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The K-SVD algorithm has been successfully utilized for adaptively learning the sparse dictionary in 2-D seismic denoising. Because of the high computational cost of many singular value decompositions (SVDs) in the K-SVD algorithm, it is not applicable in practical situations, especially in 3-D or 5-D problems. In this paper, I extend the dictionary learning based denoising approach from 2-D to 3-D. To address the computational efficiency problem in K-SVD, I propose a fast dictionary learning approach based on the sequential generalized K-means (SGK) algorithm for denoising multidimensional seismic data. The SGK algorithm updates each dictionary atom by taking an arithmetic average of several training signals instead of calculating an SVD as used in K-SVD algorithm. I summarize the sparse dictionary learning algorithm using K-SVD, and introduce SGK algorithm together with its detailed mathematical implications. 3-D synthetic, 2-D and 3-D field data examples are used to demonstrate the performance of both K-SVD and SGK algorithms. It has been shown that SGK algorithm can significantly increase the computational efficiency while only slightly degrading the denoising performance. [ABSTRACT FROM AUTHOR]

A Kepler solver is an analytical method used to solve a two-body problem. In this paper, we propose a new correction method by slightly modifying the Kepler solver. The only change to the analytical solutions is that the obtainment of the eccentric anomaly relies on the true anomaly that is associated with a unit radial vector calculated by an integrator. This scheme rigorously conserves all integrals and orbital elements except the mean longitude. However, the Kepler energy, angular momentum vector, and Laplace–Runge–Lenz vector for perturbed Kepler problems are slowly varying quantities. However, their integral invariant relations give the quantities high-precision values that directly govern five slowly varying orbital elements. These elements combined with the eccentric anomaly determine the desired numerical solutions. The newly proposed method can considerably reduce various errors for a post-Newtonian two-body problem compared with an uncorrected integrator, making it suitable for a dissipative two-body problem. Spurious secular changes of some elements or quasi-integrals in the outer Solar system may be caused by short integration times of the fourth-order Runge–Kutta algorithm. However, they can be eliminated in a long integration time of 108 yr by the proposed method, similar to Wisdom–Holman second-order symplectic integrator. The proposed method has an advantage over the symplectic algorithm in the accuracy but gives a larger slope to the phase error growth. [ABSTRACT FROM AUTHOR]

Motivation The generalized linear mixed model (GLMM) is an extension of the generalized linear model (GLM) in which the linear predictor takes random effects into account. Given its power of precisely modeling the mixed effects from multiple sources of random variations, the method has been widely used in biomedical computation, for instance in the genome-wide association studies (GWASs) that aim to detect genetic variance significantly associated with phenotypes such as human diseases. Collaborative GWAS on large cohorts of patients across multiple institutions is often impeded by the privacy concerns of sharing personal genomic and other health data. To address such concerns, we present in this paper a privacy-preserving Expectation–Maximization (EM) algorithm to build GLMM collaboratively when input data are distributed to multiple participating parties and cannot be transferred to a central server. We assume that the data are horizontally partitioned among participating parties: i.e. each party holds a subset of records (including observational values of fixed effect variables and their corresponding outcome), and for all records, the outcome is regulated by the same set of known fixed effects and random effects. Results Our collaborative EM algorithm is mathematically equivalent to the original EM algorithm commonly used in GLMM construction. The algorithm also runs efficiently when tested on simulated and real human genomic data, and thus can be practically used for privacy-preserving GLMM construction. We implemented the algorithm for collaborative GLMM (cGLMM) construction in R. The data communication was implemented using the rsocket package. Availability and implementation The software is released in open source at https://github.com/huthvincent/cGLMM. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Semi-automated segmentation algorithms hold promise for improving extraction and identification of objects in images such as tumors in medical images of human tissue, counting plants or flowers for crop yield prediction or other tasks where object numbers and appearance vary from image to image. By blending markup from human annotators to algorithmic classifiers, the accuracy and reproducability of image segmentation can be raised to very high levels. At least, that is the promise of this approach, but the reality is less than clear. In this paper, we review the state-of-the-art in semi-automated image segmentation performance assessment and demonstrate it to be lacking the level of experimental rigour needed to ensure that claims about algorithm accuracy and reproducability can be considered valid. We follow this review with two experiments that vary the type of markup that annotators make on images, either points or strokes, in tightly controlled experimental conditions in order to investigate the effect that this one particular source of variation has on the accuracy of these types of systems. In both experiments, we found that accuracy substantially increases when participants use a stroke-based interaction. In light of these results, the validity of claims about algorithm performance are brought into sharp focus, and we reflect on the need for a far more control on variables for benchmarking the impact of annotators and their context on these types of systems. [ABSTRACT FROM AUTHOR]

