CiteULike: jyuh's David

Data-driven smooth tests of the proportional hazards assumption

Kraus — 2007-03-13T02:54:58-00:00

Lifetime Data Analysis, Vol. 13, No. 1. (March 2007), pp. 1-16.

Diagnostic value of N-terminal pro-B-type natriuretic peptide (NT-proBNP) for left ventricular dysfunction in patients with chronic kidney disease stage 5 on haemodialysis.

S David — 2008-06-16T02:04:22-00:00

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association, Vol. 23, No. 4. (April 2008), pp. 1370-1377.

BACKGROUND: Natriuretic peptides such as N-terminal pro-B-type natriuretic peptide (NT-proBNP) have become increasingly important in diagnosing left ventricular dysfunction (LVD), however, in patients with chronic kidney disease (CKD), their use is confounded by concomitant volume overload and reduced renal excretion. We hypothesized that a serum NT-proBNP cut-off value adjusted for patients with CKD could serve as a biochemical marker to detect LVD in patients on haemodialysis treatment regardless of chronic fluid overload. METHODS: We assessed LV function using trans-thoracic echocardiography and indices of hydration status such as extracellular water (ECW) using bioelectrical impedance analysis (BIA) in 62 stable patients on maintenance haemodialysis. NT-proBNP cutoff values for LVD with different specificities and sensitivities were calculated by ROC curves. RESULTS: We found a significant inverse correlation between LV ejection fraction (EF) and NT-proBNP levels (r = -0.77, P < 0.0001). In the multivariate regression analysis NT-proBNP was the only independent predictor of EF (r = 0.699, P < 0.0001). NT-proBNP levels were significantly higher (P < 0.0001) in patients with LVD (n = 15; 32 760 +/- 6605 ng/L) compared to those without LVD (n = 47; 2835 +/- 428 ng/L). An NT-proBNP cut-off value of 7168 ng/L resulted in 90% specificity and 79% sensitivity for the presence of LVD, i.e. an EF <45% (AUC(ROC): 0.95 +/- 0.03, P < 0.0001). Furthermore, in patients with LVD we found a significant relationship between serum NT-proBNP and markers of fluid overload such as the ECW/body weight ratio (P < 0.0001) and the grade of peripheral oedema (P = 0.007), but not in patients without LVD. CONCLUSION: A serum NT-proBNP cut-off value of >/=7200 ng/L discriminates CKD stage 5 patients without LVD from those with LVD. In those patients with LVD, persistent post-dialytic volume overload correlates with elevated NT-proBNP levels.

Accounting for dropout bias using mixed-effects models.

CH Mallinckrodt — 2008-06-10T03:32:57-00:00

Journal of biopharmaceutical statistics, Vol. 11, No. 1-2. (y 2001), pp. 9-21.

Treatment effects are often evaluated by comparing change over time in outcome measures. However, valid analyses of longitudinal data can be problematic when subjects discontinue (dropout) prior to completing the study. This study assessed the merits of likelihood-based repeated measures analyses (MMRM) compared with fixed-effects analysis of variance where missing values were imputed using the last observation carried forward approach (LOCF) in accounting for dropout bias. Comparisons were made in simulated data and in data from a randomized clinical trial. Subject dropout was introduced in the simulated data to generate ignorable and nonignorable missingness. Estimates of treatment group differences in mean change from baseline to endpoint from MMRM were, on average, markedly closer to the true value than estimates from LOCF in every scenario simulated. Standard errors and confidence intervals from MMRM accurately reflected the uncertainty of the estimates, whereas standard errors and confidence intervals from LOCF underestimated uncertainty.

How to make clinical decisions from statistics

David — 2006-05-18T03:24:18-00:00

Clinical & Experimental Optometry, Vol. 89, No. 3. (May 2006), pp. 176-183.

Bayesian change-point analyses in ecology

Beckage — 2007-03-24T18:36:26-00:00

New Phytologist, Vol. 174, No. 2. (April 2007), pp. 456-467.

