An investigation into the effects of the feedback of knowledge of results on operator performance

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Principal Component Analysis of Results Obtained from Finite-Difference Time-Domain Algorithms

Finite-Differences Time-Domain (FDTD) algorithms are well established tools of computational electromagnetism. Because of their practical implementation as computer codes, they are affected by many numerical artefact and noise. In order to obtain better results we propose using Principal Component Analysis (PCA) based on multivariate statistical techniques. The PCA has been successfully used for the analysis of noise and spatial temporal structure in a sequence of images. It allows a straightforward discrimination between the numerical noise and the actual electromagnetic variables, and the quantitative estimation of their respective contributions. Besides, The GDTD results can be filtered to clean the effect of the noise. In this contribution we will show how the method can be applied to several FDTD simulations: the propagation of a pulse in vacuum, the analysis of two-dimensional photonic crystals. In this last case, PCA has revealed hidden electromagnetic structures related to actual modes of the photonic crystal.

High-speed label-free functional photoacoustic microscopy of mouse brain in action.

We present fast functional photoacoustic microscopy (PAM) for three-dimensional high-resolution, high-speed imaging of the mouse brain, complementary to other imaging modalities. We implemented a single-wavelength pulse-width-based method with a one-dimensional imaging rate of 100 kHz to image blood oxygenation with capillary-level resolution. We applied PAM to image the vascular morphology, blood oxygenation, blood flow and oxygen metabolism in both resting and stimulated states in the mouse brain.

Focused molecular analysis of small cell lung cancer: feasibility in routine clinical practice.

Background: There is an urgent need to identify molecular signatures in small cell lung cancer (SCLC) that may select patients who are likely to respond to molecularly targeted therapies. In this study, we investigate the feasibility of undertaking focused molecular analyses on routine diagnostic biopsies in patients with SCLC.

Methods: A series of histopathologically confirmed formalin-fixed, paraffin-embedded SCLC specimens were analysed for epidermal growth factor receptors (EGFR), KRAS, NRAS and BRAF mutations, ALK gene rearrangements and MET amplification. EGFR and KRAS mutation testing was evaluated using real time polymerase chain reaction (RT-PCR cobas®), BRAF and NRAS mutations using multiplex PCR and capillary electrophoresis-single strand conformation analysis, and ALK and MET aberrations with fluorescent in situ hybridization. All genetic aberrations detected were validated independently.

Results: A total of 105 patients diagnosed with SCLC between July 1990 and September 2006 were included. 60 (57 %) patients had suitable tumour tissue for molecular testing. 25 patients were successfully evaluated for all six pre-defined molecular aberrations. Eleven patients failed all molecular analysis. No mutations in EGFR, KRAS and NRAS were detected, and no ALK gene rearrangements or MET gene amplifications were identified. A V600E substitution in BRAF was detected in a Caucasian male smoker diagnosed with SCLC with squamoid and glandular features.

Conclusion: The paucity of patients with sufficient tumour tissue, quality of DNA extracted and low frequency of aberrations detected indicate that alternative molecular characterisation approaches are necessary, such as the use of circulating plasma DNA in patients with SCLC.

Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial.

AIMS: Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. METHODS: 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. RESULTS: Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p

A comparison of three methods for detecting KRAS mutations in formalin-fixed colorectal cancer specimens.

BACKGROUND: KRAS mutation testing is required to select patients with metastatic colorectal cancer (CRC) to receive anti-epidermal growth factor receptor antibodies, but the optimal KRAS mutation test method is uncertain. METHODS: We conducted a two-site comparison of two commercial KRAS mutation kits - the cobas KRAS Mutation Test and the Qiagen therascreen KRAS Kit - and Sanger sequencing. A panel of 120 CRC specimens was tested with all three methods. The agreement between the cobas test and each of the other methods was assessed. Specimens with discordant results were subjected to quantitative massively parallel pyrosequencing (MPP). DNA blends were tested to determine detection rates at 5% mutant alleles. RESULTS: Reproducibility of the cobas test between sites was 98%. Six mutations were detected by cobas that were not detected by Sanger, and five were confirmed by MPP. The cobas test detected eight mutations which were not detected by the therascreen test, and seven were confirmed by MPP. Detection rates with 5% mutant DNA blends were 100% for the cobas and therascreen tests and 19% for Sanger. CONCLUSION: The cobas test was reproducible between sites, and detected several mutations that were not detected by the therascreen test or Sanger. Sanger sequencing had poor sensitivity for low levels of mutation.

Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936.

