Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler

<p>Abstract</p> <p>Background</p> <p>The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. There are two bat genome projects currently underway, a circumstance that promises to speed the discovery host factors important in the coevolution of bats with their viruses. These genomes, however, are not yet assembled and one of them will provide only low coverage, making the inference of most genes of immunological interest error-prone. Many more wildlife genome projects are underway and intend to provide only shallow coverage.</p> <p>Results</p> <p>We have developed a statistical method for the assembly of gene families from partial genomes. The method takes full advantage of the quality scores generated by base-calling software, incorporating them into a complete probabilistic error model, to overcome the limitation inherent in the inference of gene family members from partial sequence information. We validated the method by inferring the human IFNA genes from the genome trace archives, and used it to infer 61 type-I interferon genes, and single type-II interferon genes in the bats <it>Pteropus vampyrus </it>and <it>Myotis lucifugus</it>. We confirmed our inferences by direct cloning and sequencing of IFNA, IFNB, IFND, and IFNK in <it>P. vampyrus</it>, and by demonstrating transcription of some of the inferred genes by known interferon-inducing stimuli.</p> <p>Conclusion</p> <p>The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.</p

Measuring thermoelectric transport properties of materials

In this review we discuss considerations regarding the common techniques used for measuring thermoelectric transport properties necessary for calculating the thermoelectric figure of merit, zT. Advice for improving the data quality in Seebeck coefficient, electrical resistivity, and thermal conductivity (from flash diffusivity and heat capacity) measurements are given together with methods for identifying possible erroneous data. Measurement of the Hall coefficient and calculation of the charge carrier concentration and mobility is also included due to its importance for understanding materials. It is not intended to be a complete record or comparison of all the different techniques employed in thermoelectrics. Rather, by providing an overview of common techniques and their inherent difficulties it is an aid to new researchers or students in the field. The focus is mainly on high temperature measurements but low temperature techniques are also briefly discussed

A Statistical Approach to the Evaluation of Covariate Effects on the Receiver Operating Characteristic Curves of Diagnostic Tests in Glaucoma

PURPOSE. To describe an approach for the evaluation of covariate effects on receiver operating characteristic (ROC) curves and to apply this methodology to the investigation of the effects of disease severity and age on the diagnostic performance of frequency doubling technology (FDT) and standard automated perimetry (SAP) visual function tests for glaucoma detection. METHODS. The study included 370 eyes of 211 participants, with 174 eyes of 110 patients having glaucomatous optic neuropathy and 196 eyes of 101 subjects being normal. All patients underwent visual function testing with FDT 24-2 Humphrey Matrix and SAP SITA (Carl Zeiss Meditec, Inc., Dublin, CA). Disease severity was evaluated by the amount of neuroretinal rim loss assessed by confocal scanning laser ophthalmoscopy. An ROC regression model was fitted to evaluate the influence of disease severity and age on the diagnostic performance of the pattern SD (PSD) index from FDT 24-2 and SAP SITA. RESULTS. After adjustment for age, the areas under the ROC curves (AUCs) for SAP SITA PSD for 10%, 30%, 50%, and 70% loss of neuroretinal rim area were 0.638, 0.756, 0.852, and 0.920, respectively. Corresponding values for FDT 24-2 PSD were 0.766, 0.857, 0.922, and 0.962. For 10% and 30% rim loss, FDT 24-2 PSD had a significantly larger AUC than did SAP SITA PSD. CONCLUSIONS. A regression methodology to evaluate covariate effects on ROC curves can be useful for assessment of diagnostic tests in glaucoma. Using the proposed methodology, a significantly better performance of FDT 24-2 compared to SAP SITA for diagnosis of early glaucoma was demonstrated. (Invest Ophthalmol Vis Sci

Progression of patterns (POP): A machine classifier algorithm to identify glaucoma progression in visual fields

Purpose. We evaluated Progression of Patterns (POP) for its ability to identify progression of glaucomatous visual field (VF) defects. Methods. POP uses variational Bayesian independent component mixture model (VIM), a machine learning classifier (MLC) developed previously. VIM separated Swedish Interactive Thresholding Algorithm (SITA) VFs from a set of 2,085 normal and glaucomatous eyes into nine axes (VF patterns): seven glaucomatous. Stable glaucoma was simulated in a second set of 55 patient eyes with five VFs each, collected within four weeks. A third set of 628 eyes with 4,186 VFs (mean ± SD of 6.7 ± 1.7 VFs over 4.0 ± 1.4 years) was tested for progression. Tested eyes were placed into suspect and glaucoma categories at baseline, based on VFs and disk stereoscopic photographs; a subset of eyes had stereophotographic evidence of progressive glaucomatous optic neuropathy (PGON). Each sequence of fields was projected along seven VIM glaucoma axes. Linear regression (LR) slopes generated from projections onto each axis yielded a degree of confidence (DOC) that there was progression. At 95% specificity, progression cutoffs were established for POP, visual field index (VFI), and mean deviation (MD). Guided progression analysis (GPA) was also compared. Results. POP identified a statistically similar number of eyes (P \u3e 0.05) as progressing compared with VFI, MD, and GPA in suspects (3.8%, 2.7%, 5.6%, and 2.9%, respectively), and more eyes than GPA (P = 0.01) in glaucoma (16.0%, 15.3%, 12.0%, and 7.3%, respectively), and more eyes than GPA (P = 0.05) in PGON eyes (26.3%, 23.7%, 27.6%, and 14.5%, respectively). Conclusions. POP, with its display of DOC of progression and its identification of progressing VF defect pattern, adds to the information available to the clinician for detecting VF progression. © 2012 The Association for Research in Vision and Ophthalmology, Inc

