Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins

<p>Laminopathies yield tissue-specific pathologies, yet arise from mutation of ubiquitously-expressed genes. A little investigated hypothesis to explain this is that the mutated proteins or their partners have tissue-specific splice variants. To test this, we analyzed RNA-Seq datasets, finding novel isoforms or isoform tissue-specificity for: Lap2, linked to cardiomyopathy; Nesprin 2, linked to Emery-Dreifuss muscular dystrophy and Lmo7, that regulates the Emery-Dreifuss muscular dystrophy linked emerin gene. Interestingly, the muscle-specific Lmo7 exon is rich in serine phosphorylation motifs, suggesting regulatory function. Muscle-specific splice variants in non-nuclear envelope proteins linked to other muscular dystrophies were also found. Nucleoporins tissue-specific variants were found for Nup54, Nup133, Nup153 and Nup358/RanBP2. RT-PCR confirmed novel Lmo7 and RanBP2 variants and specific knockdown of the Lmo7 variantreduced myogenic index. Nuclear envelope proteins were enriched for tissue-specific splice variants compared to the rest of the genome, suggesting that splice variants contribute to its tissue-specific functions.</p

Intermittency and regularity issues in 3D Navier-Stokes turbulence

Two related open problems in the theory of 3D Navier-Stokes turbulence are discussed in this paper. The first is the phenomenon of intermittency in the dissipation field. Dissipation-range intermittency was first discovered experimentally by Batchelor and Townsend over fifty years ago. It is characterized by spatio-temporal binary behaviour in which long, quiescent periods in the velocity signal are interrupted by short, active `events' during which there are violent fluctuations away from the average. The second and related problem is whether solutions of the 3D Navier-Stokes equations develop finite time singularities during these events. This paper shows that Leray's weak solutions of the three-dimensional incompressible Navier-Stokes equations can have a binary character in time. The time-axis is split into `good' and `bad' intervals: on the `good' intervals solutions are bounded and regular, whereas singularities are still possible within the `bad' intervals. An estimate for the width of the latter is very small and decreases with increasing Reynolds number. It also decreases relative to the lengths of the good intervals as the Reynolds number increases. Within these `bad' intervals, lower bounds on the local energy dissipation rate and other quantities, such as \|\bu(\cdot, t)\|_{\infty} and \|\nabla\bu(\cdot, t)\|_{\infty}, are very large, resulting in strong dynamics at sub-Kolmogorov scales. Intersections of bad intervals for $n\geq 1$ are related to Scheffer's potentially singular set in time. It is also proved that the Navier-Stokes equations are conditionally regular provided, in a given `bad' interval, the energy has a lower bound that is decaying exponentially in time.Comment: 36 pages, 3 figures and 6 Table

Chronic Mycobacterium abscessus infection and lung function decline in cystic fibrosis

Although nontuberculous mycobacteria (NTM) are recognized pathogens in cystic fibrosis (CF), associations with clinical outcomes remain unclear

Progression to chronic atrial fibrillation after pacing: the Canadian Trial of Physiologic Pacing

AbstractOBJECTIVESThis study examined the effect of physiologic pacing on the development of chronic atrial fibrillation (CAF) in the Canadian Trial Of Physiologic Pacing (CTOPP).BACKGROUNDThe role of physiologic pacing to prevent CAF remains unclear. Small randomized studies have suggested a benefit for patients with sick sinus syndrome. No data from a large randomized trial are available.METHODSThe CTOPP randomized patients undergoing first pacemaker implant to ventricular-based or physiologic pacing (AAI or DDD). Patients who were prospectively found to have persistent atrial fibrillation (AF) lasting greater than or equal to one week were defined as having CAF. Kaplan-Meier plots for the development of CAF were compared by log-rank test. The effect of baseline variables on the benefit of physiologic pacing was evaluated by Cox proportional hazards modeling.RESULTSPhysiologic pacing reduced the development of CAF by 27.1%, from 3.84% per year to 2.8% per year (p = 0.016). Three clinical factors predicted the development of CAF: age ≥74 years (p = 0.057), sinoatrial (SA) node disease (p < 0.001) and prior AF (p < 0.001). Subgroup analysis demonstrated a trend for patients with no history of myocardial infarction or coronary disease (p = 0.09) as well as apparently normal left ventricular function (p = 0.11) to derive greatest benefit.CONCLUSIONSPhysiologic pacing reduces the annual rate of development of chronic AF in patients undergoing first pacemaker implant. Age ≥74 years, SA node disease and prior AF predicted the development of CAF. Patients with structurally normal hearts appear to derive greatest benefits

The Mass and Structure of the Pleiades Star Cluster from 2MASS

We present the results of a large scale search for new members of the Pleiades star cluster using 2MASS near-infrared photometry and proper motions derived from POSS plates digitized by the USNO PMM program. The search extends to a 10 degree radius around the cluster, well beyond the presumed tidal radius, to a limiting magnitude of R ~ 20, corresponding to ~ 0.07 M_sun at the distance and age of the Pleiades. Multi-object spectroscopy for 528 candidates verifies that the search was extremely effective at detecting cluster stars in the 1 - 0.1 M_sun mass range using the distribution of H_alpha emission strengths as an estimate of sample contamination by field stars. When combined with previously identified, higher mass stars, this search provides a sensitive measurement of the stellar mass function and dynamical structure of the Pleiades. The degree of tidal elongation of the halo agrees well with current N body simulation results. Tidal truncation affects masses below ~ 1 M_sun. The cluster contains a total mass ~ 800 M_sun. Evidence for a flatter mass function in the core than in the halo indicates the depletion of stars in the core with mass less than ~ 0.5 M_sun, relative to stars with mass \~1 - 0.5 M_sun, and implies a preference for very low mass objects to populate the halo or escape. The overall mass function is best fitted with a lognormal form that becomes flat at ~ 0.1 M_sun. Whether sufficient dynamical evaporation has occurred to detectably flatten the initial mass function, via preferential escape of very low mass stars and brown dwarfs, is undetermined, pending better membership information for stars at large radial distances.Comment: 19 pages, 14 figures, 2 tables, accepted by AJ, to appear April 200

