Probability Of Alignment Research Articles

Probabilistic 3D alignment optimization of underground transport infrastructure integrating GIS-based subsurface characterization

Underground Transport construction is affected by various sources of uncertainty. These uncertainties must be identified, quantified and inherent risks assessed and managed. A crucial step in underground risk management is the planning and design phase. This paper presents an innovative probabilistic alignment optimization tool for underground tunnel construction, which considers uncertainties associated with geology and construction processes. It consists of an integrated approach of two existing tools; an interactive support system, the Decision Aids for Tunneling (DAT), and an optimization tool for linear infrastructure (Opt), which uses GIS-derived maps as input. The capabilities of the approach are demonstrated through an application to the optimization of a subway line at Masdar City, Abu Dhabi in the United Arab Emirates.

Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads

BackgroundGenome sequencing provides a powerful tool for pathogen detection and can help resolve outbreaks that pose public safety and health risks. Mapping of DNA reads to genomes plays a fundamental role in this approach, where accurate alignment and classification of sequencing data is crucial. Standard mapping methods crudely treat bases as independent from their neighbors. Accuracy might be improved by using higher order paired hidden Markov models (HMMs), which model neighbor effects, but introduce design and implementation issues that have typically made them impractical for read mapping applications. We present a variable-order paired HMM that we term VarHMM, which addresses central issues involved with higher order modeling for sequence alignment.ResultsCompared with existing alignment methods, VarHMM is able to model higher order distributions and quantify alignment probabilities with greater detail and accuracy. In a series of comparison tests, in which Ion Torrent sequenced DNA was mapped to similar bacterial strains, VarHMM consistently provided better strain discrimination than any of the other alignment methods that we compared with.ConclusionsOur results demonstrate the advantages of higher ordered probability distribution modeling and also suggest that further development of such models would benefit read mapping in a range of other applications as well.

Analyzing the teeth next to the alveolar cleft: Examination and treatment proposal prior to bone grafting based on three-dimensional versus two-dimensional diagnosis—A diagnostic study

PurposeThe objective was to evaluate the diagnostic and prognostic value of three-dimensional (3D) cone beam computed tomography (CBCT) on information about the cleft and alignment of cleft neighboring teeth. Materials and methodsPanoramic X-rays, small-volume CBCTs, and study casts of 20 patients with a total of 22 alveolar clefts were analyzed prior to secondary bone grafting. Six maxillofacial surgeons and 6 orthodontists rated the following parameters: visibility of alveolar cleft expansion, position and probability of alignment of cleft neighbored teeth. Two-dimensional (2D) X-rays and casts were rated first; CBCT and casts followed at least 4 weeks later. Radiologic bone height in the region of the former alveolar cleft, as well as alignment and reasons for nonalignment of cleft neighbored teeth, were recorded 4 years later. ResultsThe rate of proper proposals regarding the real treatment outcome using 2D- or 3D-material did not differ statistically. Although 5%–45% of the proposals were changed when using 3D instead of 2D records, Fleiss multirater kappas showed no essential differences. Raters' profession and experience had no influence on the rate of correct proposals. ConclusionIn orthodontics, small-volume CBCT may be justified only as supplement to a routine panoramic X-ray, and only in selected cases or for surgical preparation.

Figure of Merit for the Optimization of Wireless Power Transfer System Against Misalignment Tolerance

Optimization of wireless power transfer (WPT) systems with high performance and misalignment tolerance is investigated in this paper. Key performance indices of WPT are power transfer efficiency (PTE), transferred power (TP), and misalignment tolerance. Misalignment can be radial, axial, or angular, depending on the WPT receiver's degrees of freedom (DoF). A figure of merit (FOM) is proposed to optimize PTE, TP, and six-DoF (6DoF) misalignment tolerances simultaneously. Misalignments in 6DoF are segmented into subregions, and performance within each region is prioritized based on probability of alignment in deriving the FOM. A WPT system with tri-spiral repeater is introduced with the use of proposed FOM as the optimization objective. Theoretical analysis is experimentally validated.

Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds

BackgroundSpaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several alignment-free related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates. Moreover, it can be altered by a set of arbitrary chosen parameters from the probabilistic alignment models used. In this general context, Dominant seeds have been introduced by Mak and Benson (Bioinformatics 25:302–308, 2009) on the Bernoulli model, in order to reduce the number of spaced seed candidates that are further processed in a parameter-free calculation of the sensitivity.ResultsWe expand the scope of work of Mak and Benson on single and multiple seeds by considering the Hit Integration model of Chung and Park (BMC Bioinform 11:31, 2010), demonstrate that the same dominance definition can be applied, and that a parameter-free study can be performed without any significant additional cost. We also consider two new discrete models, namely the Heaviside and the Dirac models, where lossless seeds can be integrated. From a theoretical standpoint, we establish a generic framework on all the proposed models, by applying a counting semi-ring to quickly compute large polynomial coefficients needed by the dominance filter. From a practical standpoint, we confirm that dominant seeds reduce the set of, either single seeds to thoroughly analyse, or multiple seeds to store. Moreover, in http://bioinfo.cristal.univ-lille.fr/yass/iedera_dominance, we provide a full list of spaced seeds computed on the four aforementioned models, with one (continuous) parameter left free for each model, and with several (discrete) alignment lengths.

A Search for Binary Star Companions to the KELT Planet Hosts and a Comparison Sample. I. Results of DSSI Observations

Abstract We are conducting a search for binary companions around 11 hot-Jupiter hosts from the Kilodegree Extremely Little Telescope (KELT) survey and a large comparison sample of stars shown by KELT to not host a transiting hot Jupiter. The primary stars are bright (7.5 < V < 11) and of similar distance from Earth (100 < d < 300 pc). In this paper, we present the results of our observations using the Differential Speckle Survey Instrument. We observed 9 of the 14 KELT planet hosts that are visible from the northern hemisphere and 51 comparison stars, discovering two new potential companions and re-observing two previously known possible binary systems and one confirmed binary system. We provide an estimate of the chance alignment probability for our observed candidate binaries.

Discovery of wide low and very low-mass binary systems using Virtual Observatory tools

The frequency of multiple systems and their properties are key constraints of stellar formation and evolution. Formation mechanisms of very low-mass (VLM) objects are still under considerable debate and an accurate assessment of their multiplicity and orbital properties are essential for constraining current theoretical models. Taking advantage of the Virtual Observatory capabilities, we looked for comoving low and VLM binary (or multiple) systems using the Large Area Survey of the UKIDSS LAS DR10, SDSS DR9, and the 2MASS Catalogues. Other catalogues (WISE, GLIMPSE, SuperCosmos ...) were used to derive the physical parameters of the systems. We report the identification of 36 low and VLM (~M0-L0 spectral types) candidates to binary/multiple system (separations between 200 and 92000 AU), whose physical association is confirmed through common proper motion, distance and low probability of chance alignment. This new system list notably increases the previous sampling in their mass-separation parameter space (~100). We have also found 50 low-mass objects that we can classify as ~L0-T2 according to their photometric information. Only one of these objects presents a common proper motion high-mass companion. Although we could not constrain the age of the majority of the candidates, probably most of them are still bound except four that may be under disruption processes. We suggest that our sample could be divided in two populations: one tightly bound wide VLM systems that are expected to last more than 10 Gyr, and other formed by weak bound wide VLM systems that will dissipate within a few Gyr.

Erratum to: General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?

Erratum to: General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?

General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation.

BackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a method to reliably calculate the occurrence probabilities of sequence alignments via evolutionary processes on an entire sequence. Previously, we presented a perturbative formulation that facilitates the ab initio calculation of alignment probabilities under a continuous-time Markov model, which describes the stochastic evolution of an entire sequence via indels with quite general rate parameters. And we demonstrated that, under some conditions, the ab initio probability of an alignment can be factorized into the product of an overall factor and contributions from regions (or local alignments) delimited by gapless columns.ResultsHere, using our formulation, we attempt to approximately calculate the probabilities of local alignments under space-homogeneous cases. First, for each of all types of local pairwise alignments (PWAs) and some typical types of local multiple sequence alignments (MSAs), we numerically computed the total contribution from all parsimonious indel histories and that from all next-parsimonious histories, and compared them. Second, for some common types of local PWAs, we derived two integral equation systems that can be numerically solved to give practically exact solutions. We compared the total parsimonious contribution with the practically exact solution for each such local PWA. Third, we developed an algorithm that calculates the first-approximate MSA probability by multiplying total parsimonious contributions from all local MSAs. Then we compared the first-approximate probability of each local MSA with its absolute frequency in the MSAs created via a genuine sequence evolution simulator, Dawg. In all these analyses, the total parsimonious contributions approximated the multiplication factors fairly well, as long as gap sizes and branch lengths are at most moderate. Examination of the accuracy of another indel probabilistic model in the light of our formulation indicated some modifications necessary for the model’s accuracy improvement.ConclusionsAt least under moderate conditions, the approximate methods can quite accurately calculate ab initio alignment probabilities under biologically more realistic models than before. Thus, our formulation will provide other indel probabilistic models with a sound reference point.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1167-6) contains supplementary material, which is available to authorized users.

FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners.

Despite RNA-seq reads provide quality scores that represent the probability of calling a correct base, these values are not probabilistically integrated in most alignment algorithms. Based on the quality scores of the reads, we propose to calculate a lower bound of the probability of alignment of any fast alignment algorithm that generates SAM files. This bound is called Fast Bayesian Bound (FBB) and serves as a canonical reference to compare alignment results across different algorithms. This Bayesian Bound intends to provide additional support to the current state-of-the-art aligners, not to replace them. We propose a feasible Bayesian bound that uses quality scores of the reads to align them to a genome of reference. Two theorems are provided to efficiently calculate the Bayesian bound that under some conditions becomes the equality. The algorithm reads the SAM files generated by the alignment algorithms using multiple command option values. The program options are mapped into the FBB reference values, and all the aligners can be compared respect to the same accuracy values provided by the FBB. Stranded paired read RNA-seq data was used for evaluation purposes. The errors of the alignments can be calculated based on the information contained in the distance between the pairs given by Theorem 2, and the alignments to the incorrect strand. Most of the algorithms (Bowtie, Bowtie 2, SHRiMP2, Soap 2, Novoalign) provide similar results with subtle variations. Current version of the FBB software is provided at https://bitbucket.org/irenerodriguez/fbb CONTACT: rhuerta@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online.

General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?

BackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. Recently, indel probabilistic models are mostly based on either hidden Markov models (HMMs) or transducer theories, both of which give the indel component of the probability of a given sequence alignment as a product of either probabilities of column-to-column transitions or block-wise contributions along the alignment. However, it is not a priori clear how these models are related with any genuine stochastic evolutionary model, which describes the stochastic evolution of an entire sequence along the time-axis. Moreover, currently none of these models can fully accommodate biologically realistic features, such as overlapping indels, power-law indel-length distributions, and indel rate variation across regions.ResultsHere, we theoretically dissect the ab initio calculation of the probability of a given sequence alignment under a genuine stochastic evolutionary model, more specifically, a general continuous-time Markov model of the evolution of an entire sequence via insertions and deletions. Our model is a simple extension of the general “substitution/insertion/deletion (SID) model”. Using the operator representation of indels and the technique of time-dependent perturbation theory, we express the ab initio probability as a summation over all alignment-consistent indel histories. Exploiting the equivalence relations between different indel histories, we find a “sufficient and nearly necessary” set of conditions under which the probability can be factorized into the product of an overall factor and the contributions from regions separated by gapless columns of the alignment, thus providing a sort of generalized HMM. The conditions distinguish evolutionary models with factorable alignment probabilities from those without ones. The former category includes the “long indel” model (a space-homogeneous SID model) and the model used by Dawg, a genuine sequence evolution simulator.ConclusionsWith intuitive clarity and mathematical preciseness, our theoretical formulation will help further advance the ab initio calculation of alignment probabilities under biologically realistic models of sequence evolution via indels.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1105-7) contains supplementary material, which is available to authorized users.

