Separating DNA with different topologies by atomic force microscopy in comparison with gel electrophoresis.

Atomic force microscopy, which is normally used for DNA imaging to gain qualitative results, can also be used for quantitative DNA research, at a single-molecular level. Here, we evaluate the performance of AFM imaging specifically for quantifying supercoiled and relaxed plasmid DNA fractions within a mixture, and compare the results with the bulk material analysis method, gel electrophoresis. The advantages and shortcomings of both methods are discussed in detail. Gel electrophoresis is a quick and well-established quantification method. However, it requires a large amount of DNA, and needs to be carefully calibrated for even slightly different experimental conditions for accurate quantification. AFM imaging is accurate, in that single DNA molecules in different conformations can be seen and counted. When used carefully with necessary correction, both methods provide consistent results. Thus, AFM imaging can be used for DNA quantification, as an alternative to gel electrophoresis.

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.

BACKGROUND: There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently expensive that cost effective alternatives are important. RESULTS: Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants, and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40% of exonic variants identified by whole genome sequencing were captured using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data, especially at higher levels of coverage. CONCLUSIONS: We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels.

Improving supply chain performance: Real-time demand information and flexible deliveries

In some supply chains, materials are ordered periodically according to local information. This paper investigates how to improve the performance of such a supply chain. Specifically, we consider a serial inventory system in which each stage implements a local reorder interval policy; i.e., each stage orders up to a local basestock level according to a fixed-interval schedule. A fixed cost is incurred for placing an order. Two improvement strategies are considered: (1) expanding the information flow by acquiring real-time demand information and (2) accelerating the material flow via flexible deliveries. The first strategy leads to a reorder interval policy with full information; the second strategy leads to a reorder point policy with local information. Both policies have been studied in the literature. Thus, to assess the benefit of these strategies, we analyze the local reorder interval policy. We develop a bottom-up recursion to evaluate the system cost and provide a method to obtain the optimal policy. A numerical study shows the following: Increasing the flexibility of deliveries lowers costs more than does expanding information flow; the fixed order costs and the system lead times are key drivers that determine the effectiveness of these improvement strategies. In addition, we find that using optimal batch sizes in the reorder point policy and demand rate to infer reorder intervals may lead to significant cost inefficiency. © 2010 INFORMS.

Comparison of dynamic balance in adolescent male soccer players from rwanda and the United States.

PURPOSE/BACKGROUND: Dynamic balance is an important component of motor skill development. Poor dynamic balance has previously been associated with sport related injury. However, the vast majority of dynamic balance studies as they relate to sport injury have occurred in developed North American or European countries. Thus, the purpose of this study was to compare dynamic balance in adolescent male soccer players from Rwanda to a matched group from the United States. METHODS: Twenty-six adolescent male soccer players from Rwanda and 26 age- and gender-matched control subjects from the United States were screened using the Lower Quarter Y Balance Test during their pre-participation physical. Reach asymmetry (cm) between limbs was examined for all reach directions. In addition, reach distance in each direction (normalized to limb length, %LL) and the composite reach score (also normalized to %LL) were examined. Dependent samples t-tests were performed with significant differences identified at p<0.05. RESULTS: Twenty-six male soccer players from Rwanda (R) were matched to twenty-six male soccer players from the United States (US). The Rwandan soccer players performed better in the anterior (R: 83.9 ± 3.2 %LL; US: 76.5 ± 6.6 %LL, p<0.01), posterolateral (R: 114.4 ± 8.3 %LL ; US: 106.5 ± 8.2 %LL, p<0.01) and composite (R: 105.6 ± 1.3 %LL; US: 97.8 ± 6.2 %LL, p<0.01) reach scores. No significant differences between groups were observed for reach asymmetry. CONCLUSIONS: Adolescent soccer players from Rwanda exhibit superior performance on a standardized dynamic balance test as comparison to similar athletes from the United States. The examination of movement abilities of athletes from countries of various origins may allow for a greater understanding of the range of true normative values for dynamic balance. LEVELS OF EVIDENCE: 3b.

