Parallelized Latent Dirichlet Allocation Provides a Novel Interpretability of Mutation Signatures in Cancer Genomes

Global Mapping of Interventions to Improve Quality of Life of Patients with Cancer: A Protocol for Literature Mining and Meta-Analysis

Cancer led to nearly 10 million deaths in 2020, as reported by the World Health Organization (WHO). Consequently, both biomedical therapeutics and psychological interventions have been implemented to decrease the burden of this non-communicable disease. However, the research conducted so far has only described some aspects of these interventions, which may increase the health-related quality of life of cancer patients. Therefore, a systematic review is necessary to depict an overall picture of the cancer interventions globally. Then, the impact of these interventions on the preference-based health-related quality of life of cancer patients may be synthesized. The protocol is developed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The Web of Science database is used to retrieve the literature using four keyword terms: quality of life (QoL), cancer, interventions, and health utility. Then, we draw the global mapping diagram and conduct the meta-analysis for this research. Additionally, longitudinal measurements are used to estimate the changes in the health utility of patients during the interventions. Thus, this systematic review can provide insight into the impact of interventions on increasing the health-related quality of life (HRQL) of cancer patients.

A Comprehensive Approach of Exploring Usability Problems in Enterprise Resource Planning Systems

Enterprise Resource Planning (ERP) is a frequently used system among organizations to automate their workflows, and companies’ performances are highly dependent on the ERP system. The usability issues of ERP systems may cause performance degradation, resulting in the company’s loss in terms of cost. Previously, several studies reported many usability problems of ERP systems. It can be helpful for the developers and designers of ERP systems to use design recommendations as a quick reference to avoid recurrent usability problems of ERP systems. Currently, this area lacks effective consolidation of the previously reported usability problems data. This paper presents a unique approach to developing a precise checklist of ERP usability problems using the topic modeling technique. Our analysis found six different usability problem-related topics that can be generalized for various ERP systems. We have successfully validated our checklist in three different usability studies of ERP systems. The most found usability problems are “difficulty searching and finding desired item/information in interface and error handling” and “missing data and information”. The outcome of our paper is the provision of recommendations to avoid the usability problems of ERP systems and help organizations efficiently prevent frequent issues during the development and maintenance of ERP systems.

Clone decomposition based on mutation signatures provides novel insights into mutational processes

Intra-tumor heterogeneity is a phenomenon in which mutation profiles differ from cell to cell within the same tumor and is observed in almost all tumors. Understanding intra-tumor heterogeneity is essential from the clinical perspective. Numerous methods have been developed to predict this phenomenon based on variant allele frequency. Among the methods, CloneSig models the variant allele frequency and mutation signatures simultaneously and provides an accurate clone decomposition. However, this method has limitations in terms of clone number selection and modeling. We propose SigTracer, a novel hierarchical Bayesian approach for analyzing intra-tumor heterogeneity based on mutation signatures to tackle these issues. We show that SigTracer predicts more reasonable clone decompositions than the existing methods against artificial data that mimic cancer genomes. We applied SigTracer to whole-genome sequences of blood cancer samples. The results were consistent with past findings that single base substitutions caused by a specific signature (previously reported as SBS9) related to the activation-induced cytidine deaminase intensively lie within immunoglobulin-coding regions for chronic lymphocytic leukemia samples. Furthermore, we showed that this signature mutates regions responsible for cell-cell adhesion. Accurate assignments of mutations to signatures by SigTracer can provide novel insights into signature origins and mutational processes.