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Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.

Foreign language teachers’ recognition of their identity is essential to their professional development. Drawing on bicultural theories, this study investigated two American teachers who recounted ...

L’abolition de l’Apartheid en Afrique du Sud marque une victoire importante pour les idées démocratiques et pacifiques. Cette passation politique est l’aboutissement de plus de dix ans de mobilisation populaire contre les classifications dites chromatiques: « black », « white », « colored ». Aujourd’hui il subsiste une zone d’ombre sur ces forces antiapartheid. Quel fut le rôle des personnes classées « white » ? Ce livre décrit les trajectoires de trois associations: Black Sash, End Conscription Campaign, Five freedoms Forum. De plus, sont examinées les importantes contributions apportées par les historiens et les artistes. Enfin, l’analyse des symboles d’unité nationale permet de comprendre comment a pu naître une nouvelle identité sud-africaine.

The current study investigated the effect of percep-tual training on the production of English tense-lax vowels by native Chinese speakers. 16-session phonetic category identification training was conducted, and the tokens from 10 English tense-lax vowels produced by Chinese speakers were recorded before and after training. A series of acoustic measures and analyses demonstrated that there was no significant formant quality change for the Chinese speakers after training, and the formant trajectories of individual vowels did not become more native-like either. Although small changes in vowel duration were found after training, the conclusion that training generally had limited effects on Chinese speakers’ vowel production was clear.

Purpose: Radiation risk communication is a critical component of radiation protection and the public’s understanding of radiation risks and benefits. Risk communication becomes even more complicated when considering cultural and language differences. In the US, many diverse communities face risk communication challenges. We obtained radon testing data to evaluate patterns of radon testing in Allentown, the third largest city in Pennsylvania. Radon exposure is the second leading cause of lung cancer after smoking and is associated with over 21,000 lung cancer deaths in the US annually. It is estimated that 1 in every 15 homes in the US has elevated radon levels above the recommended action level set by the US Environmental Protection Agency. Allentown has some of the highest reported levels of indoor radon in the country, yet only a small portion of the population has tested their homes. This is true particularly among self-identified Hispanics, who make up nearly half of the city’s population. This study seeks to (1) characterize the difference in testing rates between self-identified Hispanics and non-Hispanics in Allentown, (2) quantify the level of radon awareness and knowledge, (3) identify potential obstacles to radon testing among the Allentown population that self-identifies as Hispanic, and (4) determine whether more effective risk communication is needed. Method: Radon test results in Allentown were analyzed to better understand the nature of radon testing. To evaluate radon awareness and knowledge, a cross-sectional study was conducted using a face-to-face survey. This data was informative in assessing testing and mitigation practices, ethnicity, income level, age, education level, homeowner status, zip code and primary language. Results: Ethnicity was an independent predictor of radon awareness and knowledge. Statistically significant differences were found between the number of self-identified Hispanics (39%) and non-Hispanics (84%) who indicated that they had ever heard of radon; 13% of Hispanics and 49% of non-Hispanics knew that they lived in an area with typically high radon levels. There was a statistically significant association between self-reported ethnicity and radon testing with non-Hispanics (43%) more likely to test their homes for radon than Hispanics (32%). Conclusion: Individual and community understanding of the risks of exposure to radiation sources such as radon is dependent upon communication that informs and spurs appropriate action. This study demonstrates the need for culturally appropriate radon risk communication strategies targeted to a Hispanic population. Successful communication will raise awareness and knowledge that can lead to better public health protection.

