Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine 14 pathogen or host-pathogen differential gene expression data sets to assess whether using longer reads is warranted. A variety of data sets was used to assess what genomic attributes might affect the outcome of differential gene expression analysis including: gene density, operons, gene length, number of introns/exons and intron length. No genome attribute was found to influence the data in principal components analysis, hierarchical clustering with bootstrap support, or regression analyses of pairwise comparisons that were undertaken on the same reads, looking at all combinations of paired and unpaired reads trimmed to 36, 54, 72 and 101 bp. Read pairing had the greatest effect when there was little variation in the samples from different conditions or in their replicates (e.g. little differential gene expression). But overall, 54 and 72 bp reads were typically most similar. Given differences in costs and mapping percentages, we recommend 54 bp reads for organisms with no or few introns and 72 bp reads for all others. In a third of the data sets, read pairing had absolutely no effect, despite paired reads having twice as much data. Therefore, single-end reads seem robust for differential-expression analyses, but in eukaryotes paired-end reads are likely desired to analyse splice variants and should be preferred for data sets that are acquired with the intent to be community resources that might be used in secondary data analyses

Evolutionary history of mammalian sucking lice (Phthiraptera: Anoplura)

<p>Abstract</p> <p>Background</p> <p>Sucking lice (Phthiraptera: Anoplura) are obligate, permanent ectoparasites of eutherian mammals, parasitizing members of 12 of the 29 recognized mammalian orders and approximately 20% of all mammalian species. These host specific, blood-sucking insects are morphologically adapted for life on mammals: they are wingless, dorso-ventrally flattened, possess tibio-tarsal claws for clinging to host hair, and have piercing mouthparts for feeding. Although there are more than 540 described species of Anoplura and despite the potential economical and medical implications of sucking louse infestations, this study represents the first attempt to examine higher-level anopluran relationships using molecular data. In this study, we use molecular data to reconstruct the evolutionary history of 65 sucking louse taxa with phylogenetic analyses and compare the results to findings based on morphological data. We also estimate divergence times among anopluran taxa and compare our results to host (mammal) relationships.</p> <p>Results</p> <p>This study represents the first phylogenetic hypothesis of sucking louse relationships using molecular data and we find significant conflict between phylogenies constructed using molecular and morphological data. We also find that multiple families and genera of sucking lice are not monophyletic and that extensive taxonomic revision will be necessary for this group. Based on our divergence dating analyses, sucking lice diversified in the late Cretaceous, approximately 77 Ma, and soon after the Cretaceous-Paleogene boundary (ca. 65 Ma) these lice proliferated rapidly to parasitize multiple mammalian orders and families.</p> <p>Conclusions</p> <p>The diversification time of sucking lice approximately 77 Ma is in agreement with mammalian evolutionary history: all modern mammal orders are hypothesized to have diverged by 75 Ma thus providing suitable habitat for the colonization and radiation of sucking lice. Despite the concordant timing of diversification events early in the association between anoplurans and mammals, there is substantial conflict between the host and parasite phylogenies. This conflict is likely the result of a complex history of host switching and extinction events that occurred throughout the evolutionary association between sucking lice and their mammalian hosts. It is unlikely that there are any ectoparasite groups (including lice) that tracked the early and rapid radiation of eutherian mammals.</p

Insomnia as an Independent Predictor of Incident Cardiovascular Disease in HIV: Data from the Veterans Aging Cohort Study

Background: Insomnia is associated with increased cardiovascular disease (CVD) risk in the general population and is highly prevalent in people with HIV. The CVD risk conferred by insomnia in the HIV population is unknown. Methods: Using the Veterans Aging Cohort Study-Survey Cohort, insomnia symptoms were measured and dummy coded with the item, “Difficulty falling or staying asleep?” (5-point scale from no difficulty to bothers a lot). Incident CVD event ICD-9 codes (acute myocardial infarction, stroke, or coronary artery revascularization) were identified with VA and Medicare administrative data and VA fee-for-service data. Those with baseline CVD were excluded. Results: HIV-infected (N=3,108) veterans had a median follow-up time of 10.8 years, during which 267 CVD events occurred. Compared to HIV-infected veterans with no difficulty falling or staying asleep, HIV-infected veterans bothered a lot by insomnia symptoms had an increased risk of incident CVD after adjusting for demographics (HR=1.64, 95%CI=1.16-2.31, p=.005), CVD risk factors (HR=1.62, 95%CI=1.14-2.30, p=.007), additional potential confounders (hepatitis C infection, renal disease, anemia, alcohol use, cocaine use; HR=1.70, 95%CI=1.19-2.43, p=.003), and HIV-specific factors (HIV-1 RNA, CD4+ T-cell count, ART; HR=1.66, 95%CI=1.16-2.37, p=.005). Additional adjustment for non-benzodiazepine sleep medication (HR=1.62, 95%CI=1.13-2.32, p=.009) did not attenuate the association; however, it fell short of significance at p < .01 after adjustment for depressive symptoms (HR=1.51, 95%CI=0.98-2.32, p=.060) or antidepressant medication (HR=1.51, 95%CI=1.04-2.19, p=.031). Conclusion: Highly bothersome insomnia symptoms were significantly associated with incident CVD in HIV-infected veterans, suggesting that insomnia may be a novel, modifiable risk factor for CVD in HIV

