251 research outputs found
Cerulean: A hybrid assembly using high throughput short and long reads
Genome assembly using high throughput data with short reads, arguably,
remains an unresolvable task in repetitive genomes, since when the length of a
repeat exceeds the read length, it becomes difficult to unambiguously connect
the flanking regions. The emergence of third generation sequencing (Pacific
Biosciences) with long reads enables the opportunity to resolve complicated
repeats that could not be resolved by the short read data. However, these long
reads have high error rate and it is an uphill task to assemble the genome
without using additional high quality short reads. Recently, Koren et al. 2012
proposed an approach to use high quality short reads data to correct these long
reads and, thus, make the assembly from long reads possible. However, due to
the large size of both dataset (short and long reads), error-correction of
these long reads requires excessively high computational resources, even on
small bacterial genomes. In this work, instead of error correction of long
reads, we first assemble the short reads and later map these long reads on the
assembly graph to resolve repeats.
Contribution: We present a hybrid assembly approach that is both
computationally effective and produces high quality assemblies. Our algorithm
first operates with a simplified version of the assembly graph consisting only
of long contigs and gradually improves the assembly by adding smaller contigs
in each iteration. In contrast to the state-of-the-art long reads error
correction technique, which requires high computational resources and long
running time on a supercomputer even for bacterial genome datasets, our
software can produce comparable assembly using only a standard desktop in a
short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Health Risk of the Walpole Island First Nation Community from Exposure to Environmental Contaminants: A Community-based Participatory Research Partnership
The Five Factor Model of personality and evaluation of drug consumption risk
The problem of evaluating an individual's risk of drug consumption and misuse
is highly important. An online survey methodology was employed to collect data
including Big Five personality traits (NEO-FFI-R), impulsivity (BIS-11),
sensation seeking (ImpSS), and demographic information. The data set contained
information on the consumption of 18 central nervous system psychoactive drugs.
Correlation analysis demonstrated the existence of groups of drugs with
strongly correlated consumption patterns. Three correlation pleiades were
identified, named by the central drug in the pleiade: ecstasy, heroin, and
benzodiazepines pleiades. An exhaustive search was performed to select the most
effective subset of input features and data mining methods to classify users
and non-users for each drug and pleiad. A number of classification methods were
employed (decision tree, random forest, -nearest neighbors, linear
discriminant analysis, Gaussian mixture, probability density function
estimation, logistic regression and na{\"i}ve Bayes) and the most effective
classifier was selected for each drug. The quality of classification was
surprisingly high with sensitivity and specificity (evaluated by leave-one-out
cross-validation) being greater than 70\% for almost all classification tasks.
The best results with sensitivity and specificity being greater than 75\% were
achieved for cannabis, crack, ecstasy, legal highs, LSD, and volatile substance
abuse (VSA).Comment: Significantly extended report with 67 pages, 27 tables, 21 figure
Search for Spontaneous Nucleation of Magnetic Flux During Rapid Cooling of YBCO films Through Tc
We describe an experimental search for spontaneous formation of flux lines
during a rapid quench of thin YBaCuO films through Tc. This effect is expected
according to the Kibble-Zurek mechanism of a creation of topological defects of
the order parameter during a symmetry breaking phase transition. Spontaneously
formed vortices were previously observed in superfluid 3He, while a similar
experiment in superfluid 4He gave negative results. Using a high Tc SQUID, we
measured both the magnetic flux in the sample during a quench with a
sensitivity of 20 phi-0/cm^2, and the field noise which one would expect from
flux lines pinned in the film. The sensitivity was sufficient to detect
spontaneous flux at a level corresponding to 10^(-3) of the prediction. Within
our resolution, we saw no evidence for this effect.Comment: Manuscript and 4 figure
Effect of left ventricular hypertrophy on long-term survival of patients with coronary artery disease following percutaneous coronary intervention
The impact of left ventricular hypertrophy (LVH) on survival among patients with established coronary artery disease (CAD) is not well understood. We sought to evaluate the effect of LVH on the survival of patients with CAD following percutaneous coronary intervention (PCI). Three hospitals in New York City contributed prospectively defined data on 4284 consecutive patients undergoing PCI. Allcause mortality at a mean follow-up of three years was the primary endpoint. LVH was present in 383 patients (8.9%). LVH patients had a greater prevalence of hypertension (88% vs. 68%, p<0.001), vascular disease (21% vs. 6.6%, p=0.001), and prior heart failure (10% vs. 5.5%, p<0.001). LVH patients presented less often with one-vessel disease (38% vs. 50%, p=0.040) and more often with two- (34% vs. 29%, p=0.014) or three-vessel (22% vs. 18%, p=0.044) disease. Ejection fractions and angiographic success were similar in both groups. In-hospital mortality did not differ between groups. At three-year follow-up, the survival rate for patients with LVH was 86% vs. 91% in patients without LVH (log-rank p=0.001). However, after adjustment for differences in baseline characteristics using Cox proportional hazards analysis, LVH was found not to be an independent predictor of mortality (hazard ratio, 0.93; 95% confidence interval, 0.68–1.28; p=0.67). We conclude that LVH at the time of PCI is not independently associated with an increase in the hazard of death at three years
The position of graptolites within Lower Palaeozoic planktic ecosystems.