We report the results of an international external quality assessment (EQA) program to assess the performance of laboratories in genotyping Legionella pneumophila isolates using the standard European Working Group for Legionella Infections sequence-based typing protocol. Three coded distributions of L. pneumophila isolates were sent to laboratories in 12, 14, and 20 countries, respectively. The data were returned by 11 of 16, 18 of 19, and 27 of 29 centers, respectively. Incomplete submission of data resulted in exclusion from certain aspects of the analyses. The number of centers achieving 100% score, for all loci tested, rose successively from 50% (5 of 10) for the first EQA distribution, to 56% (9 of 16) for the second EQA distribution, to 76% (19 of 25) for the third EQA distribution. A number of additional centers made only a few errors (one to three) in each distribution. Sequence data from the first two distributions were collected in flat text file format and using specially developed software, the sequence quality tool (SQT), in the third distribution. The SQT allows users to upload trace files in standard file formats, automates basecalling using phred and phrap software, contig assembly, trimming, and matching against a reference library. The program described here allow users an independent measure of sequence quality, and such schemes are vital in order to identify strengths and weakness in centers responsible for the generation of genotyping data in legionella outbreak investigation. The present study demonstrates that DNA sequence data can be highly reproducible but, when independently assessed, in practice frequently falls short of this goal. However, experience and training in the methodology results in increased performance.

Assessment of the sequence quality is a skilled task and can often be very subjective. Therefore, the primary aim of the study described in this paper was to develop novel web-based tools to facilitate: (i) database curation, designation of novel allele types, and allelic profiles; (ii) automated quality assessment of sequence chromatograms. The outcome of the study is an online tool, which is now accessible via the European Working Group for Legionella infections website to allow users to assemble sequence traces (from the sequence-based typing (SBT) scheme) and to identify matching preexisting alleles. Most SBT types are derived from at least two sequences, typically one forward and one reverse sequence. Extensive sequence analysis and manipulation of the sequences and assembled contig is carried out using the BioPerl toolkit of objects. The processes involved include quality-trimming, assessment of the proportion of the contig that is double-stranded, and consensus generation. Data analysis from multicenter proficiency SBT analysis has confirmed that misidentification readily occurs when poor-quality trace files are used. This online tool will help systemically check sequence quality and will assist in the determination of minimum standards for a range of sequence quality parameters, ensuring that only high-quality data is accepted for allele and profile identification.

This chapter investigates the feasibility of providing a dedicated database allowing the online identification of putative Legionella spp. following standard PCR amplification and sequencing using a previously published identification scheme for Legionella. A standard PCR and sequencing protocol based on a previously published sequence-based identification scheme was used to generate a DNA sequence from the macrophage infectivity potentiator gene (mip). Identification of user-generated sequences was performed using tools showing: (i) an alignment of all the sequences from the reference alignment, top five database matches, and the user sequence; (ii) a neighbor-joining tree of the alignment, including the reference species, five closest matches from the database, and the user sequence; and (iii) an alignment of the eight sequences from the combined alignment that are most similar to the user sequence together with percentage similarity scores. It is anticipated that additional genes, including those coding for 16S rRNA, RpoB, and RnpB, will be added to the current identification system to aid in the characterization and identification of known and potential novel members of this genus.

The main reason for typing Legionella pneumophila is to help identify environmental sources giving rise to cases of legionellosis, thus allowing control measures to be implemented and further cases to be prevented in a timely manner. Monoclonal antibody (mAB) subgrouping is probably the most rapid and reliable phenotypic method available and is excellent for initial screening of isolates. Only a few of the many genotypic methods described have been shown to meet these exacting requirements. Of these, pulsed-field gel electrophoresis is the most widely applied, but others have also been used. For example, a restriction-fragment length polymorphism (RFLP) typing method was used as the standard method in the United Kingdom for almost 20 years. Investigation of travel-associated legionellosis requires even more rigorously standardized systems, as not only must the types be clearly defined but they also must be recognizable and reproducible in laboratories in different countries (different laboratories, different times). The standardized sequence-based typing (SBT) method targets part of six genes (flaA, pilE, asd, mip, mompS, proA), each of which shows considerable allelic variation, thus providing an extremely discriminatory typing system. Furthermore, of the seven major-outbreak-associated strains for which SBT data are available, five are SBT 3,4,1,1,14,9. However, if substantiated, these observations have important and widespread implications for our understanding of the epidemiology of legionellosis and for the monitoring and control of L. pneumophila in the built environment.

This paper describes the use of a Nexys2 board in a Digital Logic Design course to create three brain teaser games as students' final project to enhance their interest, motivation and academic abilities. The integration of these games into our Digital Logic Design course will take place in Fall 2011 semester.

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