mutations and depleted for TP53 and RB1 mutations. A GC trained to identify these LPL-C3 patients showed robust performance in two validation cohorts. Conclusions Using lncRNA expression profiles, we identified a biologically distinct subgroup of luminal-papillary MIBC with a favorable prognosis. These data suggest that lncRNAs provide additional information for higher-resolution subtyping, potentially improving precision patient management.

Introduction Deep venous thrombosis (DVT) is a common vascular disease with an annual incidence of 0.1% among the general population, and more than 1% among hospitalized individuals (1). Pulmonary embolism--the [...], Deep venous thrombosis (DVT) and secondary pulmonary embolism cause approximately 100,000 deaths per year in the United States. Physical immobility is the most significant risk factor for DVT, but a molecular and cellular basis for this link has not been defined. We found that the endothelial cells surrounding the venous valve, where DVTs originate, express high levels of FOXC2 and PROX1, transcription factors known to be activated by oscillatory shear stress. The perivalvular venous endothelial cells exhibited a powerful antithrombotic phenotype characterized by low levels of the prothrombotic proteins vWF, P-selectin, and ICAM1 and high levels of the antithrombotic proteins thrombomodulin (THBD), endothelial protein C receptor (EPCR), and tissue factor pathway inhibitor (TFPI). The perivalvular antithrombotic phenotype was lost following genetic deletion of FOXC2 or femoral artery ligation to reduce venous flow in mice, and at the site of origin of human DVT associated with fatal pulmonary embolism. Oscillatory blood flow was detected at perivalvular sites in human veins following muscular activity, but not in the immobile state or after activation of an intermittent compression device designed to prevent DVT. These findings support a mechanism of DVT pathogenesis in which loss of muscular activity results in loss of oscillatory shear-dependent transcriptional and antithrombotic phenotypes in perivalvular venous endothelial cells, and suggest that prevention of DVT and pulmonary embolism may be improved by mechanical devices specifically designed to restore perivalvular oscillatory flow.