Origin of spectral purity and tuning sensitivity in a vortex-based spin transfer nano-oscillator

We investigate the microwave characteristics of a spin transfer nano-oscillator (STNO) based on coupled vortices as a function of the perpendicular magnetic field $H_\perp$. While the generation linewidth displays strong variations on $H_\perp$ (from 40 kHz to 1 MHz), the frequency tunability in current remains almost constant (~7 MHz/mA). We demonstrate that our vortex-based oscillator is quasi-isochronous independently of $H_\perp$, so that the severe nonlinear broadening usually observed in STNOs does not exist. Interestingly, this does not imply a loss of frequency tunability, which is here governed by the current induced Oersted field. Nevertheless this is not sufficient to achieve the highest spectral purity in the full range of $H_\perp$ either: we show that the observed linewidth broadenings are due to the excited mode interacting with a lower energy overdamped mode, which occurs at the successive crossings between harmonics of these two modes. These findings open new possibilities for the design of STNOs and the optimization of their performance

Exercise capacity and incidence of myocardial perfusion defects after Kawasaki disease in children and adolescents

Objectives.This study evaluated exercise performance and myocardial perfusion during exercise in patients with Kawasaki disease who had a broad spectrum of residual coronary abnormalities.Background.Reports of exercise performance after Kawasaki disease have generally included a small number of patients evaluated by various protocols, frequently with incomplete data. Myocardial perfusion studies have usually been limited to those using pharmacologically induced coronary vasodilation. Therefore, to our knowledge there has not been a large study directly correlating exercise performance, electrocardiographic (ECG) changes and myocardial perfusion imaging.Methods.Forty-six patients were classified into three groups on the basis of coronary artery status: group 1 (n = 27) had no objective evidence of coronary artery lesions; group 2 (n = 11) had resolved aneurysms; group 3 (n = 8) had persistent coronary aneurysms. All patients underwent exercise testing with monitor ing of ECG changes and oxygen consumption. Single-photon emission computed tomographic imaging was performed at rest and during peak exercise using technetium-99m sestamibi.Results.Maximal oxygen consumption was within normal limits and was similar for all three groups. Five patients had mild ST segment changes at peak exercise. Two of these patients had stress-induced perfusion defects. Myocardial perfusion defects were present in 37% of patients in group 1, 63% in group 2 and 100% in group 3. Perfusion defects corresponded to the coronary artery lesion site in all but three patients.Conclusions.Maximal oxygen consumption is normal after Kawasaki disease regardless of coronary artery status. Stressinduced perfusion defects are frequent even in the absence of coronary abnormalities and are common in the absence of ST segment changes suggestive of ischemia

721-6 Pulmonary Balloon Valvuloplasty: Effective Palliation for Infants with Tetralogy of Fallot and Small Pulmonary Arteries

Infants with tetralogy of Fallot (TOF) and small pulmonary arteries (PAs) may need palliation to improve pulmonary blood flow and allow growth of the PAs prior to complete repair. Shunts may become occluded, distort the PAs or cause pulmonary overcirculation. As an alternative palliation, we performed pulmonary balloon valvuloplasty (PBV) on infants with TOF and small PAs.20 infants, ages 1.8±1.5 mo and weights 4.1±1.6kg, undervvent PBV as initial palliation for persistent cyanosis or “spells”. 4/20 pts were intubated prior to or for PBV All pts had pre and post-PBV angiograms. In all pts, single balloon valvuloplasty was performed. The ratio of balloon: pulmonary valve annulus (PVA) diameter was 1.51±0.32. Post-PBV, there was no change in the PYA diameter (5.2±1.1mm vs 5.6 + 1.1mm; p=0.1) or PA branch diameter(4.1±1.6mm vs 4.5±1.7mm, p&gt;0.05). The systemic 02 saturation increased from 81±8% to 93±6%. (p&lt;0.001)7/20 pts undervvent follow-up (F/U) cath 8.2±2.4 mo post-PBV Compared to pre-PBV measurements, the PYA diameter increased from 5.2 ± 1.1mm to 7.1±1.4mm (p&lt;0.03) and the McGoon ratio increased from 1.4±0.4 to 2.1±0.3 (p&lt;0.02).Of the 20 pts, 11 pts undervvent corrective surgery 8.0±3.1 mo post-PBV with no surgical deaths; 5 pts remain in stable condition awaiting surgery; 3 pts required shunt placement 9-66 days post-PBV; 1 pt died due to other congenital anomalies.ConclusionsPulmonary balloon valvuloplasty promotes growth of the PAs and PYA in infants with TOF and small PAs, offering a safe and effective alternative palliation for infants who are not yet candidates for complete repair