The effect of alignment on the electric mobility of soot

ABSTRACTThe effect of an aligning electric field on the mobility of both flame generated smoke and smolder generated smoke was studied. A pulsed differential mobility analyzer was used to study the alignment without changing the DMA flows. No detectable change in the mobility was observed for the smolder smoke, while a small but detectable effect of up to 5% decrease in the mobility diameter with increasing field was observed for the largest aggregates with a mobility diameter of 200 nm. We modeled the friction coefficient tensor of soot fractal aggregates as an equivalent prolate spheroid to obtain the field induced mobility as a function of aspect ratio. The alignment probability distribution function was determined by computing the polarizability tensor for simulated fractal aggregates. One interesting result was the smallness of the prolate sphere aspect ratio of 1.2 to 1.3 compared to the much larger aspect ratio from TEM analysis and from the polarizability ratio. An explanation for the low value ba...

Interplay between Intrinsic Conformational Propensities and Intermolecular Interactions in the Self-Assembly of Short Surfactant-like Peptides Composed of Leucine/Isoleucine.

To study how the conformational propensities of individual amino acid residues, primary structures (i.e., adjacent residues and molecular lengths), and intermolecular interactions of peptides affect their self-assembly properties, we report the use of replica exchange molecular dynamics (REMD) to investigate the monomers, dimers, and trimers of a series of short surfactant-like peptides (I3K, L3K, L4K, and L5K). For four-residue peptides X3K (I3K and L3K), the results show that their different aggregation behaviors arise from the different intrinsic conformational propensities of isoleucine and leucine. For LmK peptides (L3K, L4K, and L5K), the molecular length is found to dictate their aggregation via primarily modulating intermolecular interactions. Increasing the number of hydrophobic amino acid residues of LmK peptides enhances their intermolecular H-bonding and promotes the formation of β-strands in dimer and trimer aggregates, overwhelming the intrinsic preference of Leu for helical structures. Thus, the interplay between the conformational propensities of individual amino acid residues for secondary structures and molecular interactions determines the self-assembly properties of the peptides, and the competition between intramolecular and intermolecular H-bonding interactions determines the probability of β-sheet alignment of peptide molecules. These results are validated by comparing simulated and experimental CD spectra of the peptides. This study will aid the design of short peptide amphiphiles and improve the mechanistic understanding of their self-assembly behavior.

Velocity Condensation for Magnetotactic Bacteria.

Magnetotactic swimmers tend to align along magnetic field lines against stochastic reorientations. We show that the swimming strategy, e.g., active Brownian motion versus run-and-tumble dynamics, strongly affects the orientation statistics. The latter can exhibit a velocity condensation whereby the alignment probability density diverges. As a consequence, we find that the swimming strategy affects the nature of the phase transition to collective motion, indicating that Lévy run-and-tumble walks can outperform active Brownian processes as strategies to trigger collective behavior.

Alignments of radio galaxies in deep radio imaging of ELAIS N1

Abstract We present a study of the distribution of radio jet position angles of radio galaxies over an area of 1 square degree in the ELAIS N1 field. ELAIS N1 was observed with the Giant Metrewave Radio Telescope at 612 MHz to an rms noise level of 10 μJy and angular resolution of 6 arcsec × 5 arcsec. The image contains 65 resolved radio galaxy jets. The spatial distribution reveals a prominent alignment of jet position angles along a ‘filament’ of about 1°. We examine the possibility that the apparent alignment arises from an underlying random distribution and find that the probability of chance alignment is less than 0.1 per cent. An angular covariance analysis of the data indicates the presence of spatially coherence in position angles on scales >0 $_{.}^{\circ}$5. This angular scales translates to a comoving scale of >20 Mpc at a redshift of 1. The implied alignment of the spin axes of massive black holes that give rise to the radio jets suggest the presence of large-scale spatial coherence in angular momentum. Our results reinforce prior evidence for large-scale spatial alignments of quasar optical polarization position angles.

