A robust method for estimating gene expression states using Affymetrix microarray probe level data

<p>Abstract</p> <p>Background</p> <p>Microarray technology is a high-throughput method for measuring the expression levels of thousand of genes simultaneously. The observed intensities combine a non-specific binding, which is a major disadvantage with microarray data. The Affymetrix GeneChip assigned a mismatch (MM) probe with the intention of measuring non-specific binding, but various opinions exist regarding usefulness of MM measures. It should be noted that not all observed intensities are associated with expressed genes and many of those are associated with unexpressed genes, of which measured values express mere noise due to non-specific binding, cross-hybridization, or stray signals. The implicit assumption that all genes are expressed leads to poor performance of microarray data analyses. We assume two functional states of a gene - expressed or unexpressed - and propose a robust method to estimate gene expression states using an order relationship between PM and MM measures.</p> <p>Results</p> <p>An indicator 'probability of a gene being expressed' was obtained using the number of probe pairs within a probe set where the PM measure exceeds the MM measure. We examined the validity of the proposed indicator using Human Genome U95 data sets provided by Affymetrix. The usefulness of 'probability of a gene being expressed' is illustrated through an exploration of candidate genes involved in neuroblastoma prognosis. We identified the candidate genes for which expression states differed (un-expressed or expressed) when compared between two outcomes. The validity of this result was subsequently confirmed by quantitative RT-PCR.</p> <p>Conclusion</p> <p>The proposed qualitative evaluation, 'probability of a gene being expressed', is a useful indicator for improving microarray data analysis. It is useful to reduce the number of false discoveries. Expression states - expressed or unexpressed - correspond to the most fundamental gene function 'On' and 'Off', which can lead to biologically meaningful results.</p

マンセイ シッカン デ セイシン ショウジョウ オ テイスル カンジャ エノ チイキ セイシンカ イリョウ モデル ジギョウ オヨビ ソノ ヒョウカ : セイシン カンゴ センモン カンゴフ ト リエゾン チーム ノ ヤクワリ

The purpose of this study was to show the effectiveness of psychiatric liaison consultation team for the people with chronic illness in the general hospital. Psychiatric liaison consultation team was constructed by certified nurse specialist (CNS), psychiatrist, clinical psychologist, nurse and social worker. Case manager was CNS and team intervened to the patients according to the standard of intervention by team. Intervention had been implemented by CNS mainly. Thirty one patients who consented to this study were intervened by CNS and team between July of 2007 and Feb.2008. They had chronic illness which was SLE, cancer and other physical illness without mental illness. BPRS, GAF, and LSP were written by CNS at the time of baseline before intervention and at the end time of intervention. Furthermore patients wrote CES-D and SF-36 by themselves at the baseline and the end point of intervention. Those questionnaires were returned by mail. CSQ was written by patients at the end of intervention. Thirty one patients had high depression score at the baseline and after intervention depressive state was improved. And they had lower SF-36 compared with that of the people who had chronic illness in another study. Furthermore they needed to be supported psychosocially by CNS to prevent worse their symptom. And they had psychosocial needs and those needs should be intervened by interdisciplinary team. In conclusion, the role of CNS and interdisciplinary team were discussed in order to meet the patients\u27 needs and to prevent worse their symptom in the general hospitals

Immunohistochemical Detection of Telomerase (hTERT) Protein in Human Cancer Tissues and a Subset of Cells in Normal Tissues

We examined human telomerase reverse transcriptase (hTERT) protein distribution by immunohistochemistry in cultured cells and tissue sections. Cells with telomerase activity had nuclear positive signals whereas cells without telomerase activity did not. In most normal epithelial tissues, hTERT expression was prominent in the early proliferative descendent progenitor cells. In cancers with high telomerase activity, hTERT expression was detected in almost all neoplastic cells and correlated with telomerase activity levels, whereas cancers with low telomerase activity had fewer hTERT-positive cancer cells. In pediatric neuroblastomas with a favorable outcome, both the percentage of positive cells and the signal intensity of each hTERT-expressing cell decreased. These studies indicate that detection of telomerase at the cellular level is achievable and may have utility in cancer diagnostics

Two Asymptomatic Cases with Sarcoidosis Demonstrated Sequential Evolution from Radiographic Stage I to III within Five Years

There are no guidelines regarding the treatment of pulmonary sarcoidosis. Generally, oral corticosteroids are considered the first-line treatment for symptomatic patients with pulmonary sarcoidosis. We report here two Japanese cases with pulmonary sarcoidosis who demonstrated sequential evolution from radiographic stage I to III within five years. Although these two cases had no symptoms, persistent, progressive pulmonary involvements were observed on chest X-ray. Considering the effectiveness of corticosteroids on patients with radiographic type II or III sarcoidosis reported by the British Thoracic Society, corticosteroid therapy might be a choice even in asymptomatic cases, if they demonstrate developing pulmonary involvement

Exploration of the genes responsible for unlimited proliferation of immortalized lung fibroblasts

Regulation mechanism of lung fibroblast proliferation remains unknown. To elucidate the key molecules in it, we here established mortal and immortal non-transformed lung fibroblast cell line/strains with elongated lifespan by telomerase reversetranscriptase gene transfection. Comparing the expression profiles of them, 51 genes were explored to be the candidates responsible for regulation of cellular proliferation of lung fibroblasts. This set of fibrobrast strains of same origin with different proliferative capacities may become useful model cells for research on lung fibroblast growth regulation and the candidate genes explored in this study may provide biomarkers or therapeutic targets of pulmonary fibrosis