Experiences of health tracking in mobile apps for multiple sclerosis: A qualitative content analysis of user reviews.

BACKGROUND: Mobile health applications (apps) are promising condition self-management tools for people living with multiple sclerosis (MS). However, most existing apps do not include health tracking features. This gap has been raised as a priority research topic, but the development of new self-management apps will require designers to understand the context and needs of those living with MS. Our aim was to conduct a content analysis of publicly available user reviews of existing MS self-management apps to understand desired features and guide the design of future apps. METHODS: We systematically reviewed MS self-management apps which were publicly available in English on the Google Play and iOS app stores. We then conducted sentiment and content analysis of recent user reviews which referenced health tracking and data visualization to understand self-reported experiences and feedback. RESULTS: Searches identified 75 unique apps, of which six met eligibility criteria and had reviews. One hundred and thirty-seven user reviews of these apps were eligible, though most were associated with a single app (n=108). Overall, ratings and sentiment scores skewed highly positive (Median [IQR]: Ratings - 5 [4-5], Sentiment scores - 0.70 [0.44-0.86]), though scores of individual apps varied. Content analysis revealed five themes: reasons for app usage, simple user experience, customization and flexibility, feature requests, and technical issues. Reviewers suggested that app customization, interconnectivity, and consolidated access to desired features should be considered in the design of future apps. User ratings weakly correlated with review sentiment scores (ρ = 0.27 [0.11-0.42]). CONCLUSIONS: Self-tracking options in MS apps are currently limited, though the apps that offer these functions are considered useful by individuals with MS. Additional qualitative research is required to understand how specific app features and opportunities for personalization should be incorporated into new self-management tools for this population.

Health Tracking via Mobile Apps for Depression Self-management: Qualitative Content Analysis of User Reviews.

BACKGROUND: Tracking and visualizing health data using mobile apps can be an effective self-management strategy for mental health conditions. However, little evidence is available to guide the design of mental health-tracking mechanisms. OBJECTIVE: The aim of this study was to analyze the content of user reviews of depression self-management apps to guide the design of data tracking and visualization mechanisms for future apps. METHODS: We systematically reviewed depression self-management apps on Google Play and iOS App stores. English-language reviews of eligible apps published between January 1, 2018, and December 31, 2021, were extracted from the app stores. Reviews that referenced health tracking and data visualization were included in sentiment and qualitative framework analyses. RESULTS: The search identified 130 unique apps, 26 (20%) of which were eligible for inclusion. We included 783 reviews in the framework analysis, revealing 3 themes. Impact of app-based mental health tracking described how apps increased reviewers' self-awareness and ultimately enabled condition self-management. The theme designing impactful mental health-tracking apps described reviewers' feedback and requests for app features during data reporting, review, and visualization. It also described the desire for customization and contexts that moderated reviewer preference. Finally, implementing impactful mental health-tracking apps described considerations for integrating apps into a larger health ecosystem, as well as the influence of paywalls and technical issues on mental health tracking. CONCLUSIONS: App-based mental health tracking supports depression self-management when features align with users' individual needs and goals. Heterogeneous needs and preferences raise the need for flexibility in app design, posing challenges for app developers. Further research should prioritize the features based on their importance and impact on users.

Data Visualization for Chronic Neurological and Mental Health Condition Self-management: Systematic Review of User Perspectives.

