Simulation assisted machine learning

Motivation: In a predictive modeling setting, if sufficient details of the system behavior are known, one can build and use a simulation for making predictions. When sufficient system details are not known, one typically turns to machine learning, which builds a black-box model of the system using a large dataset of input sample features and outputs. We consider a setting which is between these two extremes: some details of the system mechanics are known but not enough for creating simulations that can be used to make high quality predictions. In this context we propose using approximate simulations to build a kernel for use in kernelized machine learning methods, such as support vector machines. The results of multiple simulations (under various uncertainty scenarios) are used to compute similarity measures between every pair of samples: sample pairs are given a high similarity score if they behave similarly under a wide range of simulation parameters. These similarity values, rather than the original high dimensional feature data, are used to build the kernel. Results: We demonstrate and explore the simulation based kernel (SimKern) concept using four synthetic complex systems--three biologically inspired models and one network flow optimization model. We show that, when the number of training samples is small compared to the number of features, the SimKern approach dominates over no-prior-knowledge methods. This approach should be applicable in all disciplines where predictive models are sought and informative yet approximate simulations are available. Availability: The Python SimKern software, the demonstration models (in MATLAB, R), and the datasets are available at https://github.com/davidcraft/SimKern.Comment: This manuscript has been accepted for publication in Bioinformatics published by Oxford University Press: https://doi.org/10.1093/bioinformatics/btz199 (open access). Timo M. Deist and Andrew Patti contributed equally to this wor

Endo-Porter–Mediated Delivery of Phosphorodiamidate Morpholino Oligos (PMOs) in Erythrocyte Suspension Cultures from Cope\u27s Gray Treefrog Hyla Chrysoscelis

Cope\u27s gray treefrog, Hyla chrysoscelis, is a freeze-tolerant anuran that accumulates cryoprotective glycerol during cold acclimation. H. chrysoscelis erythrocytes express the aquaglyceroporin HC-3, which facilitates transmembrane glycerol and water movement. Aquaglyceroporins have no pharmacological inhibitors, and no genetic knockout tools currently exist for H. chrysoscelis. A phosphorodiamidate morpholino oligo (PMO)–mediated expression knockdown approach was therefore pursued to provide a model for testing the role of HC-3. We describe a novel procedure optimized for specific, efficient knockdown of HC-3 expression in amphibian erythrocyte suspensions cultured at nonmammalian physiological temperatures using Endo-Porter. Our protocol includes three critical components: pre-incubation at 37°C, two rounds of Endo-Porter and HC-3 PMO administration at ~23°C, and continuous shaking at 190 rpm. This combination of steps resulted in 94% reduction in HC-3 protein expression (Western blot), substantial decrease in HC-3 expression in \u3e65% of erythrocytes, and no detectable expression in an additional 30% of cells (immunocytochemistry)

Recommendations for Care of the Asymptomatic Patient

We present a set of reasonable guidelines for the care of healthy, asymptomatic individuals based upon recommendations prepared by an Internal Medicine review committee of Henry Ford Hospital. There recommendations have four goals: to prevent disease, to detect disease in an asymptomatic and potentially curable state, to enhance the patient\u27s quality of life, and to help physicians teach patients good health habits. Recommendations are made for infectious diseases, cancer, metabolic diseases, neurosensory conditions like visual and hearing loss, and general health habits. Some recommendations are at variance with those of well recognized authorities and should be viewed only as a suggested protocol for the care of the asymptomatic patient. Results of ongoing studies may alter our understanding of some areas of controversy and mandate revision of these guidelines periodically

Cannabinoids, cannabis, and cannabis-based medicines for pain management: an overview of systematic reviews

Cannabinoids, cannabis, and cannabis-based medicines (CBM) are increasingly used to manage pain, with limited understanding of their efficacy and safety. We assessed methodological quality, scope, and results of systematic reviews of randomised controlled trials of these treatments. Several search strategies sought self-declared systematic reviews. Methodological quality was assessed using both AMSTAR-2 and techniques important for bias reduction in pain studies. Of the 106 articles read, 57 were self-declared systematic reviews, most published since 2010. They included any type of cannabinoid, cannabis, or CBM, at any dose, however administered, in a broad range of pain conditions. No review examined the effects of a particular cannabinoid, at a particular dose, using a particular route of administration, for a particular pain condition, reporting a particular analgesic outcome. Confidence in the results in the systematic reviews using AMSTAR-2 definitions was critically low (41), low (8), moderate (6), or high (2). Few used criteria important for bias reduction in pain. Cochrane reviews typically provided higher confidence; all industry-conflicted reviews provided critically low confidence. Meta-analyses typically pooled widely disparate studies, and, where assessable, were subject to potential publication bias. Systematic reviews with positive or negative recommendation for use of cannabinoids, cannabis, or CBM in pain typically rated critically low or low (24/25 [96%] positive; 10/12 [83%] negative). Current reviews are mostly lacking in quality and cannot provide a basis for decision-making. A new high-quality systematic review of randomised controlled trials is needed to critically assess the clinical evidence for cannabinoids, cannabis, or CBM in pain

Cannabinoids, cannabis and cannabis-based medicine for pain management: a systematic review of randomised controlled trials

