simple version of megaprimer pcr for site directed mutagenesis

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In-situ monitoring of defects in extrusion-based bioprinting processes using visible light imaging

Tissue engineering techniques are central for the development of biomedical scaffolds, which are primarily employed in the biofabrication of various artificial human tissue and organ models. Bioprinting is a new technique of creating tissue constructs that can sustain cell proliferation. The development of printing techniques proceeds together with the development of the biomaterials to be printed, which is why studying the printability of these specific biomaterials must be explored. An appropriate hydrogel used as bioink should have numerous rheological, mechanical, and biological properties for producing appropriate tissue constructs. However, reaching the right trade-off between a desirable bioactivity and high printability is challenging, and despite numerous optimization studies for different materials, printing defects often occur during printing. Herein, methods are proposed to automatically identify these drifting processes in commonly used geometries and how they affected subsequent layers, as well as printing defects within each layer. Several structures were printed with standard commercial bioink as proof of concept. The constructs were analyzed using optical images from a coaxial camera. The images were then digitally processed to get geometrical data from which patterns of defectology to be monitored were derived. This automation should decrease the time in post-processing characterization of constructs and should provide a standardized tool to compare different bioinks

Data preparation and interannotator agreement: BioCreAtIvE Task 1B

<p>Abstract</p> <p>Background</p> <p>We prepared and evaluated training and test materials for an assessment of text mining methods in molecular biology. The goal of the assessment was to evaluate the ability of automated systems to generate a list of unique gene identifiers from PubMed abstracts for the three model organisms Fly, Mouse, and Yeast. This paper describes the preparation and evaluation of answer keys for training and testing. These consisted of lists of normalized gene names found in the abstracts, generated by adapting the gene list for the full journal articles found in the model organism databases. For the training dataset, the gene list was pruned automatically to remove gene names not found in the abstract; for the testing dataset, it was further refined by manual annotation by annotators provided with guidelines. A critical step in interpreting the results of an assessment is to evaluate the quality of the data preparation. We did this by careful assessment of interannotator agreement and the use of answer pooling of participant results to improve the quality of the final testing dataset.</p> <p>Results</p> <p>Interannotator analysis on a small dataset showed that our gene lists for Fly and Yeast were good (87% and 91% three-way agreement) but the Mouse gene list had many conflicts (mostly omissions), which resulted in errors (69% interannotator agreement). By comparing and pooling answers from the participant systems, we were able to add an additional check on the test data; this allowed us to find additional errors, especially in Mouse. This led to 1% change in the Yeast and Fly "gold standard" answer keys, but to an 8% change in the mouse answer key.</p> <p>Conclusion</p> <p>We found that clear annotation guidelines are important, along with careful interannotator experiments, to validate the generated gene lists. Also, abstracts alone are a poor resource for identifying genes in paper, containing only a fraction of genes mentioned in the full text (25% for Fly, 36% for Mouse). We found that there are intrinsic differences between the model organism databases related to the number of synonymous terms and also to curation criteria. Finally, we found that answer pooling was much faster and allowed us to identify more conflicting genes than interannotator analysis.</p

new morphologic variants of the hand motor cortex as seen with mr imaging in a large study population

BACKGROUND AND PURPOSE: The hand motor cortex (HMC) has been classically described as having an omega or epsilon shape in axial-plane images obtained with CT and MR imaging. The aim of this study was to use MR imaging and Talairach normalization in a large sample population that was homogeneous for age and handedness to evaluate in a sex model a new classification with 5 morphologic variants of the HMC in the axial plane (omega, medially asymmetric epsilon, epsilon, laterally asymmetric epsilon, and null). MATERIALS AND METHODS: Structural brain MR images were obtained from 257 right-handed healthy subjects (143 men and 114 women; mean age, 23.1 ± 1.1 years) via a Talairach space transformed 3D magnetization-prepared rapid acquisition of gradient echo sequence. The frequencies of the different HMC variants were reported for hemisphere and sex. RESULTS: The new variants of the HMC (medially asymmetric epsilon, laterally asymmetric epsilon, and null) were observed in 2.9%, 7.0%, and 1.8% of the hemispheres, respectively. Statistically significant sex differences were observed: The epsilon variant was twice as frequent in men, and an interhemispheric concordance for morphologic variants was observed only for women. CONCLUSION: The large study population permitted the description of a new morphologic classification that included 3 new variants of the HMC. This new morphologic classification should facilitate the identification of the precentral gyrus in subsequent studies and in everyday practice

From Profile to Surface Monitoring: SPC for Cylindrical Surfaces Via Gaussian Processes

