Detecting substitution-rate heterogeneity among regions of a nucleotide sequence

Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rate among regions of a DNA sequence. The tests examine three-sequence phylogenies, and two specific tests are proposed: a test to detect rate heterogeneity among genic regions within a sequence, over all evolutionary lineages; and a test to detect rate heterogeneity among regions in a specific evolutionary lineage. Simulations examine the ability of tests to detect a single region that varies in nucleotide substitution rate relative to the remainder of the sequence. A 50-bp region with a fivefold substitution-rate increase can be detected > or = 90% of the time when it is found in all three lineages of the phylogeny, and a 50-bp region of fivefold rate increase can be detected with approximately 70% power when it is found in only one evolutionary lineage. Simulation also examines the effect of transition- and transversion-rate differences. The tests are applied to published DNA sequences. While the tests are powerful, significant results can be difficult to interpret biologically.      

Predictors of mortality of patients newly diagnosed with clinical type 2 diabetes: a 5-year follow up study

Background

At diabetes diagnosis major decisions about life-style changes and treatments are made based on characteristics measured shortly after diagnosis. The predictive value for mortality of these early characteristics is widely unknown. We examined the predictive value of patient characteristics measured shortly after diabetes diagnosis for 5-year all-cause and cardiovascular mortality with special reference to self-rated general health.

Methods

Data were from a population-based sample of 1,323 persons newly diagnosed with clinical diabetes and aged 40 years or over. Possible predictors of mortality were investigated in Cox regression models.

Results

Multivariately patients who rated their health less than excellent experienced increased all-cause and cardiovascular mortality. These end-points also increased with sedentary life-style, relatively young age at diagnosis and presence of cardiovascular disease (CVD) at diagnosis. Further predictors of all-cause mortality were male sex, low body mass index and cancer, while cardiovascular mortality increased with urinary albumin concentration.

Conclusions

We found that patients who rated their health as less than excellent had increased 5-year mortality, similar to that of patients with prevalent CVD, even when biochemical, clinical and life-style variables were controlled for. This finding could motivate doctors to discuss perceptions of health with newly diagnosed diabetic patients and be attentive to patients with suboptimal health ratings. Our findings also confirm that life-style changes and optimizing treatment are particularly relevant for relatively young and inactive patients and those who already have CVD or (micro)albuminuria at the time of diabetes diagnosis.     

Durable remission of diabetes after bariatric surgery: What is the underlying pathway?

Background: In the past, type 2 diabetes mellitus (DM) was regarded as a progressive, incurable disease for which palliative therapy could not, over the long term, prevent the associated amputations, blindness, renal failure, and early mortality. This is no longer true. Full and durable remission of type 2 DM, with major decreases in morbidity and mortality, is now achieved regularly with several types of surgery that reduce contact between food and the foregut.Objectives: The aims of this article are to review the impact of bariatric surgery on obesity, remission of DM, and obesity-related morbidity and mortality, and the possible mechanisms for this advance.Methods: This article is based on our 2 meta-analyses of the literature published through April 30, 2006, as well as the most significant reports in the bariatric surgical literature that have been published in English since April 30, 2006. The studies included in our second meta-analysis provided the details of the methodology for the present literature review, including the levels of evidence.Results: Results of our 2 meta-analyses were published previously. Briefly, the analyses revealed that the clinical and laboratory manifestations of type 2 DM resolved or improved in most of the patients who underwent bariatric surgery; the responses were greatest in the patients who lost the most excess body weight; and the improvements were maintained for ≥2 years. The studies reported that intestinal operations such as gastric bypass reduced contact between food and the foregut, produced full and durable remission of DM, reduced mortality, and reversed other comorbidities associated with severe obesity (eg, asthma, gastroesophageal reflux, hypertension, stress incontinence). Insulin levels decreased markedly after surgery, as did glycosylated hemoglobin (A1C) and fasting blood glucose levels. Although these effects were initially attributed to weight loss, the rapid reversal of DM within a matter of days after surgery suggest that bariatric surgery changes the signaling mechanism of the gut with pancreatic islet cells, muscles, fat, the liver, and other organs.Conclusions: Bariatric surgery has opened new vistas, producing durable full remission of type 2 DM—a breakthrough previously considered impossible—with normalization of A1C levels over time and discontinuation of all antidiabetes medication for many patients. These advances create new opportunities for exploring the mechanisms of type 2 DM and its control through pharmaceutical approaches. DM is no longer an irreversible, incurable, or hopeless disease.     