Testing with synthetic data sets is a vital stage in an algorithm's development for benchmarking the algorithm's performance. A common addition to synthetic data sets is White, Gaussian Noise (WGN) which is used to mimic noise that would be present in recorded data sets. The first section of this paper focuses on comparing the effects of WGN and realistic modelled noise on standard microseismic event detection and imaging algorithms using synthetic data sets with recorded noise as a benchmark. The data sets with WGN underperform on the trace-by-trace algorithm while overperforming on algorithms utilizing the full array. Throughout, the data sets with realistic modelled noise perform near identically to the recorded noise data sets. The study concludes by testing an algorithm that simultaneously solves for the source location and moment tensor of a microseismic event. Not only does the algorithm fail to perform at the signal-to-noise ratios indicated by the WGN results but the results with realistic modelled noise highlight pitfalls of the algorithm not previously identified. The misleading results from the WGN data sets highlight the need to test algorithms under realistic noise conditions to gain an understanding of the conditions under which an algorithm can perform and to minimize the risk of misinterpretation of the results. [ABSTRACT FROM AUTHOR]

The use of signalling pathway hypergraphs represented as process description diagrams is steadily becoming more pervasive in the field of biology. This makes ever more evident the necessity for an effective automated layout that can replicate high-quality manually drawn diagrams. The complexity and idiosyncrasies of these diagrams, as well as the specific tasks the end users perform with them, mean that a layout must meet many requirements beyond the simple metrics used in existing automated computational approaches. In this paper we outline these requirements, examine existing ones and describe new ones. We demonstrate state-of-the-art layout techniques enhanced with novel functionalities to meet part of the requirements. For comparatively small signalling pathways our enhanced algorithm provides results close to manually drawn layouts. In addition, we suggest technical approaches that may be suited for fulfilling the identified requirements currently not covered. [ABSTRACT FROM AUTHOR]

In this paper, an efficient algorithm is developed to automatically detect and extract coronal loops. First of all, in the algorithm, three characteristics associated with coronal loops are used to construct a match filter able to enhance the loops. Secondly, the method combining a high-pass filter (unsharp-mask enhancement) with a global threshold is used to further enhance and segment the loops. Thirdly, to extract every individual coronal loop and obtain their parameters (the 2D projected space coordinates and lengths) from the segmented loops, a clustering method of the pixels with approximate local direction and connected domain is further used. Fourthly, to evaluate the performance of the developed algorithm, images observed by the Transition Region and Coronal Explorer (TRACE), the Atmospheric Imaging Assembly (AIA) of the Solar Dynamics Observatory (SDO) and the High-Resolution Coronal Imager (Hi-C) are used, and comparison experiments between the existing algorithms and the developed algorithm are performed. Finally, it is found that the developed algorithm is commensurate with the two most promising algorithms, oriented coronal curved loop tracing (OCCULT) and its improved version, OCCULT-2, in performance. Therefore, for scientific applications associated with coronal loops, the developed algorithm will be a powerful tool. [ABSTRACT FROM AUTHOR]

Motivation In high dimensional genetic data analysis, the objective is to select important biomarkers which are involved in some biological processes, such as disease progression, immune response, etc. The experimental data are often collected from different platforms including microarray experiments and proteomic experiments. The conventional single-platform approach lacks the capability to learn from multiple platforms, and the resulted lists of biomarkers vary across different platforms. There is a great need to develop an algorithm which can aggregate information across platforms and provide a consolidated list of biomarkers across different platforms. Results In this paper, we introduce an R package FusionLearn , which implements a fusion learning algorithm to analyze cross-platform data. The consolidated list of biomarkers is selected by the technique of group penalization. We first apply the algorithm on a collection of breast cancer microarray experiments from the NCBI (National Centre for Biotechnology Information) microarray database and the resulted list of selected genes have higher classification accuracy rate across different datasets than the lists generated from each single dataset. Secondly, we use the software to analyze a combined microarray and proteomic dataset for the study of the growth phase versus the stationary phase in Streptomyces coelicolor. The selected biomarkers demonstrate consistent differential behavior across different platforms. Availability and implementation R package: https://cran.r-project.org/package=FusionLearn. [ABSTRACT FROM AUTHOR]

