1,469 research outputs found
Using cascading Bloom filters to improve the memory usage for de Brujin graphs
De Brujin graphs are widely used in bioinformatics for processing
next-generation sequencing data. Due to a very large size of NGS datasets, it
is essential to represent de Bruijn graphs compactly, and several approaches to
this problem have been proposed recently. In this work, we show how to reduce
the memory required by the algorithm of [3] that represents de Brujin graphs
using Bloom filters. Our method requires 30% to 40% less memory with respect to
the method of [3], with insignificant impact to construction time. At the same
time, our experiments showed a better query time compared to [3]. This is, to
our knowledge, the best practical representation for de Bruijn graphs.Comment: 12 pages, submitte
Network patterns and strength of orbital currents in layered cuprates
In a frame of the model we derive the microscopical expression for
the circulating orbital currents in layered cuprates using the anomalous
correlation functions. In agreement with -on spin relaxation (SR),
nuclear quadrupolar resonance (NQR) and inelastic neutron scattering(INS)
experiments in YBaCuO we successfully explain the order of
magnitude and the monotonous increase of the {\it internal} magnetic fields
resulting from these currents upon cooling. However, the jump in the intensity
of the magnetic fields at T reported recently seems to indicate a
non-mean-field feature in the coexistence of current and superconducting states
and the deviation of the extended charge density wave vector instability from
its commensurate value {\bf Q}) in accordance with the
reported topology of the Fermi surface
U.S. Inhibitor Pilot Project: Study Design And Methods Validation
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106090/1/jth01876.pd
Biological aspects of the leafminer Liriomyza sativae (Diptera: Agromyzidae) on melon (Cucumis melo L.)
A review of Monte Carlo simulations of polymers with PERM
In this review, we describe applications of the pruned-enriched Rosenbluth
method (PERM), a sequential Monte Carlo algorithm with resampling, to various
problems in polymer physics. PERM produces samples according to any given
prescribed weight distribution, by growing configurations step by step with
controlled bias, and correcting "bad" configurations by "population control".
The latter is implemented, in contrast to other population based algorithms
like e.g. genetic algorithms, by depth-first recursion which avoids storing all
members of the population at the same time in computer memory. The problems we
discuss all concern single polymers (with one exception), but under various
conditions: Homopolymers in good solvents and at the point, semi-stiff
polymers, polymers in confining geometries, stretched polymers undergoing a
forced globule-linear transition, star polymers, bottle brushes, lattice
animals as a model for randomly branched polymers, DNA melting, and finally --
as the only system at low temperatures, lattice heteropolymers as simple models
for protein folding. PERM is for some of these problems the method of choice,
but it can also fail. We discuss how to recognize when a result is reliable,
and we discuss also some types of bias that can be crucial in guiding the
growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011
Increasing rates of fluoroquinolone resistance in escherichia coli isolated from the blood and urine of patients with hematologic malignancies and stem cell transplant recipients
Fluoroquinolone (FQ) antibiotics have been shown to reduce mortality and the number of febrile episodes when used as prophylaxis during neutropenia. Prior studies suggest that prophylaxis may result in increasing rates of FQ resistance. Fluoroquinolone non-susceptibility trends in Escherichia coli isolated from blood and urine cultures were evaluated over a 16-year period during which prophylaxis was initiated in patients with hematologic malignancies and stem cell transplants. Non-susceptibility rates increased after the introduction of prophylaxis, with yearly non-susceptibility rates rising from 30%–33% to 40%–88% in blood isolates. The high rates of non-susceptibility now observed raise concerns about the continued efficacy of FQ prophylaxis. This concern exists particularly in those patients undergoing stem cell transplants where the total FQ non-susceptibility rates over the study period were 82.3%. Further evaluation of the effect of FQ prophylaxis on antibiotic resistance and its efficacy in the setting of increased rates of resistance is warranted