Experimental study of vorticity-strain rate interaction in turbulent partially premixed jet flames using tomographic particle image velocimetry

In turbulent flows, the interaction between vorticity, ω, and strain rate, s, is considered a primary mechanism for the transfer of energy from large to small scales through vortex stretching. The ω-s coupling in turbulent jet flames is investigated using tomographic particle image velocimetry (TPIV). TPIV provides a direct measurement of the three-dimensional velocity field from which ω and s are determined. The effects of combustion and mean shear on the ω-s interaction are investigated in turbulent partially premixed methane/air jet flames with high and low probabilities of localized extinction as well as in a non-reacting isothermal air jet with Reynolds number of approximately 13 000. Results show that combustion causes structures of high vorticity and strain rate to agglomerate in highly correlated, elongated layers that span the height of the probe volume. In the non-reacting jet, these structures have a more varied morphology, greater fragmentation, and are not as well correlated. The enhanced spatiotemporal correlation of vorticity and strain rate in the stable flame results in stronger ω-s interaction characterized by increased enstrophy and strain-rate production rates via vortex stretching and straining, respectively. The probability of preferential local alignment between ω and the eigenvector of the intermediate principal strain rate, s2, which is intrinsic to the ω-s coupling in turbulent flows, is larger in the flames and increases with the flame stability. The larger mean shear in the flame imposes a preferential orientation of ω and s2 tangential to the shear layer. The extensive and compressive principal strain rates, s1 and s3, respectively, are preferentially oriented at approximately 45° with respect to the jet axis. The production rates of strain and vorticity tend to be dominated by instances in which ω is parallel to the s1¯-s2¯ plane and orthogonal to s3¯.

Higher-order Lexical Semantic Models for Non-factoid Answer Reranking

Lexical semantic models provide robust performance for question answering, but, in general, can only capitalize on direct evidence seen during training. For example, monolingual alignment models acquire term alignment probabilities from semi-structured data such as question-answer pairs; neural network language models learn term embeddings from unstructured text. All this knowledge is then used to estimate the semantic similarity between question and answer candidates. We introduce a higher-order formalism that allows all these lexical semantic models to chain direct evidence to construct indirect associations between question and answer texts, by casting the task as the traversal of graphs that encode direct term associations. Using a corpus of 10,000 questions from Yahoo! Answers, we experimentally demonstrate that higher-order methods are broadly applicable to alignment and language models, across both word and syntactic representations. We show that an important criterion for success is controlling for the semantic drift that accumulates during graph traversal. All in all, the proposed higher-order approach improves five out of the six lexical semantic models investigated, with relative gains of up to +13% over their first-order variants.

Supervoids in the WISE–2MASS catalogue imprinting cold spots in the cosmic microwave background

The Cold Spot (CS) is a clear feature in the Cosmic Microwave Background (CMB); it could be of primordial origin, or caused by a intervening structure along the line of sight. We identified a large projected underdensity in the recently constructed WISE-2MASS all-sky infrared galaxy catalogue aligned with the Cold Spot direction at $(l,b)\approx(209^\circ,-57^\circ)$. It has an angular size of tens of degrees, and shows a $\sim20\%$ galaxy underdensity in the center. Moreover, we find another large underdensity in the projected WISE-2MASS galaxy map at $(l,b)\approx(101^\circ,46^\circ)$ (hereafter Draco Supervoid), also aligned with a CMB decrement, although less significant than that of the CS direction. Motivated by these findings, we develop spherically symmetric Lemaitre-Tolman-Bondi (LTB) compensated void models to explain the observed CMB decrements with these two underdensities, or "supervoids". Within our perturbative treatment of the LTB voids, we find that the Integrated Sachs-Wolfe and Riess-Sciama effects due to the Draco Supervoid can account for the CMB decrement observed in the same direction. On the contrary, the extremely deep CMB decrement in the CS direction is more difficult to explain by the presence of the CS supervoid only. Nevertheless, the probability of a random alignment between the CS and the corresponding supervoid is disfavored, and thus its contribution as a secondary anisotropy cannot be neglected. We comment on how the approximations used in this paper, in particular the assumption of spherical symmetry, could change quantitatively our conclusions and might provide a better explanation for the CMB CS.