In a European BIOMED-2 collaborative study, multiplex PCR assays have successfully been developed and standardized for the detection of clonally rearranged immunoglobulin (Ig) and T-cell receptor (TCR) genes and the chromosome aberrations t(11;14) and t(14;18). This has resulted in 107 different primers in only 18 multiplex PCR tubes: three VH-JH, two DH-JH, two Ig kappa (IGK), one Ig lambda (IGL), three TCR beta (TCRB), two TCR gamma (TCRG), one TCR delta (TCRD), three BCL1-Ig heavy chain (IGH), and one BCL2-IGH. The PCR products of Ig/TCR genes can be analyzed for clonality assessment by heteroduplex analysis or GeneScanning. The detection rate of clonal rearrangements using the BIOMED-2 primer sets is unprecedentedly high. This is mainly based on the complementarity of the various BIOMED-2 tubes. In particular, combined application of IGH (VH-JH and DH-JH) and IGK tubes can detect virtually all clonal B-cell proliferations, even in B-cell malignancies with high levels of somatic mutations. The contribution of IGL gene rearrangements seems limited. Combined usage of the TCRB and TCRG tubes detects virtually all clonal T-cell populations, whereas the TCRD tube has added value in case of TCRgammadelta(+) T-cell proliferations. The BIOMED-2 multiplex tubes can now be used for diagnostic clonality studies as well as for the identification of PCR targets suitable for the detection of minimal residual disease.

Gene scanning of VDJH-amplified segments is a clinically relevant technique to detect contaminating tumor cells in the apheresis products of multiple myeloma patients undergoing autologous peripheral blood stem cell transplantation.

Contaminating tumour cells in apheresis products have proved to influence the outcome of patients with multiple myeloma (MM) undergoing autologous stem cell transplantation (APBSCT). The gene scanning of clonally rearranged VDJ segments of the heavy chain immunoglobulin gene (VDJH) is a reproducible and easy to perform technique that can be optimised for clinical laboratories. We used it to analyse the aphereses of 27 MM patients undergoing APBSCT with clonally detectable VDJH segments, and 14 of them yielded monoclonal peaks in at least one apheresis product. The presence of positive results was not related to any pre-transplant characteristics, except the age at diagnosis (lower in patients with negative products, P = 0.04). Moreover, a better pre-transplant response trended to associate with a negative result (P = 0.069). Patients with clonally free products were more likely to obtain a better response to transplant (complete remission, 54% vs 28%; >90% reduction in the M-component, 93% vs 43% P = 0.028). In addition, patients transplanted with polyclonal products had longer progression-free survival, (39 vs 19 months, P = 0.037) and overall survival (81% vs 28% at 5 years, P = 0.045) than those transplanted with monoclonal apheresis. In summary, the gene scanning of apheresis products is a useful and clinically relevant technique in MM transplanted patients.

Measuring attachment to life in old age: the Portuguese version of the Positive Valuation of Life Scale (Positive VOL)

Purpose This study aims to present the psychometric properties of the Portuguese version of the Positive Valuation of Life Scale (Lawton et al. in J Aging Ment Healt 13:3–31, 2001). Method Sample included 207 community-dwelling elders (129 women; MAge = 77.2 years, SD = 7.5). The data collection included the translated and adapted Portuguese version of Positive Valuation of Life Scale, Life Satisfac- tion Index Z, Meaning in Life Questionnaire and Geriatric Depression Scale. Results From exploratory factor analysis, two factors emerged, existential beliefs and perceived control, ex- plaining 49 % of the total variance. Both factors were positively related with meaning in life and life satisfaction and negatively related with depression (p\0.05). The values obtained for internal consistency for the total scale and for each subscale were good (a [ 0.75). Conclusion The Portuguese version of Positive VOL Scale represents a reliable and valid measure to capture the subjective experience of attachment to one’s life. The two-factor structure is an update to Lawton’s previous work and in line with findings obtained in the USA (Dennis et al. in What is valuation of life for frail community-dwelling older adults: factor structure and criterion validity of the VOL, Thomas Jefferson University, Center for Applied Research on Aging and Health Research, 2005) and Japan (Nakagawa et al. in Shinrigaku Kenkyu 84:37–46, 2013). Future research is required to investigate VOL predictors and the potential changes toward the end of the life span.

The problem posed by exam choice on the comparability of results in the Finnish matriculation examination

The article focuses on the upper secondary matriculation examination in Finland as a school leaving and university entrance examination. The presented research addresses the question of whether increased choice of the subject-specific examinations has the potential to undermine the comparability of examination results and to direct students’ choices not only in the examination but already beforehand at school. The authors refer to Finland’s tradition of more than 160 years of a national examination connecting the academic track of upper secondary schools with universities. The authors explain the Finnish system by describing the adoption of a course-based (vs. class- or year-based) curriculum for the three-year upper secondary education and the subsequent reforms in the matriculation examination. This increases students’ choices considerably with regard to the subject-specific exams included in the examination (a minimum of four). As a result, high-achieving students compete against each other in the more demanding subjects while the less able share the same normal distribution of grades in the less demanding subjects. As a consequence, students tend to strategic exam-planning, which in turn affects their study choices at school, often to the detriment of the more demanding subjects and, subsequently, of students’ career opportunities, endangering the traditional national objective of an all-round pre-academic upper secondary education. This contribution provides an overview of Finnish upper secondary education and of the matriculation examination (cf. Klein, 2013) while studying three separate but related issues by using data from several years of Finnish matriculation results: the relation of the matriculation examination and the curriculum; the problems of comparability vis-à-vis university entry due to the increased choice within the examination; the relations between students’ examination choices and their course selection and achievement during upper secondary school. (DIPF/Orig.)

