Search results for "Algorithm"
showing 10 items of 4887 documents
On Approximate Jumbled Pattern Matching in Strings
2011
Given a string s, the Parikh vector of s, denoted p(s), counts the multiplicity of each character in s. Searching for a match of a Parikh vector q in the text s requires finding a substring t of s with p(t) = q. This can be viewed as the task of finding a jumbled (permuted) version of a query pattern, hence the term Jumbled Pattern Matching. We present several algorithms for the approximate version of the problem: Given a string s and two Parikh vectors u, v (the query bounds), find all maximal occurrences in s of some Parikh vector q such that u <= q <= v. This definition encompasses several natural versions of approximate Parikh vector search. We present an algorithm solving this problem …
Optimization of the KNN Supervised Classification Algorithm as a Support Tool for the Implantation of Deep Brain Stimulators in Patients with Parkins…
2019
Deep Brain Stimulation (DBS) of the Subthalamic Nuclei (STN) is the most used surgical treatment to improve motor skills in patients with Parkinson&rsquo
Multiple Protein Sequence Alignment with MSAProbs
2013
Multiple sequence alignment (MSA) generally constitutes the foundation of many bioinformatics studies involving functional, structural, and evolutionary relationship analysis between sequences. As a result of the exponential computational complexity of the exact approach to producing optimal multiple alignments, the majority of state-of-the-art MSA algorithms are designed based on the progressive alignment heuristic. In this chapter, we outline MSAProbs, a parallelized MSA algorithm for protein sequences based on progressive alignment. To achieve high alignment accuracy, this algorithm employs a hybrid combination of a pair hidden Markov model and a partition function to calculate posterior…
Strong antiapostatic selection against novel rare aposematic prey
2001
The evolution of aposematism, a phenomenon where prey species conspicuously advertise their unprofitability to predators, is puzzling. How did conspicuousness evolve, if it simultaneously increased the likelihood of an inexperienced predator to detect the prey and presumably kill it? Antiapostatic selection, where rare prey is predated relatively more often, is considered as another major difficulty for aposematism to evolve. However, the risk of being conspicuous in low frequencies has not been experimentally tested. We designed an experiment to test how frequency (4%, 12%, 32%) of conspicuous aposematic prey and its dispersion type (solitary vs. aggregated) affect an initial predation ri…
Selection for cryptic coloration in a visually heterogeneous habitat.
2001
We studied selection by predators for cryptic prey coloration in a visually heterogeneous habitat that consists of two microhabitats. It has been suggested that the probability of escaping detection in such habitats might be optimized by maximizing crypsis in one of the microhabitats. However, a recent model indicates that a coloration that compromises the requirements of different microhabitats might sometimes be the optimal solution. To experimentally study these hypotheses, we allowed great tits (Parus major L.) to search for artificial prey items in two different microhabitats (background boards): small patterned and large patterned. On each board there was one prey item that was either…
Can experienced birds select for Müllerian mimicry?
2008
Field experiments have shown that avian predators in the wild can select for similarity of warning signals in aposematic prey (Müllerian mimicry) because a common signal is better protected than a signal that is novel and rare. The original theory of Müllerian mimicry assumes that the mechanism promoting mimicry is predator learning; by sharing a signal, the comimic species share the mortality that is due to sampling by inexperienced predators. Predation events have not been observed in the wild, and learning experiments with naive bird predators in a laboratory have not unambiguously shown a benefit of a uniform signal compared with different signals. As predators in the field experiments …
Estimation of Passenger Car Equivalents for single-lane roundabouts using a microsimulation-based procedure
2017
Calibration of microscopic traffic simulation models for single-lane roundabouts.Use of a meta-analytical estimation of critical and follow up headways.Use of a genetic algorithm-based procedure.Calculation of passenger car equivalents for single-lane roundabouts. Passenger car equivalents for heavy vehicles are required to carry out capacity calculations and perform operational analysis of any road entity (roadway segments or intersections). At single-lane roundabouts, the constraints to the vehicular trajectories imposed by the curvilinear geometric design and the driver's gap acceptance behaviour are expected to produce an impact of the heavy vehicles on the quality of traffic flow diffe…
Modulation of voltage-gated K(+) channels Kv11 and Kv1 4 by forskolin.
2002
Forskolin (FSK) affects voltage-gated K + (Kv) currents in different cell types, but it is not known which of the various subunits form FSK-sensitive Kv channels. We compared the effect of the compound at Kv1.1 and Kv1.4 channels ectopically expressed in HEK 293 cells. Low FSK concentrations induced a phosphorylation-dependent potentiation of Kv1.1 currents. At higher concentrations, this effect was superimposed by a fast, cAMP-independent channel block. Kv1.4 currents were inhibited with lower potency by FSK but were not modified by phosphorylation. The variable effect of the compound might help to distinguish between Kv subunits expressed by native cells. 2002 Elsevier Science Ltd. All …
Quantification of the heterogeneity of prognostic cellular biomarkers in ewing sarcoma using automated image and random survival forest analysis
2014
Driven by genomic somatic variation, tumour tissues are typically heterogeneous, yet unbiased quantitative methods are rarely used to analyse heterogeneity at the protein level. Motivated by this problem, we developed automated image segmentation of images of multiple biomarkers in Ewing sarcoma to generate distributions of biomarkers between and within tumour cells. We further integrate high dimensional data with patient clinical outcomes utilising random survival forest (RSF) machine learning. Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithm…
Quantification of vesicles in differentiating human SH-SY5Y neuroblastoma cells by automated image analysis
2005
A new automated image analysis method for quantification of fluorescent dots is presented. This method facilitates counting the number of fluorescent puncta in specific locations of individual cells and also enables estimation of the number of cells by detecting the labeled nuclei. The method is here used for counting the AM1-43 labeled fluorescent puncta in human SH-SY5Y neuroblastoma cells induced to differentiate with all-trans retinoic acid (RA), and further stimulated with high potassium (K+) containing solution. The automated quantification results correlate well with the results obtained manually through visual inspection. The manual method has the disadvantage of being slow, labor-i…