Utility of multispectral imaging for nuclear classification of routine clinical histopathology imagery

Background

We present an analysis of the utility of multispectral versus standard RGB imagery for routine H&;E stained histopathology images, in particular for pixel-level classification of nuclei. Our multispectral imagery has 29 spectral bands, spaced 10 nm within the visual range of 420–700 nm. It has been hypothesized that the additional spectral bands contain further information useful for classification as compared to the 3 standard bands of RGB imagery. We present analyses of our data designed to test this hypothesis.

Results

For classification using all available image bands, we find the best performance (equal tradeoff between detection rate and false alarm rate) is obtained from either the multispectral or our "ccd" RGB imagery, with an overall increase in performance of 0.79% compared to the next best performing image type. For classification using single image bands, the single best multispectral band (in the red portion of the spectrum) gave a performance increase of 0.57%, compared to performance of the single best RGB band (red). Additionally, red bands had the highest coefficients/preference in our classifiers. Principal components analysis of the multispectral imagery indicates only two significant image bands, which is not surprising given the presence of two stains.

Conclusion

Our results indicate that multispectral imagery for routine H&;E stained histopathology provides minimal additional spectral information for a pixel-level nuclear classification task than would standard RGB imagery.

     

Obesity‐related hypertension: Pathogenesis,cardiovascular risk,and treatment—A position paper of the The Obesity Society and the American Society of Hypertension

In light of the worldwide epidemic of obesity, and in recognition of hypertension as a major factor in the cardiovascular morbidity and mortality associated with obesity, The Obesity Society and The American Society of Hypertension agreed to jointly sponsor a position paper on obesity‐related hypertension to be published jointly in the journals of each society. The purpose is to inform the members of both societies, as well as practicing clinicians, with a timely review of the association between obesity and high blood pressure, the risk that this association entails, and the options for rational, evidenced‐based treatment. The position paper is divided into six sections plus a summary as follows: pathophysiology, epidemiology and cardiovascular risk, the metabolic syndrome, lifestyle management in prevention and treatment, pharmacologic treatment of hypertension in the obese, and the medical and surgical treatment of obesity in obese hypertensive patients. Obesity (2012)     

The role of site-specific N-glycosylation in secretion of soluble forms of rabies virus glycoprotein

Rabies virus glycoprotein is important in the biology and pathogenesis of neurotropic rabies virus infection. This transmembrane glycoprotein is the only viral protein on the surface of virus particles, is the viral attachment protein that facilitates virus uptake by the infected cell, and is the target of the host humoral immune response to infection. The extracellular domain of this glycoprotein has N- glycosylation sequons at Asn37, Asn247, and Asn319. Appropriate glycosylation of these sequons is important in the expression of the glycoprotein. Soluble forms of rabies virus glycoprotein were constructed by insertion of a stop codon just external to the transmembrane domain. Using site-directed mutagenesis and expression in transfected eukaryotic cells, it was possible to compare the effects of site-specific glycosylation on the cell-surface expression and secretion of transmembrane and soluble forms, respectively, of the same glycoprotein. These studies yielded the surprising finding that although any of the three sequons permitted cell surface expression of full-length rabies virus glycoprotein, only the N-glycan at Asn319 permitted secretion of soluble rabies virus glycoprotein. Despite its biological and medical importance, it has not yet been possible to determine the crystal structure of the full-length transmembrane form of rabies virus glycoprotein which contains heterogeneous oligosaccharides. The current studies demonstrate that a soluble form of rabies virus glycoprotein containing only one sequon at Asn319 is efficiently secreted in the presence of the N-glycan processing inhibitor 1-deoxymannojirimycin. Thus, it is possible to purify a conformationally relevant form of rabies virus glycoprotein that contains only one N-glycan with a substantial reduction in its microheterogeneity. This form of the glycoprotein may be particularly useful for future studies aimed at elucidating the three-dimensional structure of this important glycoprotein.