An integrated approach has been used to assess the palaeoecology of graptolites both as a discrete group and also as a part of the biota present within Ordovician and Silurian planktic realms. Study of the functional morphology of graptolites and comparisons with recent ecological analogues demonstrates that graptolites most probably filled a variety of niches as primary consumers, with modes of life related to the colony morphotype. Graptolite coloniality was extremely ordered, lacking any close morphological analogues in Recent faunas. To obtain maximum functional efficiency, graptolites would have needed varying degrees of coordinated automobility. A change in lifestyle related to ontogenetic changes was prevalent within many graptolite groups. Differing lifestyle was reflected by differing reproductive strategies, with synrhabdosomes most likely being a method for rapid asexual reproduction. Direct evidence in the form of graptolithophage 'coprolitic' bodies, as well as indirect evidence in the form of probable defensive adaptations, indicate that graptolites comprised a food item for a variety of predators. Graptolites were also hosts to a variety of parasitic organisms and provided an important nutrient source for scavenging organisms
Combination of searches for Higgs boson pairs in pp collisions at \sqrts = 13 TeV with the ATLAS detector
This letter presents a combination of searches for Higgs boson pair production using up to 36.1 fb(-1) of proton-proton collision data at a centre-of-mass energy root s = 13 TeV recorded with the ATLAS detector at the LHC. The combination is performed using six analyses searching for Higgs boson pairs decaying into the b (b) over barb (b) over bar, b (b) over barW(+)W(-), b (b) over bar tau(+)tau(-), W+W-W+W-, b (b) over bar gamma gamma and W+W-gamma gamma final states. Results are presented for non-resonant and resonant Higgs boson pair production modes. No statistically significant excess in data above the Standard Model predictions is found. The combined observed (expected) limit at 95% confidence level on the non-resonant Higgs boson pair production cross-section is 6.9 (10) times the predicted Standard Model cross-section. Limits are also set on the ratio (kappa(lambda)) of the Higgs boson self-coupling to its Standard Model value. This ratio is constrained at 95% confidence level in observation (expectation) to -5.0 < kappa(lambda) < 12.0 (-5.8 < kappa(lambda) < 12.0). In addition, limits are set on the production of narrow scalar resonances and spin-2 Kaluza-Klein Randall-Sundrum gravitons. Exclusion regions are also provided in the parameter space of the habemus Minimal Supersymmetric Standard Model and the Electroweak Singlet Model. For complete list of authors see http://dx.doi.org/10.1016/j.physletb.2019.135103</p
Searches for lepton-flavour-violating decays of the Higgs boson in TeV collisions with the ATLAS detector
This Letter presents direct searches for lepton flavour violation in Higgs boson decays, H → eτ and
H → μτ , performed with the ATLAS detector at the LHC. The searches are based on a data sample
of proton–proton collisions at a centre-of-mass energy √s = 13 TeV, corresponding to an integrated
luminosity of 36.1 fb−1. No significant excess is observed above the expected background from Standard
Model processes. The observed (median expected) 95% confidence-level upper limits on the leptonflavour-violating branching ratios are 0.47% (0.34+0.13−0.10%) and 0.28% (0.37+0.14−0.10%) for H → eτ and H → μτ , respectively.publishedVersio
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