ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

Computing Variances from Data with Complex Sampling Designs: A Comparison of Stata and SPSS

Most of the data sets available through the National Center for Education Statistics (NCES) are based on complex sampling designs involving multi-stage sampling, stratification, and clustering. These complex designs require appropriate statistical techniques to calculate the variance. Stata employs specialized methods that appropriately adjust for the complex designs, while SPSS does not. Researchers using SPSS must obtain the design effects through NCES and adjust the standard errors generated by SPSS with these values. This presentation addresses the pros and cons of recommending Stata or SPSS to novice researchers. The first presenter teaches research methods to doctoral students and uses Stata to conduct research with NCES data. She uses SPSS to teach her research methods course, due to its user-friendly interface. The second presenter is a doctoral student conducting dissertation research with NCES data. In his professional life as an institutional researcher, he uses SPSS. NCES data sets are a rich resource, but the complex sampling designs create conceptual issues beyond the immediate grasp of most doctoral candidates in the field. The session considers and invites comment on the best approaches to introducing new researchers to complex sampling designs in order to enable them to use NCES data.

Targeting delivery in Parkinson's disease

Disease-modifying therapies for Parkinson's disease (PD), with the potential to halt the neurodegenerative process and to stimulate the protection, repair, and regeneration of dopaminergic neurons, remain a vital but unmet clinical need. Targeting the delivery of current and new therapeutics directly to the diseased brain region (in particular the nigrostriatal pathway) could result in greater improvements in the motor functions that characterise PD. Here, we highlight some of the opportunities and challenges facing the development of the next generation of therapies for patients with PD

Healing the health care system: Summaries from the Department of Health Policy Summer Seminar

Editorial Introduction: The disease management field continues to evolve. The range of chronic diseases treated has expanded to include such conditions as obesity and pain management, and the care continuum now encompasses wellness, prevention, and population health. One population that is an ideal candidate for our collective efforts is that of older adults. Global and national population projections reveal the impending staggering increase in the age 65+ cohort, which will cause a sharp increase in the demand for health care and other services due to such age-related issues as multiple chronic conditions, falls, and depression. To begin to address these issues, the Department of Health Policy at Jefferson Medical College devoted its annual Summer Seminar to providing a forum for collaborative discussion focusing on the needs of the aging population. Two of the presentations focused on Pennsylvania, although the demographics presented by Nora Dowd Eisenhower reflect national and global trends, and the recently passed legislation outlined by Rosemarie Greco can be used as a yardstick against which other states can judge their own progress. Dr Susan Reinhard\u27s presentation keys in on the need for expansion of scope of practice and consumer-oriented care. Our keynote speaker, Dr Robert Butler, details the challenging issues we must face and resolve in order to cope with the impending crisis. And finally, a panel, comprising representatives from payor, practitioner, and consumer groups, offer their candid, unscripted reactions to the presentations in a segment titled Bridging the Gap Between the Vision and Implementation. Summaries of these presentations follow. I hope that you will invest your time in reviewing these materials, and begin to think about the significant role that disease management can play in reforming the health care system to meet the needs of the older adult population. I am, as always, interested in your feedback. You can reach me via email at [email protected]

Cathodoluminescence as a method of extracting detailed information from nanophotonics systems: a study of silicon nanocrystals

We investigated Si nanocaystal samples produced by high dose 600 keV Si+ implantation of fused silica and annealing using cathodoluminescence (CL). CL spectra collected under 5-25 keV electron irradiation show similar features to reported photoluminescenc

Strategies to control the spectral properties of Au-Ni thin films

Gold and nickel have quite different dielectric functions. Here we use a combination of calculation and sample manufacture to assess two strategies by which thin films of these elements can be produced with a controlled range of far-field optical properties. In the first approach, control can be achieved by manipulating the density of states of metastable solid solutions, which in turn controls the dielectric function. In the second approach the optical properties of the films are controlled by varying the geometry of stacks fabricated from the constituent elements. We show that the two approaches can produce equivalent results so both are viable options in practice. Modeling is used to reveal how the structure controls the optical properties and to map out the possible color gamut. Predictions are tested with thin film samples fabricated by magnetron sputtering. © 2013 Elsevier B.V

A preliminary assessment into the utility of social networks for engaging local communities in climate adaptation policy: working paper prepared for NSW Office of Environment & Heritage, Sydney, Australia.

