A study in BMCMedicine confirms the association of chemotherapy with weight gain that may be due to alterations of bacterial flora. The gut microbiome may be a future target for intervention in preventing chemotherapy-dependent anthropometric changes.
Eggerthella
sp. showed a significant difference with a negative association with obesity , in keeping with previously published reports []. We also analyzed the Firmicutes to Bacteroidetes ratio and found no significant baseline differences between patients classified as normal weight, and overweight or obese. Normal weight patients had an F/B of 5.233, while patients classified as overweight or obese demonstrated ratios of 6.563 and 5.822, respectively .
At the species level interesting differences in relative abundance were observed between chemotherapy and endocrine therapy-treated patient groups. For instance, within the group of organisms that were altered in abundance, more species were reduced in relative abundance following treatment with chemotherapy, as opposed to endocrine therapy where the opposite was observed.
An association between intestinal microbial dysbiosis and gut inflammation has been well documented in disease states such as inflammatory bowel disease [
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KATZNCP: a miRNA–disease association prediction model integrating KATZ algorithm and network consistency projection - BMC BioinformaticsBackground Clinical studies have shown that miRNAs are closely related to human health. The study of potential associations between miRNAs and diseases will contribute to a profound understanding of the mechanism of disease development, as well as human disease prevention and treatment. MiRNA–disease associations predicted by computational methods are the best complement to biological experiments. Results In this research, a federated computational model KATZNCP was proposed on the basis of the KATZ algorithm and network consistency projection to infer the potential miRNA–disease associations. In KATZNCP, a heterogeneous network was initially constructed by integrating the known miRNA–disease association, integrated miRNA similarities, and integrated disease similarities; then, the KATZ algorithm was implemented in the heterogeneous network to obtain the estimated miRNA–disease prediction scores. Finally, the precise scores were obtained by the network consistency projection method as the final prediction results. KATZNCP achieved the reliable predictive performance in leave-one-out cross-validation (LOOCV) with an AUC value of 0.9325, which was better than the state-of-the-art comparable algorithms. Furthermore, case studies of lung neoplasms and esophageal neoplasms demonstrated the excellent predictive performance of KATZNCP. Conclusion A new computational model KATZNCP was proposed for predicting potential miRNA–drug associations based on KATZ and network consistency projections, which can effectively predict the potential miRNA–disease interactions. Therefore, KATZNCP can be used to provide guidance for future experiments.
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Infusing wellness opportunities into integrated youth services - BMC PsychiatryBackground Appropriate health services and health promotion strategies for young people with mental health and substance use (MHSU) concerns are critical for recovery. Foundry, an integrated youth services (IYS) initiative for young people ages 12-24 in British Columbia (BC), Canada, has recently added leisure and recreational activities (referred to as the Wellness Program) into its services. The objectives of this study were to: (1) describe how the Wellness Program was implemented over a two-year period into IYS (2) provide an overview of what the Wellness Program is, who accessed the program since inception and initial evaluation results. Methods This study was part of the developmental evaluation of Foundry. A phased approach was used to implement the program at nine centres. Data was accessed from Foundry’s centralized platform ‘Toolbox’ and included activity type, number of unique youth and visits, additional services sought, information about how youth found out about the centre, and demographics. Qualitative data was also accessed from focus groups (n=2) conducted with young people (n=9). Results Over the two-year period, 355 unique youth accessed the Wellness Program, with 1319 unique visits. Almost half (40%) of youth identified the Wellness Program as the first point of access to Foundry. A total of 384 different programs were offered targeting five wellness domains (physical, mental/emotional, social, spiritual, and cognitive/intellectual). The majority of youth identified as young girls/women (58.2%), 22.6% as gender diverse, and 19.2% as young men/boys. The mean age was 19 years, and most participants were between the ages of 19-24 years (43.6%). From the thematic analysis of focus groups, we found young people enjoyed the social aspect of the program with peers and facilitators, and identified program improvements that are being considered as the program grows. Conclusions This study provides insight into the development and implementation of leisure
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Systemic aspergillosis in a patient with interferon gamma receptor 1 deficiency; a case report - BMC PediatricsBackground Interferon-gamma receptor deficiency is a heterogeneous spectrum of disease which involves mutations in IFNGR1, IFNGR2 genes, and the downstream signaling proteins such as STAT1. These mutations are associated with immunodeficiency 27 A and 27B, making the patient prone to mycobacterial infections. Patients with this condition are also at increased risk for affliction with viral and bacterial infections, such as with the Herpesviridae family, Listeria, and Salmonella. Moreover, SH2B3 mutation is associated with autoimmune and lymphoproliferative conditions. Case presentation the patient was a 19-month-old infant girl who presented with a two-week history of fever. She had near-normal flowcytometry with high IgM and IgE. She had pneumonic infiltration in her chest and right hilar and para-aortic lymphadenopathy. PCR of whole blood for Aspergillus fumigatus came back positive. In her Whole Exome Sequencing she had IFNGR1 and SH2B3 mutations. Conclusion systemic fungal infections such as Aspergillosis can occur in patients with interferon-gamma receptor one deficiency. This type of immunodeficiency should be considered in treating patients with systemic Aspergillosis.
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Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment - Genome MedicineBackground The crosstalk between cancer and the tumour immune microenvironment (TIME) has attracted significant interest in the latest years because of its impact on cancer evolution and response to treatment. Despite this, cancer-specific tumour-TIME interactions and their mechanistic insights are still poorly understood. Methods Here, we compute the significant interactions occurring between cancer-specific genetic drivers and five anti- and pro-tumour TIME features in 32 cancer types using Lasso regularised ordinal regression. Focusing on head and neck squamous cancer (HNSC), we rebuild the functional networks linking specific TIME driver alterations to the TIME state they associate with. Results The 477 TIME drivers that we identify are multifunctional genes whose alterations are selected early in cancer evolution and recur across and within cancer types. Tumour suppressors and oncogenes have an opposite effect on the TIME and the overall anti-tumour TIME driver burden is predictive of response to immunotherapy. TIME driver alterations predict the immune profiles of HNSC molecular subtypes, and perturbations in keratinization, apoptosis and interferon signalling underpin specific driver-TIME interactions. Conclusions Overall, our study delivers a comprehensive resource of TIME drivers, gives mechanistic insights into their immune-regulatory role, and provides an additional framework for patient prioritisation to immunotherapy. The full list of TIME drivers and associated properties are available at http://www.network-cancer-genes.org .
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BMC Series blog Culturally Safe and Trauma-Informed Care for Indigenous Women: The Indigenous Birth Support Worker (IBSW) Program
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SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data - BMC BioinformaticsBackground Structural variations (SVs) refer to variations in an organism’s chromosome structure that exceed a length of 50 base pairs. They play a significant role in genetic diseases and evolutionary mechanisms. While long-read sequencing technology has led to the development of numerous SV caller methods, their performance results have been suboptimal. Researchers have observed that current SV callers often miss true SVs and generate many false SVs, especially in repetitive regions and areas with multi-allelic SVs. These errors are due to the messy alignments of long-read data, which are affected by their high error rate. Therefore, there is a need for a more accurate SV caller method. Result We propose a new method-SVcnn, a more accurate deep learning-based method for detecting SVs by using long-read sequencing data. We run SVcnn and other SV callers in three real datasets and find that SVcnn improves the F1-score by 2–8% compared with the second-best method when the read depth is greater than 5×. More importantly, SVcnn has better performance for detecting multi-allelic SVs. Conclusions SVcnn is an accurate deep learning-based method to detect SVs. The program is available at https://github.com/nwpuzhengyan/SVcnn .
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