FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification

Background: FCI is an R code for analyzing data from real-time PCR experiments. This algorithm estimates standard curve features as well as nucleic acid concentrations and confidence intervals according to Fieller's theorem. Results: In order to describe the features of FCI four situations were selected from real data collected during an international external quality assessment program for quantitative assays based on real-time PCR. The code generates a diagnostic figure suitable for assessing the quality of the quantification process. Conclusion: We have provided a freeware programme using this algorithm specifically designed to increase the information content of the real-time PCR assay. \ua9 2008 Verderio et al; licensee BioMed Central Ltd

The genetic aetiology of retinal degeneration in children in Finland – new founder mutations identified

Purpose To study the genetic aetiology and phenotypes of retinal degeneration (RD) in Finnish children born during 1993-2009. Methods Children with retinal degeneration (N = 68) were investigated during 2012-2014 with a targeted gene analysis or a next-generation sequencing (NGS) based gene panel. Also, a full clinical ophthalmological examination was performed. Results The cohort covered 44% (68/153) of the Finnish children with inherited RD born 1993-2009. X-linked retinoschisis, retinitis pigmentosa, Leber congenital amaurosis and cone-rod dystrophy were the most common clinical diagnoses in the study group. Pathogenic mutations were found in 17 retinal genes. The molecular genetic aetiology was identified in 77% of the patients (in 77% of the families) analysed by NGS method. Several founder mutations were detected including three novel founder mutations c.148delG in TULP1, c.2314C>R (p.Gln772Ter) in RPGRIP1 and c.533G>A (Trp178Ter) in TYR. We also confirmed the previous tentative finding of c.2944 + 1delG in GYCU2D being the most frequent cause of Leber congenital amaurosis (LCA) in Finland. Conclusions Globally, RD is genetically heterogeneous with over 260 disease genes reported so far. This was shown not to be the case in Finland, where the genetic aetiology of RD is caused by a small group of genes, due to several founder mutations that are enriched in the population. We found that X-chromosomal retinoschisis constitutes the major group in Finnish paediatric RD population and is almost exclusively caused by two founder mutations. Several other founder mutations were detected including three novel founder mutations. All in all, the genetic aetiology of 77% of families was identified which is higher than previously reported from other populations, likely due to the specific genomic constitution of the Finns.Peer reviewe

A survey of the trajectories conceptual framework: investigating theory use in HCI

We present a case study of how Human-Computer Interaction (HCI) theory is reused within the field. We analyze the HCI literature in order to reveal the impact of one particular theory, the trajectories framework that has been cited as an example of both contemporary HCI theory and a strong concept that sits between theory and design practice. Our analysis of 60 papers that seriously engaged with trajectories reveals the purposes that the framework served and which parts of it they used. We compare our findings to the originally stated goals of trajectories and to subsequent claims of its status as both theory and strong concept. The results shed new light on what we mean by theory in HCI, including its relationship to practice and to other disciplines

Methodologic European External Quality Assurance for DNA Sequencing: The EQUALseq Program

Abstract Background: DNA sequencing is a key technique in molecular diagnostics, but to date no comprehensive methodologic external quality assessment (EQA) programs have been instituted. Between 2003 and 2005, the European Union funded, as specific support actions, the EQUAL initiative to develop methodologic EQA schemes for genotyping (EQUALqual), quantitative PCR (EQUALquant), and sequencing (EQUALseq). Here we report on the results of the EQUALseq program. Methods: The participating laboratories received a 4-sample set comprising 2 DNA plasmids, a PCR product, and a finished sequencing reaction to be analyzed. Data and information from detailed questionnaires were uploaded online and evaluated by use of a scoring system for technical skills and proficiency of data interpretation. Results: Sixty laboratories from 21 European countries registered, and 43 participants (72%) returned data and samples. Capillary electrophoresis was the predominant platform (n = 39; 91%). The median contiguous correct sequence stretch was 527 nucleotides with considerable variation in quality of both primary data and data evaluation. The association between laboratory performance and the number of sequencing assays/year was statistically significant (P <0.05). Interestingly, more than 30% of participants neither added comments to their data nor made efforts to identify the gene sequences or mutational positions. Conclusions: Considerable variations exist even in a highly standardized methodology such as DNA sequencing. Methodologic EQAs are appropriate tools to uncover strengths and weaknesses in both technique and proficiency, and our results emphasize the need for mandatory EQAs. The results of EQUALseq should help improve the overall quality of molecular genetics findings obtained by DNA sequencing

Why computational models are better than verbal theories: the case of nonword repetition