BACKGROUND: Remote measurement technologies (RMT) such as mobile health devices and apps are increasingly used by those living with chronic neurological and mental health conditions. RMT enables real-world data collection and regular feedback, providing users with insights about their own conditions. Data visualizations are an integral part of RMT, although little is known about visualization design preferences from the perspectives of those living with chronic conditions. OBJECTIVE: The aim of this review was to explore the experiences and preferences of individuals with chronic neurological and mental health conditions on data visualizations derived from RMT to manage health. METHODS: In this systematic review, we searched peer-reviewed literature and conference proceedings (PubMed, IEEE Xplore, EMBASE, Web of Science, Association for Computing Machinery Computer-Human Interface proceedings, and the Cochrane Library) for original papers published between January 2007 and September 2021 that reported perspectives on data visualization of people living with chronic neurological and mental health conditions. Two reviewers independently screened each abstract and full-text article, with disagreements resolved through discussion. Studies were critically appraised, and extracted data underwent thematic synthesis. RESULTS: We identified 35 eligible publications from 31 studies representing 12 conditions. Coded data coalesced into 3 themes: desire for data visualization, impact of visualizations on condition management, and visualization design considerations. Data visualizations were viewed as an integral part of users' experiences with RMT, impacting satisfaction and engagement. However, user preferences were diverse and often conflicting both between and within conditions. CONCLUSIONS: When used effectively, data visualizations are valuable, engaging components of RMT. They can provide structure and insight, allowing individuals to manage their own health more effectively. However, visualizations are not "one-size-fits-all," and it is important to engage with potential users during visualization design to understand when, how, and with whom the visualizations will be used to manage health.

Mutation Maker, An Open Source Oligo Design Platform for Protein Engineering.

Protein engineering is the discipline of developing useful proteins for applications in research, therapeutic, and industrial processes by modification of naturally occurring proteins or by invention of de novo proteins. Modern protein engineering relies on the ability to rapidly generate and screen diverse libraries of mutant proteins. However, design of mutant libraries is typically hampered by scale and complexity, necessitating development of advanced automation and optimization tools that can improve efficiency and accuracy. At present, automated library design tools are functionally limited or not freely available. To address these issues, we developed Mutation Maker, an open source mutagenic oligo design software for large-scale protein engineering experiments. Mutation Maker is not only specifically tailored to multisite random and directed mutagenesis protocols, but also pioneers bespoke mutagenic oligo design for de novo gene synthesis workflows. Enabled by a novel bundle of orchestrated heuristics, optimization, constraint-satisfaction and backtracking algorithms, Mutation Maker offers a versatile toolbox for gene diversification design at industrial scale. Supported by in silico simulations and compelling experimental validation data, Mutation Maker oligos produce diverse gene libraries at high success rates irrespective of genes or vectors used. Finally, Mutation Maker was created as an extensible platform on the notion that directed evolution techniques will continue to evolve and revolutionize current and future-oriented applications.

Human-Centered Design Strategies for Device Selection in mHealth Programs: Development of a Novel Framework and Case Study.

BACKGROUND: Despite the increasing use of remote measurement technologies (RMT) such as wearables or biosensors in health care programs, challenges associated with selecting and implementing these technologies persist. Many health care programs that use RMT rely on commercially available, "off-the-shelf" devices to collect patient data. However, validation of these devices is sparse, the technology landscape is constantly changing, relative benefits between device options are often unclear, and research on patient and health care provider preferences is often lacking. OBJECTIVE: To address these common challenges, we propose a novel device selection framework extrapolated from human-centered design principles, which are commonly used in de novo digital health product design. We then present a case study in which we used the framework to identify, test, select, and implement off-the-shelf devices for the Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) consortium, a research program using RMT to study central nervous system disease progression. METHODS: The RADAR-CNS device selection framework describes a human-centered approach to device selection for mobile health programs. The framework guides study designers through stakeholder engagement, technology landscaping, rapid proof of concept testing, and creative problem solving to develop device selection criteria and a robust implementation strategy. It also describes a method for considering compromises when tensions between stakeholder needs occur. RESULTS: The framework successfully guided device selection for the RADAR-CNS study on relapse in multiple sclerosis. In the initial stage, we engaged a multidisciplinary team of patients, health care professionals, researchers, and technologists to identify our primary device-related goals. We desired regular home-based measurements of gait, balance, fatigue, heart rate, and sleep over the course of the study. However, devices and measurement methods had to be user friendly, secure, and able to produce high quality data. In the second stage, we iteratively refined our strategy and selected devices based on technological and regulatory constraints, user feedback, and research goals. At several points, we used this method to devise compromises that addressed conflicting stakeholder needs. We then implemented a feedback mechanism into the study to gather lessons about devices to improve future versions of the RADAR-CNS program. CONCLUSIONS: The RADAR device selection framework provides a structured yet flexible approach to device selection for health care programs and can be used to systematically approach complex decisions that require teams to consider patient experiences alongside scientific priorities and logistical, technical, or regulatory constraints.