Pion-nucleus elastic scattering on 12C, 40Ca, 90Zr, and 208Pb at 400 and 500 MeV

Pion-nucleus elastic scattering at energies above the Delta(1232) resonance is studied using both pi+ and pi- beams on 12C, 40Ca, 90Zr, and 208Pb. The present data provide an opportunity to study the interaction of pions with nuclei at energies where second-order corrections to impulse approximation calculations should be small. The results are compared with other data sets at similar energies, and with four different first-order impulse approximation calculations. Significant disagreement exists between the calculations and the data from this experiment

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ßtubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils

Dose-Levels and First Signs of Efficacy in Contemporary Oncology Phase 1 Clinical Trials

PURPOSE: Phase 1 trials play a crucial role in oncology by translating laboratory science into efficient therapies. Molecular targeted agents (MTA) differ from traditional cytotoxics in terms of both efficacy and toxicity profiles. Recent reports suggest that higher doses are not essential to produce the optimal anti-tumor effect. This study aimed to assess if MTA could achieve clinical benefit at much lower dose than traditional cytotoxics in dose seeking phase 1 trials. PATIENTS AND METHODS: We reviewed 317 recent phase 1 oncology trials reported in the literature between January 1997 and January 2009. First sign of efficacy, maximum tolerated dose (MTD) and their associated dose level were recorded in each trial. RESULTS: Trials investigating conventional cytotoxics alone, MTA alone and combination of both represented respectively 63.0% (201/317), 23.3% (74/317) and 13.7% (42/317) of all trials. The MTD was reached in 65.9% (209/317) of all trials and was mostly observed at the fifth dose level. First sign of efficacy was less frequently observed at the first three dose-levels for MTA as compared to conventional cytotoxics or combinations regimens (48.3% versus 63.2% and 61.3%). Sign of efficacy was observed in the same proportion whatever the treatment type (73-82%). MTD was less frequently established in trials investigating MTA alone (51.3%) or combinations (42.8%) as compared to conventional cytotoxic agents (75.6%). CONCLUSION: First sign of efficacy was less frequently reported at the early dose-levels and MTD was less frequently reached in trials investigating molecular targeted therapy alone. Similar proportion of trials reported clinical benefit

Variation in centre-specific survival in patients starting renal replacement therapy in England is explained by enhanced comorbidity information from hospitalization data

Background Unadjusted survival on renal replacement therapy (RRT) varies widely from centre to centre in England. Until now, missing data on case mix have made it impossible to determine whether this variation reflects genuine differences in the quality of care. Data linkage has the capacity to reduce missing data. Methods Modelling of survival using Cox proportional hazards of data returned to the UK Renal Registry on patients starting RRT for established renal failure in England. Data on ethnicity, socioeconomic status and comorbidity were obtained by linkage to the Hospital Episode Statistics database, using data from hospitalizations prior to starting RRT. Results Patients with missing data were reduced from 61 to 4%. The prevalence of comorbid conditions was remarkably similar across centres. When centre-specific survival was compared after adjustment solely for age, survival was below the 95% limit for 6 of 46 centres. The addition of variables into the multivariable model altered the number of centres that appeared to be ‘outliers’ with worse than expected survival as follows: ethnic origin four outliers, socioeconomic status eight outliers and year of the start of RRT four outliers. The addition of a combination of 16 comorbid conditions present at the start of RRT reduced the number of centres with worse than expected survival to one. Conclusions Linked data between a national registry and hospital admission dramatically reduced missing data, and allowed us to show that nearly all the variation between English renal centres in 3-year survival on RRT was explained by demographic factors and by comorbidity

GeV Gamma-ray Flux Upper Limits from Clusters of Galaxies

The detection of diffuse radio emission associated with clusters of galaxies indicates populations of relativistic leptons infusing the intracluster medium. Those electrons and positrons are either injected into and accelerated directly in the intracluster medium, or produced as secondary pairs by cosmic-ray ions scattering on ambient protons. Radiation mechanisms involving the energetic leptons together with decay of neutral pions produced by hadronic interactions have the potential to produce abundant GeV photons. Here, we report on the search for GeV emission from clusters of galaxies using data collected by the Large Area Telescope (LAT) on the Fermi Gamma-ray Space Telescope (Fermi) from August 2008 to February 2010. Thirty-three galaxy clusters have been selected according to their proximity and high mass, X-ray flux and temperature, and indications of non-thermal activity for this study. We report upper limits on the photon flux in the range 0.2-100 GeV towards a sample of observed clusters (typical values 1-5 x 10^-9 ph cm^-2 s^-1) considering both point-like and spatially resolved models for the high-energy emission, and discuss how these results constrain the characteristics of energetic leptons and hadrons, and magnetic fields in the intracluster medium. The volume-averaged relativistic-hadron-to-thermal energy density ratio is found to be < 5-10% in several clusters.Comment: 9 pages, 3 tables, 1 figure, accepted for publication in ApJ Letter