Tests of nonword repetition (NWR) have often been used to examine children’s phonological knowledge and word learning abilities. However, theories of NWR primarily explain performance either in terms of phonological working memory or long-term knowledge, with little consideration of how these processes interact. One theoretical account that focuses specifically on the interaction between short-term and long-term memory is the chunking hypothesis. Chunking occurs because of repeated exposure to meaningful stimulus items, resulting in the items becoming grouped (or chunked); once chunked, the items can be represented in short-term memory using one chunk rather than one chunk per item. We tested several predictions of the chunking hypothesis by presenting 5-6 year-old children with three tests of NWR that were either high, medium, or low in wordlikeness. The results did not show strong support for the chunking hypothesis, suggesting that chunking fails to fully explain children’s NWR behavior. However, simulations using a computational implementation of chunking (namely CLASSIC, or Chunking Lexical And Sublexical Sequences In Children) show that, when the linguistic input to 5-6 year old children is estimated in a reasonable way, the children’s data is matched across all three NWR tests. These results have three implications for the field: (a) a chunking account can explain key NWR phenomena in 5-6 year old children; (b) tests of chunking accounts require a detailed specification both of the chunking mechanism itself and of the input on which the chunking mechanism operates; and (c) verbal theories emphasizing the role of long-term knowledge (such as chunking) are not precise enough to make detailed predictions about experimental data, but computational implementations of the theories can bridge the gap

Do natural enemies really make a difference?:field scale impacts of parasitoid wasps and hoverfly larvae on cereal aphid populations

1. Naturally occurring predators and parasitoids are known to reduce the abundance of pest invertebrates in arable crops, yet current treatment thresholds do not account for this contribution to pest management. 2. Here, we provide evidence for the presence of natural enemies correlating with a subsequent reduction in pest population growth. 3. The abundance of cereal aphid pests and two key aphidophagous natural enemies, parasitoid wasps (Aphidiinae) and hoverfly larvae (Syrphinae) were assessed at field boundaries and interiors in southeast England. 4. The highest rate of aphid population growth was associated with locations where no natural enemies were found. The presence of either Aphidiinae wasps or predatory Syrphinae larvae was associated with a reduction in the rate of aphid population growth irrespective of location within the field, and overall aphid population growth was negatively correlated with increasing natural enemy abundance. 5. This work indicates that natural enemies contribute significantly to pest control, and provides further evidence in support of using management strategies to promote their occurrence in agro-ecosystems. 6. Aphid predators and parasitoids make an important contribution to aphid pest control within cereal fields, and thresholds for insecticide application should account for this to avoid unnecessary treatments

Do Pareto-Zipf and Gibrat laws hold true? An analysis with European Firms

By employing exhaustive lists of large firms in European countries, we show that the upper-tail of the distribution of firm size can be fitted with a power-law (Pareto-Zipf law), and that in this region the growth rate of each firm is independent of the firm's size (Gibrat's law of proportionate effect). We also find that detailed balance holds in the large-size region for periods we investigated; the empirical probability for a firm to change its size from a value to another is statistically the same as that for its reverse process. We prove several relationships among Pareto-Zipf's law, Gibrat's law and the condition of detailed balance. As a consequence, we show that the distribution of growth rate possesses a non-trivial relation between the positive side of the distribution and the negative side, through the value of Pareto index, as is confirmed empirically

Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases.

BACKGROUND: Diagnostic use of gene panel next-generation sequencing (NGS) techniques is commonplace for individuals with inherited retinal dystrophies (IRDs), a highly genetically heterogeneous group of disorders. However, these techniques have often failed to capture the complete spectrum of genomic variation causing IRD, including CNVs. This study assessed the applicability of introducing CNV surveillance into first-tier diagnostic gene panel NGS services for IRD. METHODS: Three read-depth algorithms were applied to gene panel NGS data sets for 550 referred individuals, and informatics strategies used for quality assurance and CNV filtering. CNV events were confirmed and reported to referring clinicians through an accredited diagnostic laboratory. RESULTS: We confirmed the presence of 33 deletions and 11 duplications, determining these findings to contribute to the confirmed or provisional molecular diagnosis of IRD for 25 individuals. We show that at least 7% of individuals referred for diagnostic testing for IRD have a CNV within genes relevant to their clinical diagnosis, and determined a positive predictive value of 79% for the employed CNV filtering techniques. CONCLUSION: Incorporation of CNV analysis increases diagnostic yield of gene panel NGS diagnostic tests for IRD, increases clarity in diagnostic reporting and expands the spectrum of known disease-causing mutations