Numerical prediction of flow induced fibers orientation in injection molded polymer composites

Since the filling stage of injection molding process has important effect on the determination of the orientation state of the fibers, accurate analysis of the flow field for the mold filling stage becomes a necessity. The aim of the paper is to characterize the flow induced orientation state of short fibers in injection molding cavities. A dog-bone shaped model is considered for the simulation and experiment. The numerical model for determination of the fibers orientation during mold-filling stage of injection molding process was solved using Computational Fluid Dynamics (CFD) software called MoldFlow. Both the simulation and experimental results showed that two different regions (or three layers of orientation structures) across the thickness of the specimen could be found: a shell region which is near to the mold cavity wall, and a core region at the middle of the cross section. The simulation results support the experimental observations that for thin plates the probability of fiber alignment to the flow direction near the mold cavity walls is high but low at the core region. It is apparent that the results of this study could assist in decisions regarding short fiber reinforced polymer composites.

Correlation between cervical spine sagittal alignment and clinical outcome after cervical laminoplasty for ossification of the posterior longitudinal ligament.

The goal of this study was to determine the relationship between cervical spine sagittal alignment and clinical outcomes after cervical laminoplasty in patients with ossification of the posterior longitudinal ligament (OPLL). Fifty consecutive patients who underwent a cervical laminoplasty for OPLL between January 2012 and January 2013 and who were followed up for at least 1 year were analyzed in this study. Standing plain radiographs of the cervical spine, CT (midsagittal view), and MRI (T2-weighted sagittal view) were obtained (anteroposterior, lateral, flexion, and extension) pre- and postoperatively. Cervical spine alignment was assessed with the following 3 parameters: the C2-7 Cobb angle, C2-7 sagittal vertical axis (SVA), and T-1 slope minus C2-7 Cobb angle. The change in cervical sagittal alignment was defined as the difference between the post- and preoperative C2-7 Cobb angles, C2-7 SVAs, and T-1 slope minus C2-7 Cobb angles. Outcome assessments (visual analog scale [VAS], Oswestry Neck Disability Index [NDI], 36-Item Short-Form Health Survey [SF-36], and Japanese Orthopaedic Association [JOA] scores) were obtained in all patients pre- and postoperatively. The average patient age was 56.3 years (range 38-72 years). There were 34 male patients and 16 female patients. Cervical laminoplasty for OPLL helped alleviate radiculomyelopathy. Compared with the preoperative scores, improvement was seen in postoperative VAS and JOA scores. After laminoplasty, 35 patients had kyphotic changes, and 15 had lordotic changes. However, cervical sagittal alignment after laminoplasty was not significantly associated with clinical outcomes in terms of postoperative improvement of the JOA score (C2-7 Cobb angle: p = 0.633; C2-7 SVA: p = 0.817; T-1 slope minus C2-7 lordosis: p = 0.554), the SF-36 score (C2-7 Cobb angle: p = 0.554; C2-7 SVA: p = 0.793; T-1 slope minus C2-7 lordosis: p = 0.829), the VAS neck score (C2-7 Cobb angle: p = 0.263; C2-7 SVA: p = 0.716; T-1 slope minus C2-7 lordosis: p = 0.497), or the NDI score (C2-7 Cobb angle: p = 0.568; C2-7 SVA: p = 0.279; T-1 slope minus C2-7 lordosis: p = 0.966). Similarly, the change in cervical sagittal alignment was not related to the JOA (p = 0.604), SF-36 (p = 0.308), VAS neck (p = 0.832), or NDI (p = 0.608) scores. Cervical laminoplasty for OPLL improved radiculomyelopathy. Cervical laminoplasty increased the probability of cervical kyphotic alignment. However, cervical sagittal alignment and clinical outcomes were not clearly related.