Objective. To formulate timely evidence-based guidelines for the management of opioid-induced bowel dysfunction. Setting. Constipation is a major untoward effect of opioids. Increasing prescription of opioids has correlated to increased incidence of opioid-induced constipation. However, the inhibitory effects of opioids are not confined to the colon, but also affect higher segments of the gastrointestinal tract, leading to the coining of the term "opioid-induced bowel dysfunction." Methods. A literature search was conducted using Medline, EMBASE, and EMBASE Classic, and the Cochrane Central Register of Controlled Trials. Predefined search terms and inclusion/exclusion criteria were used to identify and categorize relevant papers. A series of statements were formulated and justified by a comment, then labeled with the degree of agreement and their level of evidence as judged by the Strength of Recommendation Taxonomy (SORT) system. Results. From a list of 10,832 potentially relevant studies, 33 citations were identified for review. Screening the reference lists of the pertinent papers identified additional publications. Current definitions, prevalence, and mechanism of opioidinduced bowel dysfunction were reviewed, and a treatment algorithm and statements regarding patient management were developed to provide guidance on clinical best practice in the management of patients with opioid-induced constipation and opioid-induced bowel dysfunction. Conclusions. In recent years, more insight has been gained in the pathophysiology of this "entity"; new treatment approaches have been developed, but guidelines on clinical best practice are still lacking. Current knowledge is insufficient regarding management of the opioid side effects on the upper gastrointestinal tract, but recommendations can be derived from what we know at present. [ABSTRACT FROM AUTHOR]

Building Energy Internet of Things could collect and analyse various types of building energy consumption data in real time by means of low-energy consumption and high-precision sensing technology. In this paper, a low-energy consumption data transmission and fusion algorithm SMART-RR (Slice Mix Agg RegaTe-Repeatablibity Reduction) is proposed. Taking advantage of the periodic repeatability and data redundancy of building energy consumption data, a data fusion strategy with unequal long time intervals and adding repeatability reduction factor is proposed. The simulation results show that SMART-RR algorithm is a low-energy data transmission and fusion algorithm with small data traffic, high privacy protection and high accuracy. [ABSTRACT FROM AUTHOR]

The DNA is the fundamental basis of genetic information, just as bits are for computers. Whenever computers are used to represent genetic data, the computational encoding must be efficient to allow the representation of processes driving the inheritance and variability. This is especially important across simulations in view of the increasing complexity and dimensions brought by genomics. This paper introduces a new binary representation of genetic information. Algorithms as bitwise operations that mimic the inheritance of a wide range of polymorphisms are also presented. Different kinds and mixtures of polymorphisms are discussed and exemplified. Proposed algorithms and data structures were implemented in C++ programming language and is available to end users in the R package "isqg" which is available at the R repository (CRAN). Supplementary data are available online. [ABSTRACT FROM AUTHOR]

We develop a flexible and computationally efficient approach for analyzing high-throughput chemical genetic screens. In such screens, a library of genetic mutants is phenotyped in a large number of stresses. Typically, interactions between genes and stresses are detected by grouping the mutants and stresses into categories, and performing modified t-tests for each combination. This approach does not have a natural extension if mutants or stresses have quantitative or nonoverlapping annotations (e.g., if conditions have doses or a mutant falls into more than one category simultaneously). We develop a matrix linear model (MLM) framework that allows us to model relationships between mutants and conditions in a simple, yet flexible, multivariate framework. It encodes both categorical and continuous relationships to enhance detection of associations. We develop a fast estimation algorithm that takes advantage of the structure of MLMs. We evaluate our method's performance in simulations and in an Escherichia coli chemical genetic screen, comparing it with an existing univariate approach based on modified t-tests. We show that MLMs perform slightly better than the univariate approach when mutants and conditions are classified in nonoverlapping categories, and substantially better when conditions can be ordered in dosage categories. Therefore, it is an attractive alternative to current methods, and provides a computationally scalable framework for larger and complex chemical genetic screens. A Julia language implementation of MLMs and the code used for this paper are available at https://github.com/janewliang/GeneticScreen.jl and https:// bitbucket.org/jwliang/mlm_gs_supplement, respectively. [ABSTRACT FROM AUTHOR]

