Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study.

Describing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3-5 days of age (DOA) born to mass-exposed sows through live virus inoculation with the recently introduced wild-type virus two weeks prior were sampled and followed up at 17-19 DOA. Samples from 127 piglets were individually tested for PRRSV by RT-PCR and 100 sequences were generated using Oxford Nanopore Technologies chemistry. Female piglets had significantly higher median Ct values than males (15.5 vs. 13.7, Kruskal-Wallis p < 0.001) at 3-5 DOA. A 52.8% mortality between sampling points was found, and the odds of dying by 17-19 DOA decreased with every one unit increase in Ct values at 3-5 DOA (OR = 0.76, 95% CI 0.61-0.94, p = 0.01). Although the within-pig percent nucleotide identity was overall high (99.7%) between 3-5 DOA and 17-19 DOA samples, ORFs 4 and 5a showed much lower identities (97.26% and 98.53%, respectively). When looking solely at ORF5, 62% of the sequences were identical to the 3-5 DOA consensus. Ten and eight regions showed increased nucleotide and amino acid genetic diversity, respectively, all found throughout ORFs 2a/2b, 4, 5a/5, 6, and 7.

Producing personalized statin treatment plans to optimize clinical outcomes using big data and machine learning.

Almost half of Americans 65 years of age and older take statins, which are highly effective in lowering low-density lipoprotein cholesterol, preventing atherosclerotic cardiovascular disease (ASCVD), and reducing all-cause mortality. Unfortunately, ∼50% of patients prescribed statins do not obtain these critical benefits because they discontinue use within one year of treatment initiation. Therefore, statin discontinuation has been identified as a major public health concern due to the increased morbidity, mortality, and healthcare costs associated with ASCVD. In clinical practice, statin-associated symptoms (SAS) often result in dose reduction or discontinuation of these life-saving medications. Currently, physician decision-making in statin prescribing typically relies on only a few patient data elements. Physicians then employ reactive strategies to manage SAS concerns after they manifest (e.g., offering an alternative statin treatment plan or a statin holiday). A preferred approach would be a proactive strategy to identify the optimal treatment plan (statin agent + dosage) to prevent/minimize SAS and statin discontinuation risks for a particular individual prior to initiating treatment. Given that using a single patient's data to identify the optimal statin regimen is inadequate to ensure that the harms of statin use are minimized, alternative tactics must be used to address this problem. In this proof-of-concept study, we explore the use of a machine-learning personalized statin treatment plan (PSTP) platform to assess the numerous statin treatment plans available and identify the optimal treatment plan to prevent/minimize harms (SAS and statin discontinuation) for an individual. Our study leveraged de-identified administrative insurance claims data from the OptumLabs® Data Warehouse, which includes medical and pharmacy claims, laboratory results, and enrollment records for more than 130 million commercial and Medicare Advantage (MA) enrollees, to successfully develop the PSTP platform. In this study, we found three results: (1) the PSTP platform recommends statin prescription with significantly lower risks of SAS and discontinuation compared with standard-practice, (2) because machine learning can consider many more dimensions of data, the performance of the proactive prescription strategy with machine-learning support is better, especially the artificial neural network approach, and (3) we demonstrate a method of incorporating optimization constraints for individualized patient-centered medicine and shared decision making. However, more research into its clinical use is needed. These promising results show the feasibility of using machine learning and big data approaches to produce personalized healthcare treatment plans and support the precision-health agenda.

Prokaryote autoimmunity in the context of self-targeting by CRISPR-Cas systems.

Prokaryote adaptive immunity (CRISPR-Cas systems) can be a threat to its carriers. We analyze the risks of autoimmune reactions related to adaptive immunity in prokaryotes by computational methods. We found important differences between bacteria and archaea with respect to autoimmunity potential. According to the results of our analysis, CRISPR-Cas systems in bacteria are more prone to self-targeting even though they possess fewer spacers per organism on average than archaea. The results of our study provide opportunities to use self-targeting in prokaryotes for biological and medical applications.

A Population-Based Study of Simvastatin Drug-Drug Interactions in Cardiovascular Disease Patients.

Simvastatin is a commonly used medication for lipid management and cardiovascular disease, however, the risk of adverse events (AEs) with its use increases via drug-drug interaction (DDI) exposures. Patients were extracted if initially diagnosed with cardiovascular disease and newly initiated simvastatin therapy. The cohort was divided into a DDI-exposed group and a non-DDI exposed group. The DDI-exposed group was further divided into gemfibrozil, clarithromycin, and erythromycin exposure groups. The outcome was defined as a composite of predefined AEs. Our results show that the simvastatin-DDI group had a higher illness burden with longer simvastatin exposure time and more medical care follow-up compared with the simvastatin-non-DDI exposed group. AEs occurred more frequently in subjects exposed to interacting drugs with a higher risk for clarithromycin and erythromycin exposed subjects than for gemfibrozil subjects.

Personalized long-term prediction of cognitive function: Using sequential assessments to improve model performance.

Prediction of onset and progression of cognitive decline and dementia is important both for understanding the underlying disease processes and for planning health care for populations at risk. Predictors identified in research studies are typically accessed at one point in time. In this manuscript, we argue that an accurate model for predicting cognitive status over relatively long periods requires inclusion of time-varying components that are sequentially assessed at multiple time points (e.g., in multiple follow-up visits). We developed a pilot model to test the feasibility of using either estimated or observed risk factors to predict cognitive status. We developed two models, the first using a sequential estimation of risk factors originally obtained from 8 years prior, then improved by optimization. This model can predict how cognition will change over relatively long time periods. The second model uses observed rather than estimated time-varying risk factors and, as expected, results in better prediction. This model can predict when newly observed data are acquired in a follow-up visit. Performances of both models that are evaluated in10-fold cross-validation and various patient subgroups show supporting evidence for these pilot models. Each model consists of multiple base prediction units (BPUs), which were trained using the same set of data. The difference in usage and function between the two models is the source of input data: either estimated or observed data. In the next step of model refinement, we plan to integrate the two types of data together to flexibly predict dementia status and changes over time, when some time-varying predictors are measured only once and others are measured repeatedly. Computationally, both data provide upper and lower bounds for predictive performance.