A Comparison of Rates of Change in Neuroretinal Rim Area and Retinal Nerve Fiber Layer Thickness in Progressive Glaucoma

Longitudinal analyses of the rates of deterioration in both the rim area and retinal nerve fiber layer provide valuable additional information for the management of glaucoma patients. We observed in this study that the ability to discriminate progressing eyes from stable eyes was greater with nerve fiber layer measurements than with rim area measurements

Effects of Adrenomedullin on Human Myocyte Contractile Function and β-Adrenergic Response

Background: Adrenomedullin has been demonstrated to cause systemic vasodilation, and increased plasma adrenomedullin levels have been observed in cardiovascular disease states such as heart failure. While adrenomedullin receptors have been localized to the myocardium, the effects of adrenomedullin on human myocyte contractility remained unknown. Methods and Results: Left ventricular myocytes were isolated from myocardial biopsies of patients (n = 16) undergoing elective coronary artery bypass surgery with normal left ventricular ejection fractions (51 ± 1%). A total of 233 left ventricular myocytes were studied by videomicroscopy. Myocyte shortening velocity (μm/s) was measured at baseline and following the addition of either 3 nM, 30 nM, or 60 nM of adrenomedullin. The change in myocyte shortening velocity with increasing concentrations of adrenomedullin was computed. At all concentrations, adrenomedullin reduced myocyte shortening velocity from baseline values (P \u3c 0.05). Next, the potential interaction of adrenomedullin with the β-adrenergic receptor system was examined using 25 nM isoproterenol. The β-adrenergic receptor-mediated increase in the myocyte shortening velocity was blunted with adrenomedullin (29 ± 7 vs 63 ± 13 μm/s, P \u3c 0.05). Conclusions: These unique findings demonstrate that adrenomedullin reduced contractility in isolated human left ventricular myocytes and exhibited a negative interaction with the β-adrenergic receptor system. Past studies have shown that adrenomedullin induces nitric oxide synthesis and that nitric oxide can uncouple myocyte metabolism. Thus, while adrenomedullin causes systemic vasodilation, this peptide can also exert a negative contractile effect in human left ventricular myocytes

Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis.

OBJECTIVE:To estimate healthcare expenditures that could be impacted by advanced diagnostic testing for patients hospitalized with meningitis or encephalitis. METHODS:Patients hospitalized with meningitis (N = 23,933) or encephalitis (N = 7,858) in the U.S. were identified in the 2010-2014 Truven Health MarketScan Commercial Claims and Encounters Database using ICD-9-CM diagnostic codes. The database included an average of 40.8 million commercially insured enrollees under age 65 per year. Clinical, demographic and healthcare utilization criteria were used to identify patient subgroups early in their episode who were at risk to have high inpatient expenditures. Healthcare expenditures of patients within each subgroup were bifurcated: those expenditures that remained five days after the patient could be classified into the subgroup versus those that had occurred previously. RESULTS:The hospitalization episode rate per 100,000 enrollee-years for meningitis was 13.0 (95% CI: 12.9-13.2) and for encephalitis was 4.3 (95% CI: 4.2-4.4), with mean inpatient expenditures of $36,891 (SD =$92,636) and $60,181 (SD =$130,276), respectively. If advanced diagnostic testing had been administered on the day that a patient could be classified into a subgroup, then a test with a five-day turnaround time could impact the following mean inpatient expenditures that remained by subgroup for patients with meningitis or encephalitis, respectively: had a neurosurgical procedure ($83,337 and$56,020), had an ICU stay ($34,221 and$46,051), had HIV-1 infection or a previous organ transplant ($37,702 and$62,222), were age 2 days ($18,325 and$30,244). DISCUSSION:Inpatient expenditures for patients hospitalized with meningitis or encephalitis were substantial and varied widely. Patient subgroups who had high healthcare expenditures could be identified early in their stay, raising the potential for advanced diagnostic testing to lower these expenditures