Motivation Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) is a recent technology to obtain spatially resolved gene or transcript expression profiles in single cells for hundreds to thousands of genes in parallel. So far, no statistical framework to analyze MERFISH data is available. Results We present a Bayesian model for single cell transcript expression analysis on MERFISH data. We show that the model successfully captures uncertainty in MERFISH data and eliminates systematic biases that can occur in raw RNA molecule counts obtained with MERFISH. Our model accurately estimates transcript expression and additionally provides the full probability distribution and credible intervals for each transcript. We further show how this enables MERFISH to scale towards the whole genome while being able to control the uncertainty in obtained results. Availability and implementation The presented model is implemented on top of Rust-Bio (Köster, 2016) and available open-source as MERFISHtools (https://merfishtools.github.io). It can be easily installed via Bioconda (Grüning et al. 2018). The entire analysis performed in this paper is provided as a fully reproducible Snakemake (Köster and Rahmann, 2012) workflow via Zenodo (https://doi.org/10.5281/zenodo.752340). Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Large-scale sequencing projects have confirmed the hypothesis that eukaryotic DNA is rich in repetitions whose functional role needs to be elucidated. In particular, tandem repeats (TRs) (i.e. short, almost identical sequences that lie adjacent to each other) have been associated to many cellular processes and, indeed, are also involved in several genetic disorders. The need of comprehensive lists of TRs for association studies and the absence of a computational model able to capture their variability have revived research on discovery algorithms. Results Building upon the idea that sequence similarities can be easily displayed using graphical methods, we formalized the structure that TRs induce in dot-plot matrices where a sequence is compared with itself. Leveraging on the observation that a compact representation of these matrices can be built and searched in linear time, we developed Dot2dot : an accurate algorithm fast enough to be suitable for whole-genome discovery of TRs. Experiments on five manually curated collections of TRs have shown that Dot2dot is more accurate than other established methods, and completes the analysis of the biggest known reference genome in about one day on a standard PC. Availability and implementation Source code and datasets are freely available upon paper acceptance at the URL: https://github.com/Gege7177/Dot2dot. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

A recent paper by Ge et al. performs a series of experiments with two full spectral fitting codes, ppxf and starlight  , finding that the two yield consistent results when the input spectrum is not heavily reddened. For |$E(B-V) \gtrsim 0.2$|⁠, however, they claim starlight  leads to severe biases in the derived properties. Counterintuitively, and at odds with previous simulations, they find that this behaviour worsens significantly as the signal-to-noise ratio of the input spectrum increases. This communication shows that this is entirely due to an AV < 1 mag condition imposed while initializing the Markov chains in the code. This choice is normally irrelevant in real-life galaxy work but can become critical in artificial experiments. Alleviating this usually harmless initialization constraint changes the Ge et al. results completely, as was explained to the authors before their publication. We replicate their spectral fitting experiments, finding much smaller biases. Furthermore, both bias and scatter in the derived properties converge as signal to noise increases, as one would expect. We also show how the very output of the code provides ways of diagnosing anomalies in the fits. [ABSTRACT FROM AUTHOR]

A review, recently published in this journal by Fang (2019), showed that methods trained for the prediction of protein stability changes upon mutation have a very critical bias: they neglect that a protein variation (A- > B) and its reverse (B- > A) must have the opposite value of the free energy difference (ΔΔGAB = − ΔΔGBA). In this letter, we complement the Fang's paper presenting a more general view of the problem. In particular, a machine learning-based method, published in 2015 (INPS), addressed the bias issue directly. We include the analysis of the missing method, showing that INPS is nearly insensitive to the addressed problem. [ABSTRACT FROM AUTHOR]

Motivation Machine learning plays a substantial role in bioscience owing to the explosive growth in sequence data and the challenging application of computational methods. Peptide-recognition domains (PRDs) are critical as they promote coupled-binding with short peptide-motifs of functional importance through transient interactions. It is challenging to build a reliable predictor of peptide-binding residue in proteins with diverse types of PRDs from protein sequence alone. On the other hand, it is vital to cope up with the sequencing speed and to broaden the scope of study. Results In this paper, we propose a machine-learning-based tool, named PBRpredict, to predict residues in peptide-binding domains from protein sequence alone. To develop a generic predictor, we train the models on peptide-binding residues of diverse types of domains. As inputs to the models, we use a high-dimensional feature set of chemical, structural and evolutionary information extracted from protein sequence. We carefully investigate six different state-of-the-art classification algorithms for this application. Finally, we use the stacked generalization approach to non-linearly combine a set of complementary base-level learners using a meta-level learner which outperformed the winner-takes-all approach. The proposed predictor is found competitive based on statistical evaluation. Availability and implementation PBRpredict-Suite software: http://cs.uno.edu/~tamjid/Software/PBRpredict/pbrpredict-suite.zip. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Protein structure alignment is a significant tool to understand evolutionary processes and physicochemical properties of proteins. Important targets of structure alignment are not only monomeric but also oligomeric proteins that sometimes include domain swapping or fusions. Although various protein structural alignment programs have been developed, no method is applicable to any protein pair regardless of the number of chain components and oligomeric states with retaining sequential restrictions: structurally equivalent regions must be aligned in the same order along protein sequences. Results In this paper, we introduced a new sequential protein structural alignment algorithm MICAN-SQ, which is applicable to protein structures in all oligomeric states. In particular, MICAN-SQ allows the complicated structural alignments of proteins with domain swapping or fusion regions. To validate MICAN-SQ, alignment accuracies were evaluated using curated alignments of monomers and examples of domain swapping, and compared with those of pre-existing protein structural alignment programs. The results of this study show that MICAN-SQ has superior accuracy and robustness in comparison with previous programs and offers limited computational times. We also demonstrate that MICAN-SQ correctly aligns very large complexes and fused proteins. The present computations warrant the consideration of MICAN-SQ for studies of evolutionary and physicochemical properties of monomeric structures and all oligomer types. Availability and implementation The MICAN program was implemented in C. The source code and executable file can be freely downloaded from http://www.tbp.cse.nagoya-u.ac.jp/MICAN/. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

