323 research outputs found
A Bulk-Parallel Priority Queue in External Memory with STXXL
We propose the design and an implementation of a bulk-parallel external
memory priority queue to take advantage of both shared-memory parallelism and
high external memory transfer speeds to parallel disks. To achieve higher
performance by decoupling item insertions and extractions, we offer two
parallelization interfaces: one using "bulk" sequences, the other by defining
"limit" items. In the design, we discuss how to parallelize insertions using
multiple heaps, and how to calculate a dynamic prediction sequence to prefetch
blocks and apply parallel multiway merge for extraction. Our experimental
results show that in the selected benchmarks the priority queue reaches 75% of
the full parallel I/O bandwidth of rotational disks and and 65% of SSDs, or the
speed of sorting in external memory when bounded by computation.Comment: extended version of SEA'15 conference pape
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Stops making sense: translational trade-offs and stop codon reassignment
Background
Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature.
Results
In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences.
Conclusions
We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants
Lucky Imaging of M subdwarfs
The knowledge of the binary properties of metal-poor and solar-metallicity
stars can shed light on the potential differences between the formation
processes responsible for both types of objects.
The aim of the project is to determine the binary properties (separation,
mass ratio, frequency of companions) for M subdwarfs, the low-metallicity
counterparts of field M dwarfs, and investigate any potential differences
between both populations.
We have obtained high-resolution imaging in the optical for a sample of 24
early-M subdwarfs and nine extreme subdwarfs with the ``Lucky Imaging''
technique using the AstraLux instrument on the Calar Alto 2.2-m telescope.
We are sensitive to companions at separations larger than 0.1 arcsec and
differences of ~2 magnitudes at 0.1 arcsec and ~5 mag at 1 arcsec. We have
found no companion around the 24 subdwarfs under study and one close binary out
of nine extreme subdwarfs. A second image of LHS 182 taken three months later
with the same instrument confirms the common proper motion of the binary
separated by about 0.7 arcsec. Moreover, we do not confirm the common proper
motion of the faint source reported by Riaz and collaborators at ~2 arcsec from
LHS 1074. We derive a binary frequency of 3+/-3% for M subdwarfs from our
sample of 33 objects for separations larger than about five astronomical units.
Adding to our sample the additional 28 metal-poor early-M dwarfs observed with
the Hubble Space Telescope by Riaz and collaborators, we infer a binary
fraction of 3.7+/-2.6% (with a 1 sigma confidence limit), significantly lower
than the fraction of resolved binary M dwarfs (~20%) over the same mass and
separation ranges (abridged).Comment: 9 pages, 2 tables, 5 figures, accepted to A&
Avaliação semiquantitativa ecocardiográfica de dilatações vasculares intrapulmonares em candidatos a transplante hepático: correlação com avaliação de shunt e parâmetros funcionais pulmonares
Esophagectomy with gastroplasty in advanced megaesophagus: late results of omeprazole use
Laparoscopic right hemicolectomy: a SICE (Società Italiana di Chirurgia Endoscopica e Nuove tecnologie) network prospective study on the approach to right colon lymphadenectomy in Italy: is there a standard?—CoDIG 2 (ColonDx Italian Group)
Background: Colon cancer is a disease with a worldwide spread. Surgery is the best option for the treatment of advanced colon cancer, but some aspects are still debated, such as the extent of lymphadenectomy. In Japanese guidelines, the gold standard was D3 dissection to remove the central lymph nodes (203, 213, and 223), but in 2009, Hoenberger et al. introduced the concept of complete mesocolic excision, in which surgical dissection follows the embryological planes to remove the mesentery entirely to prevent leakage of cancer cells and collect more lymph nodes. Our study describes how lymphadenectomy is currently performed in major Italian centers with an unclear indication on the type of lymphadenectomy that should be performed during right hemicolectomy (RH). Methods: CoDIG 2 is an observational multicenter national study that involves 76 Italian general surgery wards highly specialized in colorectal surgery. Each center was asked not to modify their usual surgical and clinical practices. The aim of the study was to assess the preference of Italian surgeons on the type of lymphadenectomy to perform during RH and the rise of any new trends or modifications in habits compared to the findings of the CoDIG 1 study conducted 4 years ago. Results: A total of 788 patients were enrolled. The most commonly used surgical technique was laparoscopic (82.1%) with intracorporeal (73.4%), side-to-side (98.7%), or isoperistaltic (96.0%) anastomosis. The lymph nodes at the origin of the vessels were harvested in an inferior number of cases (203, 213, and 223: 42.4%, 31.1%, and 20.3%, respectively). A comparison between CoDIG 1 and CoDIG 2 showed a stable trend in surgical techniques and complications, with an increase in the robotic approach (7.7% vs. 12.3%). Conclusions: This analysis shows how lymphadenectomy is performed in Italy to achieve oncological outcomes in RH, although the technique to achieve a higher lymph node count has not yet been standardized. Trial registration (ClinicalTrials.gov) ID: NCT05943951
The role of empirical research in the study of complex forms of governance in agroindustrial systems
Law Enforcement, Municipal Budgets and Spillover Effects: Evidence from a Quasi-Experiment in Italy
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