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Since the first receiver independent exchange format (RINEX) version was released in 1989, it has gone through several versions, making the existing software, such as TEQC, incompatible with certain later versions. This study proposes a new Python package named PyRINEX, which is developed to batch process the most generally used versions of RINEX files, namely 2.0 and 3.0. The proposed package can be used to manage and edit numerous RINEX files as well as perform a data quality check function. PyRINEX can be easily imported into any Python IDE similar to any other open-source Python package, it also makes secondary development easy for users.

BackgroundPatients with substance use disorders (SUDs) are at increased risk for symptom deterioration following treatment, with up to 60% resuming substance use within the first year posttreatment. Substance use craving together with cognitive and mental health variables play important roles in the understanding of the trajectories from abstinence to substance use. ObjectiveThis prospective observational feasibility study aims to improve our understanding of specific profiles of variables explaining SUD symptom deterioration, in particular, how individual variability in mental health, cognitive functioning, and smartphone use is associated with craving and substance use in a young adult clinical population. MethodsIn this pilot study, 26 patients with SUDs were included at about 2 weeks prior to discharge from inpatient SUD treatment from 3 different treatment facilities in Norway. Patients underwent baseline neuropsychological and mental health assessments; they were equipped with smartwatches and they downloaded an app for mobile sensor data collection in their smartphones. Every 2 days for up to 8 weeks, the patients were administered mobile ecological momentary assessments (EMAs) to evaluate substance use, craving, mental health, cognition, and a mobile Go/NoGo performance task. Repeated EMAs as well as the smartphone’s battery use data were averaged across all days per individual and used as candidate input variables together with the baseline measures in models of craving intensity and the occurrence of any substance use episodes. ResultsA total of 455 momentary assessments were completed out of a potential maximum of 728 assessments. Using EMA and baseline data as candidate input variables and craving and substance use as responses, model selection identified mean craving intensity as the most important predictor of having one or more substance use episodes and with variabilities in self-reported impulsivity, mental health, and battery use as significant explanatory variables of craving intensity. ConclusionsThis prospective observational feasibility study adds novelty by collecting high-intensity data for a considerable period of time, including mental health data, mobile cognitive assessments, and mobile sensor data. Our study also contributes to our knowledge about a clinical population with the most severe SUD presentations in a vulnerable period during and after discharge from inpatient treatment. We confirmed the importance of variability in cognitive function and mood in explaining variability in craving and that smartphone usage may possibly add to this understanding. Further, we found that craving intensity is an important explanatory variable in understanding substance use episodes.

BackgroundDigital just-in-time adaptive interventions can reduce binge-drinking events (BDEs; consuming ≥4 drinks for women and ≥5 drinks for men per occasion) in young adults but need to be optimized for timing and content. Delivering just-in-time support messages in the hours prior to BDEs could improve intervention impact. ObjectiveWe aimed to determine the feasibility of developing a machine learning (ML) model to accurately predict future, that is, same-day BDEs 1 to 6 hours prior BDEs, using smartphone sensor data and to identify the most informative phone sensor features associated with BDEs on weekends and weekdays to determine the key features that explain prediction model performance. MethodsWe collected phone sensor data from 75 young adults (aged 21 to 25 years; mean 22.4, SD 1.9 years) with risky drinking behavior who reported their drinking behavior over 14 weeks. The participants in this secondary analysis were enrolled in a clinical trial. We developed ML models testing different algorithms (eg, extreme gradient boosting [XGBoost] and decision tree) to predict same-day BDEs (vs low-risk drinking events and non-drinking periods) using smartphone sensor data (eg, accelerometer and GPS). We tested various “prediction distance” time windows (more proximal: 1 hour; distant: 6 hours) from drinking onset. We also tested various analysis time windows (ie, the amount of data to be analyzed), ranging from 1 to 12 hours prior to drinking onset, because this determines the amount of data that needs to be stored on the phone to compute the model. Explainable artificial intelligence was used to explore interactions among the most informative phone sensor features contributing to the prediction of BDEs. ResultsThe XGBoost model performed the best in predicting imminent same-day BDEs, with 95% accuracy on weekends and 94.3% accuracy on weekdays (F1-score=0.95 and 0.94, respectively). This XGBoost model needed 12 and 9 hours of phone sensor data at 3- and 6-hour prediction distance from the onset of drinking on weekends and weekdays, respectively, prior to predicting same-day BDEs. The most informative phone sensor features for BDE prediction were time (eg, time of day) and GPS-derived features, such as the radius of gyration (an indicator of travel). Interactions among key features (eg, time of day and GPS-derived features) contributed to the prediction of same-day BDEs. ConclusionsWe demonstrated the feasibility and potential use of smartphone sensor data and ML for accurately predicting imminent (same-day) BDEs in young adults. The prediction model provides “windows of opportunity,” and with the adoption of explainable artificial intelligence, we identified “key contributing features” to trigger just-in-time adaptive intervention prior to the onset of BDEs, which has the potential to reduce the likelihood of BDEs in young adults. Trial RegistrationClinicalTrials.gov NCT02918565; https://clinicaltrials.gov/ct2/show/NCT02918565

Short DNA oligonucleotides (~4 mer) have been used to index samples from different sources, such as in multiplex sequencing. Presently, longer oligonucleotides (8-12 mer) are being used as molecular barcodes with which to distinguish among raw DNA molecules in many high-tech sequence analyses, including low-frequent mutation detection, quantitative transcriptome analysis, and single-cell sequencing. Despite some advantages of using molecular barcodes with random sequences, such an approach, however, makes it impossible to know the exact sequences used in an experiment and can lead to inaccurate interpretation due to misclustering of barcodes arising from the occurrence of unexpected mutations in the barcodes. The present study introduces a tool developed for selecting an optimal barcode subset during molecular barcoding. The program considers five barcode factors: GC content, homopolymers, simple sequence repeats with repeated units of dinucleotides, Hamming distance, and complementarity between barcodes. To evaluate a selected barcode set, penalty scores for the factors are defined based on their distributions observed in random barcodes. The algorithm employed in the program comprises two steps: i) random generation of an initial set and ii) optimal barcode selection via iterative replacement. Users can execute the program by inputting barcode length and the number of barcodes to be generated. Furthermore, the program accepts a user's own values for other parameters, including penalty scores, for advanced use, allowing it to be applied in various conditions. In many test runs to obtain 100000 barcodes with lengths of 12 nucleotides, the program showed fast performance, efficient enough to generate optimal barcode sequences with merely the use of a desktop PC. We also showed that VFOS has comparable performance, flexibility in program running, consideration of simple sequence repeats, and fast computation time in comparison with other two tools (DNABarcodes and FreeBarcodes). Owing to the versatility and fast performance of the program, we expect that many researchers will opt to apply it for selecting optimal barcode sets during their experiments, including next-generation sequencing.