The presence of GC-AG introns in Neurospora crassa and other euascomycetes determined from analyses of complete genomes: implications for automated gene prediction

AbstractA combination of experimental and computational approaches was employed to identify introns with noncanonical GC-AG splice sites (GC-AG introns) within euascomycete genomes. Evaluation of 2335 cDNA-confirmed introns from Neurospora crassa revealed 27 such introns (1.2%). A similar frequency (1.0%) of GC-AG introns was identified in Fusarium graminearum, in which 3 of 292 cDNA-confirmed introns contained GC-AG splice sites. Computational analyses of the N. crassa genome using a GC-AG intron consensus sequence identified an additional 20 probable GC-AG introns in this fungus. For 8 of the 47 GC-AG introns identified in N. crassa a GC donor site is also present in a homolog from Magnaporthe grisea, F. graminearum, or Aspergillus nidulans. In most cases, however, homologs in these fungi contain a GT-AG intron or no intron at the corresponding position. These findings have important implications for fungal genome annotation, as the automated annotations of euascomycete genomes incorrectly identified intron boundaries for all of the confirmed and probable GC-AG introns reported here

Quantum Bayes rule

We state a quantum version of Bayes's rule for statistical inference and give a simple general derivation within the framework of generalized measurements. The rule can be applied to measurements on N copies of a system if the initial state of the N copies is exchangeable. As an illustration, we apply the rule to N qubits. Finally, we show that quantum state estimates derived via the principle of maximum entropy are fundamentally different from those obtained via the quantum Bayes rule.Comment: REVTEX, 9 page

Temporal variability in foraminiferal morphology and geochemistry at the West Antarctic Peninsula: a sediment trap study

The West Antarctic Peninsula (WAP) exhibits strong spatial and temporal oceanographic variability, resulting in highly heterogeneous biological productivity. Calcifying organisms that live in the waters off the WAP respond to temporal and spatial variations in ocean temperature and chemistry. These marine calcifiers are potentially threatened by regional climate change with waters already naturally close to carbonate undersaturation. Future projections of carbonate production in the Southern Ocean are challenging due to the lack of historical data collection and complex, decadal climate variability. Here we present a 6-year-long record of the shell fluxes, morphology and stable isotope variability of the polar planktic foraminifera Neogloboquadrina pachyderma (sensu stricto) from near Palmer Station, Antarctica. This species is fundamental to Southern Ocean planktic carbonate production as it is one of the very few planktic foraminifer species adapted to the marine polar environments. We use these new data to obtain insights into its ecology and to derive a robust assessment of the response of this polar species to environmental change. Morphology and stable isotope composition reveal the presence of different growth stages within this tightly defined species. Inter- and intra-annual variability of foraminiferal flux and size is evident and driven by a combination of environmental forcing parameters, most importantly food availability, temperature and sea ice duration and extent. Foraminiferal growth occurs throughout the austral year and is influenced by environmental change, a large portion of which is driven by the Southern Annular Mode and El Niño–Southern Oscillation. A distinct seasonal production is observed, with the highest shell fluxes during the warmest and most productive months of the year. The sensitivity of calcifying foraminifera to environmental variability in this region, from weeks to decades, has implications both for their response to future climatic change and for their use as palaeoclimate indicators. A longer ice-free season could increase carbonate production in this region at least while carbonate saturation is still high enough to allow for thick tests to grow

Cumulative burden of depression and all-cause mortality in women living with human immunodeficiency virus

Background Research linking depression to mortality among people living with human immunodeficiency virus (PLWH) has largely focused on binary "always vs never" characterizations of depression. However, depression is chronic and is likely to have cumulative effects on mortality over time. Quantifying depression as a cumulative exposure may provide a better indication of the clinical benefit of enhanced depression treatment protocols delivered in HIV care settings. Methods Women living with HIV (WLWH), naive to antiretroviral therapy, from the Women's Interagency HIV Study were followed from their first visit in or after 1998 for up to 10 semiannual visits (5 years). Depressive symptoms were assessed using the Center for Epidemiologic Studies Depression (CES-D) scale. An area-under-the-curve approach was used to translate CES-D scores into a time-updated measure of cumulative days with depression (CDWD). We estimated the effect of CDWD on all-cause mortality using marginal structural Cox proportional hazards models. Results Overall, 818 women contributed 3292 woman-years over a median of 4.8 years of follow-up, during which the median (interquartile range) CDWD was 366 (97-853). Ninety-four women died during follow-up (2.9 deaths/100 woman-years). A dose-response relationship was observed between CDWD and mortality. Each additional 365 days spent with depression increased mortality risk by 72% (hazard ratio, 1.72; 95% confidence interval, 1.34-2.20). Conclusions In this sample of WLWH, increased CDWD elevated mortality rates in a dose-response fashion. More frequent monitoring and enhanced depression treatment protocols designed to reduce CDWD may interrupt the accumulation of mortality risk among WLWH

On realcompact topological vector spaces

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