Quality of machined products is often related to the shapes of surfaces that are constrained by geometric tolerances. In this case, statistical quality monitoring should be used to quickly detect unwanted deviations from the nominal pattern. The majority of the literature has focused on statistical profile monitoring, while there is little research on surface monitoring. This paper faces the challenging task of moving from profile to surface monitoring. To this aim, different parametric approaches and control-charting procedures are presented and compared with reference to a real case study dealing with cylindrical surfaces obtained by lathe turning. In particular, a novel method presented in this paper consists of modeling the manufactured surface via Gaussian processes models and monitoring the deviations of the actual surface from the target pattern estimated in phase I. Regardless of the specific case study in this paper, the proposed approach is general and can be extended to deal with different kinds of surfaces or profiles

Improving blood pressure control through pharmacist interventions: a meta-analysis of randomized controlled trials.

BACKGROUND: Control of blood pressure (BP) remains a major challenge in primary care. Innovative interventions to improve BP control are therefore needed. By updating and combining data from 2 previous systematic reviews, we assess the effect of pharmacist interventions on BP and identify potential determinants of heterogeneity. METHODS AND RESULTS: Randomized controlled trials (RCTs) assessing the effect of pharmacist interventions on BP among outpatients with or without diabetes were identified from MEDLINE, EMBASE, CINAHL, and CENTRAL databases. Weighted mean differences in BP were estimated using random effect models. Prediction intervals (PI) were computed to better express uncertainties in the effect estimates. Thirty-nine RCTs were included with 14 224 patients. Pharmacist interventions mainly included patient education, feedback to physician, and medication management. Compared with usual care, pharmacist interventions showed greater reduction in systolic BP (-7.6 mm Hg, 95% CI: -9.0 to -6.3; I(2)=67%) and diastolic BP (-3.9 mm Hg, 95% CI: -5.1 to -2.8; I(2)=83%). The 95% PI ranged from -13.9 to -1.4 mm Hg for systolic BP and from -9.9 to +2.0 mm Hg for diastolic BP. The effect tended to be larger if the intervention was led by the pharmacist and was done at least monthly. CONCLUSIONS: Pharmacist interventions - alone or in collaboration with other healthcare professionals - improved BP management. Nevertheless, pharmacist interventions had differential effects on BP, from very large to modest or no effect; and determinants of heterogeneity could not be identified. Determining the most efficient, cost-effective, and least time-consuming intervention should be addressed with further research

Dietary fat differentially modulate the mRNA expression levels of oxidative mitochondrial genes in skeletal muscle of healthy subjects.

Background and aims: Different types of dietary fats exert differential effects on glucose and lipid metabolism. Our aim was to evaluate the impact of different dietary fats on the expression of skeletal muscle genes regulating mitochondrial replication and function in healthy subjects. Methods and results: Ten healthy subjects (age 29±3 years; BMI 25.0±3kg/m2) received in a random order a test meal with the same energy content but different composition in macronutrients and quality of fat: Mediterranean (MED) meal, SAFA meal (Lipid 66%, saturated 36%) and MUFA meal (Lipid 63%, monounsaturated 37%). At fast and after 180min, a fine needle aspiration was performed from the vastus lateralis for determination of mitochondrial gene expression by quantitative PCR. No difference in glucose and triglyceride response was observed between the three meals, while NEFA levels were significantly higher following fat-rich meals compared to MED meal (p<0.002-0.0001). MED meal was associated with an increased expression, albeit not statistically significant, of some genes regulating both replication and function. Following MUFA meal, a significant increase in the expression of PGC1β (p=0.02) and a reduction in the transcription factor PPARδ (p=0.006) occurred with no change in the expression of COX and GLUT4 genes. In contrast, SAFA meal was associated with a marked reduction in the expression of COX (p<0.001) PFK (p<0.003), LPL (p=0.002) and GLUT4 (p=0.009) genes. Conclusion: Dietary fats differentially modulate gene transcriptional profile since saturated, but not monounsaturated fat, downregulate the expression of genes regulating muscle glucose transport and oxidation

The genetic architecture of divergence between threespine stickleback species.

The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago. Here we use this map to analyse the genetic basis of recently evolved changes in skeletal armour and feeding morphologies seen in the benthic and limnetic stickleback species from Priest Lake, British Columbia. Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification during vertebrate evolution

Linear frictional forces cause orbits to neither circularize nor precess

For the undamped Kepler potential the lack of precession has historically been understood in terms of the Runge-Lenz symmetry. For the damped Kepler problem this result may be understood in terms of the generalization of Poisson structure to damped systems suggested recently by Tarasov[1]. In this generalized algebraic structure the orbit-averaged Runge-Lenz vector remains a constant in the linearly damped Kepler problem to leading order in the damping coeComment: 16 pages. 1 figure, Rewrite for resubmissio