Comprehensive evaluation of the estrogen receptor gene reveals further evidence for association with type 2 diabetes enriched for nephropathy in an African American population

Keene — 2008-05-16T04:48:09-00:00

Human Genetics, Vol. 123, No. 4. (May 2008), pp. 333-341.

Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase.

YL Yip — 2008-05-10T09:00:00-00:00

Human mutation, Vol. 29, No. 3. (March 2008), pp. 361-366.

UniProtKB/Swiss-Prot (http://beta.uniprot.org/uniprot; last accessed: 19 October 2007) is a manually curated knowledgebase providing information on protein sequences and functional annotation. It is part of the Universal Protein Resource (UniProt). The knowledgebase currently records a total of 32,282 single amino acid polymorphisms (SAPs) touching 6,086 human proteins (Release 53.2, 26 June 2007). Nearly all SAPs are derived from literature reports using strict inclusion criteria. For each SAP, the knowledgebase provides, apart from the position of the mutation and the resulting change in amino acid, information on the effects of SAPs on protein structure and function, as well as their potential involvement in diseases. Presently, there are 16,043 disease-related SAPs, 14,266 polymorphisms, and 1,973 unclassified variants recorded in UniProtKB/Swiss-Prot. Relevant information on SAPs can be found in various sections of a UniProtKB/Swiss-Prot entry. In addition to these, cross-references to human disease databases as well as other gene-specific databases, are being added regularly. In 2003, the Swiss-Prot variant pages were created to provide a concise view of the information related to the SAPs recorded in the knowledgebase. When compared to the information on missense variants listed in other mutation databases, UniProtKB/Swiss-Prot further records information on direct protein sequencing and characterization including posttranslational modifications (PTMs). The direct links to the Online Mendelian Inheritance in Man (OMIM) database entries further enhance the integration of phenotype information with data at protein level. In this regard, SAP information in UniProtKB/Swiss-Prot complements nicely those existing in genomic and phenotypic databases, and is valuable for the understanding of SAPs and diseases.

A FrequencyConsequence-based Technique for Visualizing and Communicating Uncertainty and Perception of Risk

Slavin — 2008-05-03T22:15:41-00:00

Annals of the New York Academy of Sciences, Vol. 1128, No. 1. (April 2008), pp. 63-77.

Multivalent engagement of chromatin modifications by linked binding modules

Alexander Ruthenburg — 2007-11-26T16:26:10-00:00

Nat Rev Mol Cell Biol, Vol. 8, No. 12. (December 2007), pp. 983-994.

Production and certification of four frozen human serum certified reference materials containing creatinine and electrolytes

Barbagallo — 2008-03-04T16:00:22-00:00

Annals of Clinical Biochemistry, Vol. 45, No. 2. (March 2008), pp. 160-166.

Chemical approaches to mapping the function of post-translational modifications

Gamblin — 2008-04-23T05:03:53-00:00

FEBS Journal, Vol. 275, No. 9. (May 2008), pp. 1949-1959.

Accurate annotation of peptide modifications through unrestrictive database search.

S Tanner — 2008-04-26T15:12:50-00:00

Journal of proteome research, Vol. 7, No. 1. (January 2008), pp. 170-181.

Proteins are extensively modified after translation due to cellular regulation, signal transduction, or chemical damage. Peptide tandem mass spectrometry can discover post-translational modifications, as well as sequence polymorphisms. Recent efforts have studied modifications at the proteomic scale. In this context, it becomes crucial to assess the accuracy of modification discovery. We discuss methods to quantify the false discovery rate from a search and demonstrate how several features can be used to distinguish valid modifications from search artifacts. We present a tool, PTMFinder, which implements these methods. We summarize the corpus of post-translational modifications identified on large data sets. Thousands of known and novel modification sites are identified, including site-specific modifications conserved over vast evolutionary distances.