There has been a growing recognition regarding the use of social networks to engage the community in government actions. However, despite increasing awareness about the potential importance of social networks, there is very limited evidence for their application in relation to climate policy. This study addresses this gap by assessing the potential of social networks for engaging local communities in climate adaptation policy, drawing on a case study of the Shoalhaven region in Australia. View/download https://www.uts.edu.au/sites/default/files/Cunninghametal2014utilityofsocialnetworks.pd

FishFace: interactive atlas of zebrafish craniofacial development at cellular resolution

Background: The vertebrate craniofacial skeleton may exhibit anatomical complexity and diversity, but its genesis and evolution can be understood through careful dissection of developmental programs at cellular resolution. Resources are lacking that include introductory overviews of skeletal anatomy coupled with descriptions of craniofacial development at cellular resolution. In addition to providing analytical guidelines for other studies, such an atlas would suggest cellular mechanisms underlying development. Description We present the Fish Face Atlas, an online, 3D-interactive atlas of craniofacial development in the zebrafish Danio rerio. Alizarin red-stained skulls scanned by fluorescent optical projection tomography and segmented into individual elements provide a resource for understanding the 3D structure of the zebrafish craniofacial skeleton. These data provide the user an anatomical entry point to confocal images of Alizarin red-stained zebrafish with transgenically-labelled pharyngeal arch ectomesenchyme, chondrocytes, and osteoblasts, which illustrate the appearance, morphogenesis, and growth of the mandibular and hyoid cartilages and bones, as viewed in live, anesthetized zebrafish during embryonic and larval development. Confocal image stacks at high magnification during the same stages provide cellular detail and suggest developmental and evolutionary hypotheses. Conclusion: The FishFace Atlas is a novel learning tool for understanding craniofacial skeletal development, and can serve as a reference for a variety of studies, including comparative and mutational analyses

The effect of a 24-hour photoperiod on the survival, growth and swim bladder inflation of pre-flexion yellowfin tuna (Thunnus albacares) larvae

The effects of two different continuous photoperiod regimes on survival, growth and swim bladder inflation of pre-flexion yellowfin tuna (Thunnus albacares) larvae were investigated. Each photoperiod regime was tested twice with a different larval cohort to confirm the observed results. Trials 1 and 2 tested the effect of a reduced night-time light intensity (10-molesm-2s-1=30% of the daytime intensity) and found that those larvae reared for 8days under the 24h lighting (24-L) photoperiod exhibited a slight improvement in survival compared to those reared under the control photoperiod of 12h light (12-L), however these improvements were not significant. In addition, those larvae reared under this photoperiod regime were equal in length to those in the control. Trials 3 and 4 compared the same variables in larvae reared under a continuous photoperiod (24-L) with a constant light intensity of 30-molesm-2s-1, against those reared under the aforementioned 12-L photoperiod. Survival of larvae under the continuous photoperiods were 9±1% (n=2) and 10±2% (n=3) for Trials 3 and 4, respectively, compared to less than 1% in both control treatments; differences that in both cases were highly significant. In addition, in both trials larvae cultured under the 24-L photoperiod were significantly larger and exhibited more advanced development than those reared under the 12-L photoperiod, however swim bladder inflation was significantly lower. We suggest that the improved survival and growth achieved under a continuous photoperiod is due to the extended foraging time combined with the prevention of mortality caused by night-time sinking

Confucian Principles: A Study of Chinese Americans’ Interpersonal Relationships in Selected Children’s Picturebooks

[[abstract]]There has not been enough critical analysis of children’s literature by and about Chinese Americans, especially when compared to other minority groups in the United States. In particular, Chinese American historical books lack extensive analysis. It is important to reflect cultural accuracy in literature and to help children develop clear concepts of self and others by providing precise cultural and physical characteristics of people. While cultural authenticity allows children the opportunity to see a reflection of real experiences within a book instead of seeing stereotypes or misrepresentations, obtaining correct information about a certain time period can help children to see images of immigration accurately represented in literature. Using the Confucian delineation of interpersonal relationships as the major criterion of cultural authenticity, this article examines three currently available children’s picturebooks set in the historical period between 1848 and 1885. In addition to exploring how Chinese Americans’ interpersonal relationships are portrayed in these children’s historical books, this article argues for more proactive inclusion of the diversity in selection of picturebooks.[[notice]]補正完