An article published in BMCBioInformatics presents scEvoNet: a Python tool for predicting cell type evolution in cross-species or cancer-related single-cell RNA sequencing datasets.
]. Despite technical batch effects and biological batch effects , we have achieved a high AUC score of 0.95 for classifying zebrafish cells with our frog-based NC model []. Here, we have expanded this method: scEvoNet applies to a variety of applications, e.g., between different time points during a given organism’s development, between species, and when comparing primary tumor and metastasis.
Additionally, to reduce the effect of the different biological domains between datasets, and to reduce the effect of the scRNA-seq data sparsity, we apply a sigmoid function that smooths expression units in a more flexible manner than simple binarization, which has been shown to keep enough information for scRNA-seq data analysis []. For the model training, we use early stopping to avoid overfitting with 10 rounds which determines the actual number of estimators in the regressions.
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Inflammation and neuronal gene expression changes differ in early versus late chronic traumatic encephalopathy brain - BMC Medical GenomicsBackground Our understanding of the molecular underpinnings of chronic traumatic encephalopathy (CTE) and its associated pathology in post-mortem brain is incomplete. Factors including years of play and genetic risk variants influence the extent of tau pathology associated with disease expression, but how these factors affect gene expression, and whether those effects are consistent across the development of disease, is unknown. Methods To address these questions, we conducted an analysis of the largest post-mortem brain CTE mRNASeq whole-transcriptome dataset available to date. We examined the genes and biological processes associated with disease by comparing individuals with CTE with control individuals with a history of repetitive head impacts that lack CTE pathology. We then identified genes and biological processes associated with total years of play as a measure of exposure, amount of tau pathology present at time of death, and the presence of APOE and TMEM106B risk variants. Samples were stratified into low and high pathology groups based on McKee CTE staging criteria to model early versus late changes in response to exposure, and the relative effects associated with these factors were compared between these groups. Results Substantial gene expression changes were associated with severe disease for most of these factors, primarily implicating diverse, strongly involved neuroinflammatory and neuroimmune processes. In contrast, low pathology groups had many fewer genes and processes implicated and show striking differences for some factors when compared with severe disease. Specifically, gene expression associated with amount of tau pathology showed a nearly perfect inverse relationship when compared between these two groups. Conclusions Together, these results suggest the early CTE disease process may be mechanistically different than what occurs in late stages, that total years of play and tau pathology influence disease expression differently, and that rela
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Effectiveness of a Smartphone App (MINISTOP 2.0) integrated in primary child health care to promote healthy diet and physical activity behaviors and prevent obesity in preschool-aged children: randomized controlled trial - International Journal of Behavioral Nutrition and Physical ActivityBackground Childhood overweight and obesity is a public health priority. We have previously reported the efficacy of a parent-oriented mobile health (mHealth) app-based intervention (MINISTOP 1.0) which showed improvements in healthy lifestyle behaviors. However, the effectiveness of the MINISTOP app in real-world conditions needs to be established. Objective To evaluate the real-world effectiveness of a 6-month mHealth intervention (MINISTOP 2.0 app) on children’s intake of fruits, vegetables, sweet and savory treats, sweet drinks, moderate-to-vigorous physical activity, and screen time (primary outcomes), and on parental self-efficacy (PSE) for promoting healthy lifestyle behaviors, and children’s body mass index (BMI) (secondary outcomes). Methods A hybrid type 1 effectiveness-implementation design was utilized. For the effectiveness outcomes, a two-arm, individually randomized controlled trial was conducted. Parents (n = 552) of 2.5-to-3-year-old children were recruited from 19 child health care centers across Sweden, and, randomized to either a control (standard care) or intervention group (MINISTOP 2.0 app). The 2.0 version was adapted and translated into English, Somali and Arabic to increase reach. All recruitment and data collection were conducted by the nurses. Outcomes were assessed at baseline and after six months, using standardized measures (BMI) and a questionnaire (health behaviors, PSE). Results Among the participating parents (n = 552, age: 34.1 ± 5.0 years), 79% were mothers and 62% had a university degree. Twenty-four percent (n = 132) of children had two foreign-born parents. At follow-up, parents in the intervention group reported lower intakes of sweet and savory treats (-6.97 g/day; p = 0.001), sweet drinks (-31.52 g/day; p | 0.001), and screen time (-7.00 min/day; p = 0.012) in their children compared to the control group. The intervention group reported higher total PSE (0.91; p = 0.006), PSE for promoting healthy diet (0.34; p = 0.008) and
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Attitudes, awareness, and perceptions of general public and pharmacists toward the extended community pharmacy services and drive-thru pharmacy services: a systematic review - Journal of Pharmaceutical Policy and PracticeBackground Several extended and newly added pharmacy services were evaluated in different countries. This review aims to provide a summary of studies on attitudes, awareness, or perceptions toward various extended and drive-thru pharmacy services at community settings among pharmacists and the general public. Methods To find qualitative and descriptive quantitative studies, that reported on the attitudes, awareness, or perceptions of the general public and pharmacists toward the practice of any extended community pharmacy service and drive-thru pharmacy services in a community setting and conducted from March 2012 to March 2022. Researchers used databases such as Embase, Medline PubMed, Scopus, Web of Science, and Science Direct. The reviewers extracted data independently using the PRISMA checklist. Results There were 55 studies found according to the inclusion criteria. Various extended pharmacy services (EPS) and drive-thru pharmacy services were noted in the community setting. Pharmaceutical care services and healthcare promotion services were the noticeable performed extended services. There were positive perceptions and attitudes toward extended and drive-thru pharmacy services among pharmacists and the public. However, some factors, such as lack of time and shortage of staff, affect the practice of those services. Conclusion Understanding the major concerns toward the provision of extended and drive-thru community pharmacy services and improving pharmacists’ skills through more training programs to provide such services efficiently. In the future, more reviews for EPS practice barriers are recommended to faceup all concerns and find standardized guidelines by stakeholders and organizations for efficient EPS practices.
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