Molecular and cellular approaches for the detection of proteinprotein interactions: latest techniques and current limitations

Lalonde — 2008-02-08T00:50:26-00:00

The Plant Journal, Vol. 53, No. 4. (February 2008), pp. 610-635.

Role of urotensin II and its receptor in health and disease

Mcdonald — 2007-11-17T09:17:50-00:00

Journal of Anesthesia, Vol. 21, No. 3. (August 2007), pp. 378-389.

Use of factor analysis in Journal of Advanced Nursing: literature review

Watson — 2006-07-08T04:57:13-00:00

Journal of Advanced Nursing, Vol. 55, No. 3. (August 2006), pp. 330-341.

An angiotensin converting enzyme haplotype predicts survival in patients with end stage renal disease

Wetmore — 2006-10-05T20:22:53-00:00

Human Genetics, Vol. 120, No. 2. (September 2006), pp. 201-210.

Gprotein-coupled receptor-induced Akt activity in cellular proliferation and apoptosis

New — 2007-11-19T20:21:17-00:00

FEBS Journal, Vol. 274, No. 23. (December 2007), pp. 6025-6036.

Interferon modulation of cellular microRNAs as an antiviral mechanism

Irene Pedersen — 2007-10-19T05:10:19-00:00

Nature, Vol. 449, No. 7164., pp. 919-922.

Quality of reporting of experimental studies in medical education: a systematic review

Cook — 2007-07-29T11:55:58-00:00

Medical Education, Vol. 41, No. 8. (August 2007), pp. 737-745.

Recombinant protein production by large-scale transient gene expression in mammalian cells: state of the art and future perspectives

Baldi — 2007-05-17T17:12:34-00:00

Biotechnology Letters, Vol. 29, No. 5. (May 2007), pp. 677-684.

Fluorescent in situ hybridization on tissue microarrays: challenges and solutions

Brown — 2007-06-04T20:26:51-00:00

Journal of Molecular Histology, Vol. 38, No. 2. (May 2007), pp. 151-157.

The Role of Continuous Renal Replacement Therapy in the Treatment of Poisoning

Goodman — 2006-09-15T08:56:40-00:00

Seminars in Dialysis, Vol. 19, No. 5. (September 2006), pp. 402-407.

Phosphoinositide 3-kinase signalling in lung disease: leucocytes and beyond

Medina-Tato — 2007-07-06T05:14:28-00:00

Immunology, Vol. 121, No. 4. (August 2007), pp. 448-461.

Identifying genes for diabetic nephropathycurrent difficulties and future directions

Conway — 2006-10-17T10:32:47-00:00

Nephrology Dialysis Transplantation, Vol. 21, No. 11. (November 2006), pp. 3012-3017.

Fixed and Random Effects Selection in Linear and Logistic Models

Kinney — 2007-09-04T09:34:49-00:00

Biometrics, Vol. 63, No. 3. (September 2007), pp. 690-698.

Bayesian Covariance Selection in Generalized Linear Mixed Models

Cai — 2006-06-20T11:02:40-00:00

Biometrics, Vol. 62, No. 2. (June 2006), pp. 446-457.

Base-excision repair of oxidative DNA damage

Sheila David — 2007-06-21T10:52:28-00:00

Nature, Vol. 447, No. 7147. (21 June 2007), pp. 941-950.

Efficacy of lipid lowering drug treatment for diabetic and non-diabetic patients: meta-analysis of randomised controlled trials.

J Costa — 2006-06-15T19:12:58-00:00

BMJ, Vol. 332, No. 7550. (13 May 2006), pp. 1115-1124.

