MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling

Background Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm. Results After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively. Conclusions MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base

She Said, She Said: Differential Interpersonal Similarities Predict Unique Linguistic Mimicry in Online Word of Mouth

This research examines the antecedents, causes, and consequences of linguistic mimicry, which assesses how closely individuals match others’ word use, in online WOM. We examine mimicry of both linguistic style (how things are said) and content (what is said). To our knowledge, this research provides the first demonstration of unique linguistic mimicry, where consumers engaging in online WOM differentially mimic other posters’ word use. Two experiments and one study using field data show that when consumers are personally similar to an individual who has previously posted (e.g., same gender), they mimic this individual’s positive emotion and social word use. When consumers are similar in status to an individual who has previously posted (e.g., same forum ranking), they mimic this individual’s cognitive and descriptive word use. This differential mimicry is driven by affiliation versus achievement goals, respectively, and affects consumers’ engagement in online WOM in terms of posting incidence and volume

Archaeogenetic evidence of ancient Nubian barley evolution from six to two-row indicates local adaptation

Background Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. Methodology and Findings We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. Conclusions The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures

Wave Speed Propagation Measurements on Highly Attenuative Wax at Elevated Temperatures

Ultrasonic stress wave amplitude and time-of-flight values change drastically as a media is heated. The measurement of relatively small variations in velocity and material attenuation can detect and quantify significant variations within a material microstructure. This paper discusses experimental setups, ultrasonic wave speed tracking methods and signal analysis algorithms that document the changes within highly attenuative wax material as it is either being heated or cooled from 25˚C to 90˚C. The experimental set-up utilizes ultrasonic probes in a pulse-echo and through-transmission configuration. The ultrasonic waveforms are recorded and analyzed during long duration thermal experiments. To complement the ultrasonic data, a Discontinuous-Galerkin Model (DGM) was also created which uses unstructured meshes to determine how waves travel in these anisotropic media. This numerical method solves particle motion travel using partial differential equations and outputs a wave trace per unit time. Both experimental and analytical data is compared and presented. Finally, the paper describes a series of additional experiments that are currently under investigation which will aid code development to adjust for density variations

Finding Latent Groups in Observed Data: A Primer on Latent Profile Analysis in Mplus for Applied Researchers

The present guide provides a practical guide to conducting latent profile analysis (LPA) in the Mplus software system. This guide is intended for researchers familiar with some latent variable modeling but not LPA specifically. A general procedure for conducting LPA is provided in six steps: (a) data inspection, (b) iterative evaluation of models, (c) model fit and interpretability, (d) investigation of patterns of profiles in a retained model, (e) covariate analysis, and (f) presentation of results. A worked example is provided with syntax and results to exemplify the steps

Effects of Community Exercise Therapy on Metabolic, Brain, Physical, and Cognitive Function Following Stroke : A Randomized Controlled Pilot Trial

© The Author(s) 2014.Peer reviewedPostprintPostprin

Codesigned Shared Decision-Making Diabetes Management Plan Tool for Adolescents With Type 1 Diabetes Mellitus and Their Parents: Prototype Development and Pilot Test

Background: Adolescents with type 1 diabetes mellitus have difficulty achieving optimal glycemic control, partly due to competing priorities that interfere with diabetes self-care. Often, significant diabetes-related family conflict occurs, and adolescents’ thoughts and feelings about diabetes management may be disregarded. Patient-centered diabetes outcomes may be better when adolescents feel engaged in the decision-making process. Objective: The objective of our study was to codesign a clinic intervention using shared decision making for addressing diabetes self-care with an adolescent patient and parent advisory board. Methods: The patient and parent advisory board consisted of 6 adolescents (teens) between the ages 12 and 18 years with type 1 diabetes mellitus and their parents recruited through our institution’s Pediatric Diabetes Program. Teens and parents provided informed consent and participated in 1 or both of 2 patient and parent advisory board sessions, lasting 3 to 4 hours each. Session 1 topics were (1) patient-centered outcomes related to quality of life, parent-teen shared diabetes management, and shared family experiences; and (2) implementation and acceptability of a patient-centered diabetes care plan intervention where shared decision making was used. We analyzed audio recordings, notes, and other materials to identify and extract ideas relevant to the development of a patient-centered diabetes management plan. These data were visually coded into similar themes. We used the information to develop a prototype for a diabetes management plan tool that we pilot tested during session 2. Results: Session 1 identified 6 principal patient-centered quality-of-life measurement domains: stress, fear and worry, mealtime struggles, assumptions and judgments, feeling abnormal, and conflict. We determined 2 objectives to be principally important for a diabetes management plan intervention: (1) focusing the intervention on diabetes distress and conflict resolution strategies, and (2) working toward a verbalized common goal. In session 2, we created the diabetes management plan tool according to these findings and will use it in a clinical trial with the aim of assisting with patient-centered goal setting. Conclusions: Patients with type 1 diabetes mellitus can be effectively engaged and involved in patient-centered research design. Teens with type 1 diabetes mellitus prioritize reducing family conflict and fitting into their social milieu over health outcomes at this time in their lives. It is important to acknowledge this when designing interventions to improve health outcomes in teens with type 1 diabetes mellitus

Exercise Induces Peripheral Muscle But Not Cardiac Adaptations After Stroke: A Randomized Controlled Pilot Trial

Objective To explore the physiological factors affecting exercise-induced changes in peak oxygen consumption and function poststroke. Design Single-center, single-blind, randomized controlled pilot trial. Setting Community stroke services. Participants Adults (N=40; age>50y; independent with/without stick) with stroke (diagnosed >6mo previously) were recruited from 117 eligible participants. Twenty participants were randomized to the intervention group and 20 to the control group. No dropouts or adverse events were reported. Interventions Intervention group: 19-week (3times/wk) progressive mixed (aerobic/strength/balance/flexibility) community group exercise program. Control group: Matched duration home stretching program. Main Outcome Measures (1) Pre- and postintervention: maximal cardiopulmonary exercise testing with noninvasive (bioreactance) cardiac output measurements; and (2) functional outcome measures: 6-minute walk test; timed Up and Go test, and Berg Balance Scale. Results Exercise improved peak oxygen consumption (18±5 to 21±5mL/(kg⋅min); P<.01) and peak arterial-venous oxygen difference (9.2±2.7 to 11.4±2.9mL of O2/100mL of blood; P<.01), but did not alter cardiac output (17.2±4 to 17.7±4.2L/min; P=.44) or cardiac power output (4.8±1.3 to 5.0±1.35W; P=.45). A significant relation existed between change in peak oxygen consumption and change in peak arterial-venous oxygen difference (r=.507; P<.05), but not with cardiac output. Change in peak oxygen consumption did not strongly correlate with change in function. Conclusions Exercise induced peripheral muscle, but not cardiac output, adaptations after stroke. Implications for stroke clinical care should be explored further in a broader cohort