Vancomycin-resistant Enterococcal Bloodstream Infections in Hematopoietic Stem Cell Transplant Recipients and Patients with Hematologic Malignancies: Impact of Daptomycin MICs of 3 to 4 mg/L
Purpose Case reports of treatment failure with standard-dose daptomycin (6 mg/kg) have recently surfaced in vancomycin-resistant Enterococcus (VRE) bloodstream infection (BSI) episodes with daptomycin MICs of 3 to 4 mg/L. The clinical implications of daptomycin MICs of 3 to 4 mg/L in VRE BSIs have not been elucidated. Methods We performed a single institutional retrospective analysis of adult stem cell transplant recipients and patients with hematologic malignancies diagnosed with VRE BSI from 2006 to 2014 and compared outcomes between those with daptomycin MICs of 3 to 4 mg/L those with 2 mg/L, as determined by Etest. Findings Forty-two daptomycin-treated VRE BSI episodes, all due to Enterococcus faecium were identified; 19 episodes with daptomycin MICs of 3 to 4 mg/L and 23 episodes with a daptomycin MIC of 2 mg/L. Patients in the higher daptomycin MIC group were more likely to be male, to be stem cell transplant recipients, and to have received high-dose daptomycin treatment (>6 mg/kg). In unadjusted analyses, microbiological failure in the daptomycin MICs 3 to 4 mg/L versus 2 mg/L groups (odds ratio = 1.79, 95% CI, 0.52–6.11; P = 0.35), the median duration of bacteremia (4 days in daptomycin MICs 3–4 mg/L vs 3 days in daptomycin MIC 2 mg/L; P = 0.18) and all-cause 30-day mortality (21% in daptomycin MICs 3–4 mg/L vs 35% in daptomycin MIC 2 mg/L group; P = 0.49) were not different. In adjusted analyses, the association between higher Pitt bacteremia scores and all-cause 30-day mortality was statistically significant (P = 0.0006), whereas the association between daptomycin MICs of 3 to 4 mg/L and all-cause 30-day mortality approached statistical significance (P = 0.06). Implications Duration of bacteremia and microbiological failure rates did not differ by daptomycin MICs in VRE BSI episodes in our patients, composed of adult stem cell transplant recipients and patients with hematologic malignancies. There was a nonsignificant trend in multivariable analysis suggesting that all-cause 30-day mortality was lower in patients whose VRE bloodstream isolates were with daptomycin MICs of 3 to 4 mg/L
A radium assay technique using hydrous titanium oxide adsorbent for the Sudbury Neutrino Observatory
As photodisintegration of deuterons mimics the disintegration of deuterons by
neutrinos, the accurate measurement of the radioactivity from thorium and
uranium decay chains in the heavy water in the Sudbury Neutrino Observatory
(SNO) is essential for the determination of the total solar neutrino flux. A
radium assay technique of the required sensitivity is described that uses
hydrous titanium oxide adsorbent on a filtration membrane together with a
beta-alpha delayed coincidence counting system. For a 200 tonne assay the
detection limit for 232Th is a concentration of 3 x 10^(-16) g Th/g water and
for 238U of 3 x 10^(-16) g U/g water. Results of assays of both the heavy and
light water carried out during the first two years of data collection of SNO
are presented.Comment: 12 pages, 4 figure
A synthetic biology approach to probing nucleosome symmetry
The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell
The AMANDA Neutrino Telescope
With an effective telescope area of order m for TeV neutrinos, a
threshold near 50 GeV and a pointing accuracy of 2.5 degrees per muon
track, the AMANDA detector represents the first of a new generation of high
energy neutrino telescopes, reaching a scale envisaged over 25 years ago. We
describe early results on the calibration of natural deep ice as a particle
detector as well as on AMANDA's performance as a neutrino telescope.Comment: 12 pages, Latex2.09, uses espcrc2.sty and epsf.sty, 13 postscript
files included. Talk presented at the 18th International Conference on
Neutrino Physics and Astrophysics (Neutrino 98), Takayama, Japan, June 199
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