ABSTRACT: Cannabinoids, cannabis, and cannabis-based medicines (CBMs) are increasingly used to manage pain, with limited understanding of their efficacy and safety. We summarised efficacy and adverse events (AEs) of these types of drugs for treating pain using randomised controlled trials: in people of any age, with any type of pain, and for any treatment duration. Primary outcomes were 30% and 50% reduction in pain intensity, and AEs. We assessed risk of bias of included studies, and the overall quality of evidence using GRADE. Studies of &lt;7 and &gt;7 days treatment duration were analysed separately. We included 36 studies (7217 participants) delivering cannabinoids (8 studies), cannabis (6 studies), and CBM (22 studies); all had high and/or uncertain risk of bias. Evidence of benefit was found for cannabis &lt;7 days (risk difference 0.33, 95% confidence interval 0.20-0.46; 2 trials, 231 patients, very low-quality evidence) and nabiximols &gt;7 days (risk difference 0.06, 95% confidence interval 0.01-0.12; 6 trials, 1484 patients, very low-quality evidence). No other beneficial effects were found for other types of cannabinoids, cannabis, or CBM in our primary analyses; 81% of subgroup analyses were negative. Cannabis, nabiximols, and delta-9-tetrahydrocannabinol had more AEs than control. Studies in this field have unclear or high risk of bias, and outcomes had GRADE rating of low- or very low-quality evidence. We have little confidence in the estimates of effect. The evidence neither supports nor refutes claims of efficacy and safety for cannabinoids, cannabis, or CBM in the management of pain.</p

A grounded theory of psychological resilience in Olympic champions

Objective: Although it is well-established that the ability to manage stress is a prerequisite of sporting excellence, the construct of psychological resilience has yet to be systematically examined in athletic performers. The study reported here sought to explore and explain the relationship between psychological resilience and optimal sport performance. Design and Method: Twelve Olympic champions (8 men and 4 women) from a range of sports were interviewed regarding their experiences of withstanding pressure during their sporting careers. A grounded theory approach was employed throughout the data collection and analysis, and interview transcripts were analyzed using open, axial and selective coding. Methodological rigor was established by incorporating various verification strategies into the research process, and the resultant grounded theory was also judged using the quality criteria of fit, work, relevance, and modifiability. Results and Conclusions: Results indicate that numerous psychological factors (relating to a positive personality, motivation, confidence, focus, and perceived social support) protect the world’s best athletes from the potential negative effect of stressors by influencing their challenge appraisal and meta-cognitions. These processes promote facilitative responses that precede optimal sport performance. The emergent theory provides sport psychologists, coaches and national sport organizations with an understanding of the role of resilience in athletes’ lives and the attainment of optimal sport performance

It Takes Two

Theories of conflict emphasize dyadic interaction, yet existing empirical studies of civil war focus largely on state attributes and pay little attention to nonstate antagonists. We recast civil war in a dyadic perspective, and consider how nonstate actor attributes and their relationship to the state influence conflict dynamics. We argue that strong rebels, who pose a military challenge to the government, are likely to lead to short wars and concessions. Conflicts where rebels seem weak can become prolonged if rebels can operate in the periphery so as to defy a government victory yet are not strong enough to extract concessions. Conflicts should be shorter when potential insurgents can rely on alternative political means to violence. We examine these hypotheses in a dyadic analysis of civil war duration and outcomes, using new data on nonstate actors and conflict attributes, finding support for many of our conjectures. </jats:p

Pharmacological interventions for chronic pain in children:an overview of systematic reviews

We know little about the safety or efficacy of pharmacological medicines for children and adolescents with chronic pain, despite their common use. Our aim was to conduct an overview review of systematic reviews of pharmacological interventions that purport to reduce pain in children with chronic noncancer pain (CNCP) or chronic cancer-related pain (CCRP). We searched the Cochrane Database of Systematic Reviews, Medline, EMBASE, and DARE for systematic reviews from inception to March 2018. We conducted reference and citation searches of included reviews. We included children (0-18 years of age) with CNCP or CCRP. We extracted the review characteristics and primary outcomes of ≥30% participant-reported pain relief and patient global impression of change. We sifted 704 abstracts and included 23 systematic reviews investigating children with CNCP or CCRP. Seven of those 23 reviews included 6 trials that involved children with CNCP. There were no randomised controlled trials in reviews relating to reducing pain in CCRP. We were unable to combine data in a meta-analysis. Overall, the quality of evidence was very low, and we have very little confidence in the effect estimates. The state of evidence of randomized controlled trials in this field is poor; we have no evidence from randomised controlled trials for pharmacological interventions in children with cancer-related pain, yet cannot deny individual children access to potential pain relief. Prospero ID: CRD42018086900.</p

Comparative functional analysis of aquaporins/glyceroporins in mammals and anurans

Maintenance of fluid homeostasis is critical to establishing and maintaining normal physiology. The landmark discovery of membrane water channels (aquaporins; AQPs) ushered in a new area in osmoregulatory biology that has drawn from and contributed to diverse branches of biology, from molecular biology and genomics to systems biology and evolution, and from microbial and plant biology to animal and translational physiology. As a result, the study of AQPs provides a unique and integrated backdrop for exploring the relationships between genes and genome systems, the regulation of gene expression, and the physiologic consequences of genetic variation. The wide species distribution of AQP family members and the evolutionary conservation of the family indicate that the control of membrane water flux is a critical biological process. AQP function and regulation is proving to be central to many of the pathways involved in individual physiologic systems in both mammals and anurans. In mammals, AQPs are essential to normal secretory and absorptive functions of the eye, lung, salivary gland, sweat glands, gastrointestinal tract, and kidney. In urinary, respiratory, and gastrointestinal systems, AQPs are required for proper urine concentration, fluid reabsorption, and glandular secretions. In anurans, AQPs are important in mediating physiologic responses to changes in the external environment, including those that occur during metamorphosis and adaptation from an aquatic to terrestrial environment and thermal acclimation in anticipation of freezing. Therefore, an understanding of AQP function and regulation is an important aspect of an integrated approach to basic biological research