A COMPARISON OF MARKET CLEARING TOOLS IN ELECTRICITY SYSTEMS

To maintain a strict balance between demand and supply in the US power systems, the Independent System Operators (ISOs) schedule power plants and determine electricity prices using a market clearing model. This model determines for each time period and power plant, the times of startup, shutdown, the amount of power production, and the provisioning of spinning and non-spinning power generation reserves, etc. Such a deterministic optimization model takes as input the characteristics of all the generating units such as their power generation installed capacity, ramp rates, minimum up and down time requirements, and marginal costs for production, as well as the forecast of intermittent energy such as wind and solar, along with the minimum reserve requirement of the whole system. This reserve requirement is determined based on the likelihood of outages on the supply side and on the levels of error forecasts in demand and intermittent generation. With increased installed capacity of intermittent renewable energy, determining the appropriate level of reserve requirements has become harder. Stochastic market clearing models have been proposed as an alternative to deterministic market clearing models. Rather than using a fixed reserve targets as an input, stochastic market clearing models take different scenarios of wind power into consideration and determine reserves schedule as output. Using a scaled version of the power generation system of PJM, a regional transmission organization (RTO) that coordinates the movement of wholesale electricity in all or parts of 13 states and the District of Columbia, and wind scenarios generated from BPA (Bonneville Power Administration) data, this paper explores a comparison of the performance between a stochastic and deterministic model in market clearing. The two models are compared in their ability to contribute to the affordability, reliability and sustainability of the electricity system, measured in terms of total operational costs, load shedding and air emissions. The process of building the models and running for tests indicate that a fair comparison is difficult to obtain due to the multi-dimensional performance metrics considered here, and the difficulty in setting up the parameters of the models in a way that does not advantage or disadvantage one modeling framework. Along these lines, this study explores the effect that model assumptions such as reserve requirements, value of lost load (VOLL) and wind spillage costs have on the comparison of the performance of stochastic vs deterministic market clearing models.

A comparison of the effectiveness of the team-based learning readiness assessments completed at home to those completed in class.

PURPOSE: The readiness assurance process (RAP) of team-based learning (TBL) is an important element that ensures that students come prepared to learn. However, the RAP can use a significant amount of class time which could otherwise be used for application exercises. The authors administered the TBL-associated RAP in class or individual readiness assurance tests (iRATs) at home to compare medical student performance and learning preference for physiology content. METHODS: Using cross-over study design, the first year medical student TBL teams were divided into two groups. One group was administered iRATs and group readiness assurance tests (gRATs) consisting of physiology questions during scheduled class time. The other group was administered the same iRAT questions at home, and did not complete a gRAT. To compare effectiveness of the two administration methods, both groups completed the same 12-question physiology assessment during dedicated class time. Four weeks later, the entire process was repeated, with each group administered the RAP using the opposite method. RESULTS: The performance on the physiology assessment after at-home administration of the iRAT was equivalent to performance after traditional in-class administration of the RAP. In addition, a majority of students preferred the at-home method of administration and reported that the at-home method was more effective in helping them learn course content. CONCLUSION: The at-home administration of the iRAT proved effective. The at-home administration method is a promising alternative to conventional iRATs and gRATs with the goal of preserving valuable in-class time for TBL application exercises.

Pyramid Multi-resolution Scanning for Two-sample Comparison

Testing for two-sample differences is challenging when the differences are local and only involve a small portion of the data. To solve this problem, we apply a multi- resolution scanning framework that performs dependent local tests on subsets of the sample space. We use a nested dyadic partition of the sample space to get a collection of windows and test for sample differences within each window. We put a joint prior on the states of local hypotheses that allows both vertical and horizontal message passing among the partition tree to reflect the spatial dependency features among windows. This information passing framework is critical to detect local sample differences. We use both the loopy belief propagation algorithm and MCMC to get the posterior null probability on each window. These probabilities are then used to report sample differences based on decision procedures. Simulation studies are conducted to illustrate the performance. Multiple testing adjustment and convergence of the algorithms are also discussed.