Estressores em Unidade de Terapia Intensiva: versão brasileira do The Environmental Stressor Questionnaire

Este estudo teve como objetivo realizar a adaptação cultural do The Environmental Stressor Questionnaire - (ESQ) para a língua portuguesa do Brasil e verificar sua confiabilidade e validade. Foram empregadas as etapas metodológicas recomendadas pela literatura para adaptação cultural. A versão brasileira do ESQ foi aplicada a 106 pacientes de Unidade de Terapia Intensiva (UTI) de dois hospitais, público e privado, do interior do Estado de São Paulo. A confiabilidade foi avaliada quanto à consistência interna e estabilidade (teste e reteste); a validade convergente foi verificada por meio da correlação entre o ESQ e questão genérica sobre estresse em UTI. A confiabilidade foi satisfatória com Alfa de Crombach=0,94 e Coeficiente de Correlação Intraclasse=0,861 (IC95% 0,723; 0,933). Constatou-se correlação entre o escore total do ESQ e a questão genérica sobre estresse (r=0,70), confirmando a validade convergente. A versão brasileira do ESQ mostrou-se uma ferramenta confiável e válida para avaliação de estressores em UTI.

QUADAS e STARD: avaliação da qualidade de estudos de acurácia de testes diagnósticos

OBJETIVO: Comparar duas abordagens baseadas em critérios do Quality Assessment of Diagnostic Accuracy Studies (QUADAS) e do Standards for Reporting Studies of Diagnostic Accuracy (STARD) na avaliação de qualidade de estudos de validação do teste rápido OptiMal®, para diagnóstico de malária. MÉTODOS: Foi realizada busca de artigos de validação do teste rápido na base bibliográfica Medline acessada pelo PubMed, no ano de 2007. Treze artigos foram recuperados na busca. Foram combinados 12 critérios do QUADAS e três do STARD para comparação com os critérios do QUADAS isoladamente. Foi considerado que artigos de regular a boa qualidade atenderiam pelo menos 50% dos critérios do QUADAS. RESULTADOS: Dos 13 artigos recuperados, 12 cumpriram pelo menos 50% dos critérios do QUADAS, e apenas dois atenderam à combinação dos critérios. Considerando-se a combinação dos dois critérios (> 6 QUADAS e > 3STARD), dois estudos (15,4%) apresentaram boa qualidade metodológica. A seleção de artigos usando a combinação proposta variou de dois a oito artigos, dependendo do número de itens considerados como ponto de corte. CONCLUSÕES: A combinação do QUADAS com o STARD tem o potencial de conferir maior rigor nas avaliações da qualidade de artigos publicados sobre validação de testes diagnósticos em malária, por incorporar a checagem de informações relevantes não alcançáveis pelo uso do QUADAS isoladamente.

Confiabilidade do questionário Lista de Atividades Físicas em crianças

OBJETIVO: Avaliar a confiabilidade do questionário Lista de Atividades Físicas em crianças. MÉTODOS: O estudo é parte da adaptação transcultural do questionário, realizado com 83 escolares de sete a dez anos, matriculados do segundo ao quinto ano do ensino fundamental da cidade de São Paulo, SP, em 2008. O questionário foi respondido pela criança por meio de entrevista individual, apresenta lista com 21 atividades físicas moderadas a vigorosas realizadas no dia anterior, é dividido em períodos (antes, durante e após a escola) e possui seção de avaliação da entrevista. O questionário permite quantificar: tempo em atividades físicas e sedentárias; e custos metabólicos total e ponderado. A confiabilidade foi avaliada comparando-se duas entrevistas realizadas com intervalo médio de três horas. Para a seção C (avaliação da entrevista), compararam-se dados da primeira entrevista e de um avaliador externo. Utilizaram-se a proposta de Bland & Altman e os coeficientes de correlação intraclasse e de correlação de concordância de Lin na avaliação da confiabilidade. RESULTADOS: Os limites inferiores dos coeficientes de correlação intraclasse para os desfechos analisados variaram de 0,84 a 0,96. A precisão e concordância variaram, respectivamente, de 0,83 a 0,97 e de 0,99 a 1. A reta estimada a partir de pares de valores obtidos nas duas aplicações para atividade física indica elevada precisão dos dados. O item da entrevista com pior resultado foi a habilidade em estimar tempo (regular em 27,7% das entrevistas). Os itens da seção C apresentaram coeficientes de correlação intraclasse entre 0,60 e 0,70, exceto o nível de cooperação (0,46). CONCLUSÕES: A Lista de Atividades Físicas apresenta alta confiabilidade para aferir atividade física e sedentária do dia anterior em crianças.