OBJECTIVE: To evaluate the clinical benefit of lipid lowering drug treatment in patients with and without diabetes mellitus, for primary and secondary prevention. DESIGN: Systematic review and meta-analysis. DATA SOURCES: Cochrane, Medline, Embase, and reference lists up to April 2004. STUDY SELECTION: Randomised, placebo controlled, double blind trials with a follow-up of at least three years that evaluated lipid lowering drug treatment in patients with and without diabetes mellitus. DATA EXTRACTION: Two independent reviewers extracted data. The primary outcome was major coronary events defined as coronary heart disease death, non-fatal myocardial infarction, or myocardial revascularisation procedures. RESULTS: Twelve studies were included. Lipid lowering drug treatment was found to be at least as effective in diabetic patients as in non-diabetic patients. In primary prevention, the risk reduction for major coronary events was 21% (95% confidence interval 11% to 30%; P < 0.0001) in diabetic patients and 23% (12% to 33%; P = 0.0003) in non-diabetic patients. In secondary prevention, the corresponding risk reductions were 21% (10% to 31%; P = 0.0005) and 23% (19% to 26%; P < or = 0.00001). However, the absolute risk difference was three times higher in secondary prevention. When results were adjusted for baseline risk, diabetic patients benefited more in both primary and secondary prevention. Blood lipids were reduced to a similar degree in both groups. CONCLUSIONS: The evidence that lipid lowering drug treatment (especially statins) significantly reduce cardiovascular risk in diabetic and non-diabetic patients is strong and suggests that diabetic patients benefit more, in both primary and secondary prevention. Future research should define the threshold for treatment of these patients and the desired target lipid concentrations, especially for primary prevention.

Distinct functions of junD in cardiac hypertrophy and heart failure.

R Ricci — 2007-09-21T08:54:39-00:00

Genes Dev, Vol. 19, No. 2. (15 January 2005), pp. 208-213.

Cardiac hypertrophic stimuli induce both adaptive and maladaptive growth response pathways in heart. Here we show that mice lacking junD develop less adaptive hypertrophy in heart after mechanical pressure overload, while cardiomyocyte-specific expression of junD in mice results in spontaneous ventricular dilation and decreased contractility. In contrast, fra-1 conditional knock-out mice have a normal hypertrophic response, whereas hearts from fra-1 transgenic mice decompensate prematurely. Moreover, fra-1 transgenic mice simultaneously lacking junD reveal a spontaneous dilated cardiomyopathy associated with increased cardiomyocyte apoptosis and a primary mitochondrial defect. These data suggest that junD promotes both adaptive-protective and maladaptive hypertrophy in heart, depending on its expression levels.

A Total Error Approach for the Validation of Quantitative Analytical Methods

Hoffman — 2007-07-07T06:53:47-00:00

Pharmaceutical Research, Vol. 24, No. 6. (June 2007), pp. 1157-1164.

The influence of a cooked-meat meal on estimated glomerular filtration rate

Preiss — 2007-01-22T14:27:35-00:00

Annals of Clinical Biochemistry, Vol. 44, No. 1. (January 2007), pp. 35-42.

Association of cystatin C and estimated GFR with inflammatory biomarkers: the Heart and Soul Study

Singh — 2007-03-31T18:59:00-00:00

Nephrology Dialysis Transplantation, Vol. 22, No. 4. (1 April 2007), pp. 1087-1092.

A versatile ligation-independent cloning method suitable for high-throughput expression screening applications

Berrow — 2007-04-29T12:52:44-00:00

Nucleic Acids Research, Vol. 35, No. 6. (March 2007), pp. e45-e45.

Statistics for proteomics: experimental design and 2-DE differential analysis.

JF Chich — 2007-07-11T06:52:56-00:00

J Chromatogr B Analyt Technol Biomed Life Sci, Vol. 849, No. 1-2. (15 April 2007), pp. 261-272.

Proteomics relies on the separation of complex protein mixtures using bidimensional electrophoresis. This approach is largely used to detect the expression variations of proteins prepared from two or more samples. Recently, attention was drawn on the reliability of the results published in literature. Among the critical points identified were experimental design, differential analysis and the problem of missing data, all problems where statistics can be of help. Using examples and terms understandable by biologists, we describe how a collaboration between biologists and statisticians can improve reliability of results and confidence in conclusions.