A deep learning genome-mining strategy for biosynthetic gene cluster prediction.

Natural products represent a rich reservoir of small molecule drug candidates utilized as antimicrobial drugs, anticancer therapies, and immunomodulatory agents. These molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The increase in full microbial genomes and similar resources has led to development of BGC prediction algorithms, although their precision and ability to identify novel BGC classes could be improved. Here we present a deep learning strategy (DeepBGC) that offers reduced false positive rates in BGC identification and an improved ability to extrapolate and identify novel BGC classes compared to existing machine-learning tools. We supplemented this with random forest classifiers that accurately predicted BGC product classes and potential chemical activity. Application of DeepBGC to bacterial genomes uncovered previously undetectable putative BGCs that may code for natural products with novel biologic activities. The improved accuracy and classification ability of DeepBGC represents a major addition to in-silico BGC identification.

Novel genes in Human Asthma Based on a Mouse Model of Allergic Airway Inflammation and Human Investigations.

PURPOSE: Based on a previous gene expression study in a mouse model of asthma, we selected 60 candidate genes and investigated their possible roles in human asthma. METHODS: In these candidate genes, 90 SNPs were genotyped using MassARRAY technology from 311 asthmatic children and 360 healthy controls of the Hungarian (Caucasian) population. Moreover, gene expression levels were measured by RT PCR in the induced sputum of 13 asthmatics and 10 control individuals. t-tests, chi-square tests, and logistic regression were carried out in order to assess associations of SNP frequency and expression level with asthma. Permutation tests were performed to account for multiple hypothesis testing. RESULTS: The frequency of 4 SNPs in 2 genes differed significantly between asthmatic and control subjects: SNPs rs2240572, rs2240571, rs3735222 in gene SCIN, and rs32588 in gene PPARGC1B. Carriers of the minor alleles had reduced risk of asthma with an odds ratio of 0.64 (0.51-0.80; P=7×10(-5)) in SCIN and 0.56 (0.42-0.76; P=1.2×10(-4)) in PPARGC1B. The expression levels of SCIN, PPARGC1B and ITLN1 genes were significantly lower in the sputum of asthmatics. CONCLUSIONS: Three potentially novel asthma-associated genes were identified based on mouse experiments and human studies.

Early repositioning through compound set enrichment analysis: a knowledge-recycling strategy.

Despite famous serendipitous drug repositioning success stories, systematic projects have not yet delivered the expected results. However, repositioning technologies are gaining ground in different phases of routine drug development, together with new adaptive strategies. We demonstrate the power of the compound information pool, the ever-growing heterogeneous information repertoire of approved drugs and candidates as an invaluable catalyzer in this transition. Systematic, computational utilization of this information pool for candidates in early phases is an open research problem; we propose a novel application of the enrichment analysis statistical framework for fusion of this information pool, specifically for the prediction of indications. Pharmaceutical consequences are formulated for a systematic and continuous knowledge recycling strategy, utilizing this information pool throughout the drug-discovery pipeline.

Complex analysis of multiple single nucleotide polymorphisms as putative risk factors of tooth agenesis in the Hungarian population.