STREAMFINDER is a new algorithm that we have built to detect stellar streams in an automated and systematic way in astrophysical datasets that possess any combination of positional and kinematic information. In Paper I, we introduced the methodology and the workings of our algorithm and showed that it is capable of detecting ultra-faint and distant halo stream structures containing as few as ∼15 members (ΣG ∼ 33.6 mag arcsec−2) in the Gaia dataset. Here, we test the method with real proper motion data from the Pan-STARRS1 survey, and by selecting targets down to r 0 = 18.5 mag we show that it is able to detect the GD-1 stellar stream, whereas the structure remains below a useful detection limit when using a Matched Filter technique. The radial velocity solutions provided by STREAMFINDER for GD-1 candidate members are found to be in good agreement with observations. Furthermore, our algorithm detects a $${\sim } 40^{^\circ }$$ long structure approximately parallel to GD-1, and which fans out from it, possibly a sign of stream-fanning due to the triaxiality of the Galactic potential. This analysis shows the promise of this method for detecting and analysing stellar streams in the upcoming Gaia DR2 catalogue. [ABSTRACT FROM AUTHOR]

Summary Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome and long repeats. An accurate assessment of scaffolding tools should take into account multiple locations of the same contig on the reference scaffolding rather than matching a repeat to a single best location. This makes mapping of inferred scaffoldings onto the reference a computationally challenging problem. This paper formulates the repeat-aware scaffolding evaluation problem, which is to find a mapping of the inferred scaffolding onto the reference maximizing number of correct links and proposes a scalable algorithm capable of handling large whole-genome datasets. Our novel scaffolding validation framework has been applied to assess the most of state-of-the-art scaffolding tools on the representative subset of Genome Assembly Golden-Standard Evaluations (GAGE) datasets and some novel simulated datasets. Availability and implementation The source code of this evaluation framework is available at https://github.com/mandricigor/repeat-aware. The documentation is hosted at https://mandricigor.github.io/repeat-aware. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

The convolution of galaxy images by the point spread function (PSF) is the dominant source of bias for weak gravitational lensing studies, and an accurate estimate of the PSF is required to obtain unbiased shape measurements. The PSF estimate for a galaxy depends on its spectral energy distribution (SED), because the instrumental PSF is generally a function of the wavelength. In this paper we explore various approaches to determine the resulting 'effective' PSF using broad-band data. Considering the Euclid mission as a reference, we find that standard SED template fitting methods result in biases that depend on source redshift, although this may be remedied if the algorithms can be optimized for this purpose. Using a machine learning algorithm we show that, at least in principle, the required accuracy can be achieved with the current survey parameters. It is also possible to account for the correlations between photometric redshift and PSF estimates that arise from the use of the same photometry. We explore the impact of errors in photometric calibration, errors in the assumed wavelength dependence of the PSF model, and limitations of the adopted template libraries. Our results indicate that the required accuracy for Euclid can be achieved using the data that are planned to determine photometric redshifts. [ABSTRACT FROM AUTHOR]

