Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia

<p>Abstract</p> <p>Background</p> <p>Chronic lymphocytic leukemia (CLL) is the most common adult leukemia. It is a highly heterogeneous disease, and can be divided roughly into indolent and progressive stages based on classic clinical markers. Immunoglobin heavy chain variable region (IgV_H) mutational status was found to be associated with patient survival outcome, and biomarkers linked to the IgV_H status has been a focus in the CLL prognosis research field. However, biomarkers highly correlated with IgV_H mutational status which can accurately predict the survival outcome are yet to be discovered.</p> <p>Results</p> <p>In this paper, we investigate the use of gene co-expression network analysis to identify potential biomarkers for CLL. Specifically we focused on the co-expression network involving ZAP70, a well characterized biomarker for CLL. We selected 23 microarray datasets corresponding to multiple types of cancer from the Gene Expression Omnibus (GEO) and used the frequent network mining algorithm CODENSE to identify highly connected gene co-expression networks spanning the entire genome, then evaluated the genes in the co-expression network in which ZAP70 is involved. We then applied a set of feature selection methods to further select genes which are capable of predicting IgV_H mutation status from the ZAP70 co-expression network.</p> <p>Conclusions</p> <p>We have identified a set of genes that are potential CLL prognostic biomarkers IL2RB, CD8A, CD247, LAG3 and KLRK1, which can predict CLL patient IgV_H mutational status with high accuracies. Their prognostic capabilities were cross-validated by applying these biomarker candidates to classify patients into different outcome groups using a CLL microarray datasets with clinical information.</p

Validity of a self-administered food frequency questionnaire (FFQ) and its generalizability to the estimation of dietary folate intake in Japan

BACKGROUND: In an epidemiological study, it is essential to test the validity of the food frequency questionnaire (FFQ) for its ability to estimate dietary intake. The objectives of our study were to 1) validate a FFQ for estimating folate intake, and to identify the foods that contribute to inter-individual variation of folate intake in the Japanese population. METHODS: Validity of the FFQ was evaluated using 28-day weighed dietary records (DRs) as gold standard in the two groups independently. In the group for which the FFQ was developed, validity was evaluated by Spearman's correlation coefficients (CCs), and linear regression analysis was used to identify foods with large inter-individual variation. The cumulative mean intake of these foods was compared with total intake estimated by the DR. The external validity of the FFQ and intake from foods on the same list were evaluated in the other group to verify generalizability. Subjects were a subsample from the Japan Public Health Center-based prospective Study who volunteered to participate in the FFQ validation study. RESULTS: CCs for the internal validity of the FFQ were 0.49 for men and 0.29 and women, while CCs for external validity were 0.33 for men and 0.42 for women. CCs for cumulative folate intake from 33 foods selected by regression analysis were also applicable to an external population. CONCLUSION: Our FFQ was valid for and generalizable to the estimation of folate intake. Foods identified as predictors of inter-individual variation in folate intake were also generalizable in Japanese populations. The FFQ with 138 foods was valid for the estimation of folate intake, while that with 33 foods might be useful for estimating inter-individual variation and ranking of individual folate intake

Cerebral Bypass Surgery: Level of Evidence and Grade of Recommendation

BACKGROUND AND AIMS Cerebral bypasses are categorized according to function (flow augmentation or flow preservation) and to characteristics: direct, indirect or combined bypass, extra-to-intracranial or intra-to-intracranial bypass, and high-, moderate- or low-capacity bypass. We critically summarize the current state of evidence and grades of recommendation for cerebral bypass surgery. METHODS The current indications for cerebral bypass are discussed depending on the function of the bypass (flow preservation or augmentation) and analyzed according to level of evidence criteria. RESULTS Flow-preservation bypass plays an important role in managing complex intracranial aneurysms (level of evidence 4; grade of recommendation C). Flow-preservation bypass is currently only very rarely indicated in the treatment of cerebral tumors involving major cerebral arteries (level of evidence 5; grade of recommendation D). The trend has evolved in favor of partial resection and radiotherapy. To preserve the flow, the bypass is always a direct bypass.Flow-augmentation bypass is currently recommended for Moyamoya patients with ischemic symptoms and compromised hemodynamics (level of evidence 4; grade of recommendation C) and patients with hemorrhagic onset (level of evidence 1B; grade of recommendation A). Flow-augmentation bypass is currently not recommended for patients with recently symptomatic carotid artery occlusion, even in the setting of compromised cerebral hemodynamics (level of evidence 1A; grade of recommendation A), but may be considered in patients with hemodynamic failure and recurrent medically refractory symptoms as a final resort (level of evidence 5; grade of recommendation D). CONCLUSIONS The results of recent randomized clinical trials narrow the indication for cerebral bypass in the setting of ischemic cerebrovascular disease. However, cerebral bypass is still very useful for managing complex intracranial aneurysms (not amenable to selective clipping or endovascular therapies) and is the only treatment option for managing symptomatic patients with Moyamoya vasculopathy and impaired brain hemodynamics

Soybean Protein--Resume and Bibliography

Excerpts from the Introduction: Until recently in the United States, the primary interest in the soybean was directed to its use as a feedstuff, especially for stock and poultry. It was soon found that the oil extracted from the soybean possessed properties of value for industrial application. Consequently, the beans were processed by mechanical pressure or solvent extraction to remove the oil as completely as practical, and the meal was used as a protein concentrate in feeds. Within the past 5 years, however, the soybean acreage has steadily increased until now (1938) it approaches 7,000,000 acres which yield about 50,000,000 bushels. Certain industrial uses have been developed for the meal and protein extracted from the beans. In most cases these uses capitalize on the chemical characteristics of the protein and the relatively high percentage of protein found in soybean meal. In view of this interest it seems appropriate to review the literature on soybean protein with special emphasis on its industrial applications