OBJECTIVES: The role was studied of multiple single nucleotide polymorphisms in tooth agenesis in the Hungarian population using a complex approach. METHODS: Eight SNPs, PAX9 -912 C/T, PAX9 -1031 A/G, MSX1 3755 A/G, FGFR1 T/C rs881301, IRF6 T/C rs764093, AXIN2-8150 A/G, AXIN2-8434 A/G and AXIN2-30224 C/T, were studied in 192 hypodontia and 17 oligodontia cases and in 260 healthy volunteers. Case-control analysis was performed to test both allelic and genotypic associations as well as associations at the level of haplotypes. Multivariate exploratory Bayesian network-based multi-level analysis of relevance (BN-BMLA) as well as logistic regression analysis were performed. RESULTS: Conventional statistics showed that PAX9 SNP -912 C/T and the MSX1 SNP changed the incidence of hypodontia, although after Bonferroni correction for multiple hypothesis testing, the effects were only borderline tendencies. Using a statistical analysis better suited for handling multiple hypotheses, the BN-BMLA, PAX9 SNPs clearly showed a synergistic effect. This was confirmed by other multivariate analyses and it remained significant after corrections for multiple hypothesis testing (p < 0.0025). The PAX9-1031-A-PAX9-912-T haplotype was the most relevant combination causing hypodontia. Interaction was weaker between PAX9 and MSX1, while other SNPs had no joint effect on hypodontia. CONCLUSION: This complex analysis shows the important role of PAX9 and MSX1 SNPs and of their interactions in tooth agenesis, while IRF6, FGFR1 and AXIN2 SNPs had no detectable role in the Hungarian population. These results also reveal that risk factors in hypodontia need to be identified in various populations, since there is considerable variability among them.

Drug repositioning for treatment of movement disorders: from serendipity to rational discovery strategies.

Movement disorders are a heterogeneous group of both common and rare neurological conditions characterized by abnormalities of motor functions and movement patterns. This work overviews recent successes and ongoing studies of repositioning relating to this disease group, which underscores the challenge of integrating the voluminous and heterogeneous findings required for making suitable drug repositioning decisions. In silico drug repositioning methods hold the promise of automated fusion of heterogeneous information sources, but the controllable, flexible and transparent incorporation of the expertise of medicinal chemists throughout the repositioning process remains an open challenge. In support of a more systematic approach toward repositioning, we summarize the application of a computational repurposing method based on statistically rooted knowledge fusion. To foster the spread of this technique, we provide a step-by-step guide to the complete workflow, together with a case study in Parkinson's disease.

Evaluation of a partial genome screening of two asthma susceptibility regions using bayesian network based bayesian multilevel analysis of relevance.

Genetic studies indicate high number of potential factors related to asthma. Based on earlier linkage analyses we selected the 11q13 and 14q22 asthma susceptibility regions, for which we designed a partial genome screening study using 145 SNPs in 1201 individuals (436 asthmatic children and 765 controls). The results were evaluated with traditional frequentist methods and we applied a new statistical method, called bayesian network based bayesian multilevel analysis of relevance (BN-BMLA). This method uses bayesian network representation to provide detailed characterization of the relevance of factors, such as joint significance, the type of dependency, and multi-target aspects. We estimated posteriors for these relations within the bayesian statistical framework, in order to estimate the posteriors whether a variable is directly relevant or its association is only mediated.With frequentist methods one SNP (rs3751464 in the FRMD6 gene) provided evidence for an association with asthma (OR = 1.43(1.2-1.8); p = 3×10(-4)). The possible role of the FRMD6 gene in asthma was also confirmed in an animal model and human asthmatics.In the BN-BMLA analysis altogether 5 SNPs in 4 genes were found relevant in connection with asthma phenotype: PRPF19 on chromosome 11, and FRMD6, PTGER2 and PTGDR on chromosome 14. In a subsequent step a partial dataset containing rhinitis and further clinical parameters was used, which allowed the analysis of relevance of SNPs for asthma and multiple targets. These analyses suggested that SNPs in the AHNAK and MS4A2 genes were indirectly associated with asthma. This paper indicates that BN-BMLA explores the relevant factors more comprehensively than traditional statistical methods and extends the scope of strong relevance based methods to include partial relevance, global characterization of relevance and multi-target relevance.