This paper develops an efficient hierarchical trans-dimensional (trans-D) Bayesian algorithm to invert magnetotelluric (MT) data for subsurface geoelectrical structure, with unknown geophysical model parameterization (the number of conductivity-layer interfaces) and data- error models parameterized by an auto-regressive (AR) process to account for potential error correlations. The reversible-jump Markov-chain Monte Carlo algorithm, which adds/removes interfaces and AR parameters in birth/death steps, is applied to sample the trans-D posterior probability density for model parameterization, model parameters, error variance and AR parameters, accounting for the uncertainties of model dimension and data-error statistics in the uncertainty estimates of the conductivity profile. To provide efficient sampling over the multiple subspaces of different dimensions, advanced proposal schemes are applied. Parameter perturbations are carried out in principal-component space, defined by eigen-decomposition of the unit-lag model covariance matrix, to minimize the effect of inter-parameter correlations and provide effective perturbation directions and length scales. Parameters of new layers in birth steps are proposed from the prior, instead of focused distributions centred at existing values, to improve birth acceptance rates. Parallel tempering, based on a series of parallel interacting Markov chains with successively relaxed likelihoods, is applied to improve chain mixing over model dimensions. The trans-D inversion is applied in a simulation study to examine the resolution of model structure according to the data information content. The inversion is also applied to a measured MT data set from south-central Australia. [ABSTRACT FROM AUTHOR]

Frequency-dependent amplitude absorption and phase velocity dispersion are typically linked by the causality-imposed Kramers-Kronig relations, which inevitably degrade the quality of seismic data. Seismic attenuation compensation is an important processing approach for enhancing signal resolution and fidelity, which can be performed on either pre-stack or post-stack data so as to mitigate amplitude absorption and phase dispersion effects resulting from intrinsic anelasticity of subsurface media. Inversion-based compensation with L1 norm constraint, enlightened by the sparsity of the reflectivity series, enjoys better stability over traditional inverse Q filtering. However, constrained L1 minimization serving as the convex relaxation of the literal L0 sparsity count may not give the sparsest solution when the kernel matrix is severely ill conditioned. Recently, non-convex metric for compressed sensing has attracted considerable research interest. In this paper, we propose a nearly unbiased approximation of the vector sparsity, denoted as L1-2 minimization, for exact and stable seismic attenuation compensation. Non-convex penalty function of L1-2 normcan be decomposed into two convex subproblems via difference of convex algorithm, each subproblem can be solved efficiently by alternating direction method of multipliers. The superior performance of the proposed compensation scheme based on L1-2 metric over conventional L1 penalty is further demonstrated by both synthetic and field examples. [ABSTRACT FROM AUTHOR]

Objectives. Pain assessment in older adults with cognitive impairment is often challenging, and paramedics are not given sufficient tools/training to assess pain. The development of a mobile app may improve pain assessment and management in this vulnerable population. We conducted usability testing of a newly developed iPhone pain assessment application with potential users, in this case as a tool for clinical paramedic practice to improve pain assessment of older adults with cognitive impairment. Methods. We conducted usability testing with paramedic students and a Delphi panel of qualified paramedics. Participants studied the app and paper-based algorithm from which the app was developed. The potential use for the app was discussed. Usability testing focus groups were recorded, transcribed verbatim, and analyzed using a thematic approach. Proposed recommendations were disseminated to the Delphi panel that reviewed and confirmed them. Results. Twenty-four paramedic students from two UK ambulance services participated in the focus groups. Usability of the app and its potential were viewed positively. Four major themes were identified: 1) overall opinion of the app for use in paramedic services; 2) incorporating technological applications into the health care setting; 3) improving knowledge and governance; and 4) alternative uses for the app. Subthemes were identified and are presented. Discussion. Our results indicate that the pain assessment app constitutes a potentially useful tool in the prehospital setting. By providing access to a tool specifically developed to help identify/assess pain in a user-friendly format, paramedics are likely to have increased knowledge and confidence in assessing pain in patients with dementia. [ABSTRACT FROM AUTHOR]

We describe an OctTree algorithm for the MPI parallel, adaptive mesh refinement code FLASH, which can be used to calculate the gas self-gravity, and also the angle-averaged local optical depth, for treating ambient diffuse radiation. The algorithm communicates to the different processors only those parts of the tree that are needed to perform the tree-walk locally. The advantage of this approach is a relatively low memory requirement, important in particular for the optical depth calculation, which needs to process information from many different directions. This feature also enables a general tree-based radiation transport algorithm that will be described in a subsequent paper, and delivers excellent scaling up to at least 1500 cores. Boundary conditions for gravity can be either isolated or periodic, and they can be specified in each direction independently, using a newly developed generalization of the Ewald method. The gravity calculation can be accelerated with the adaptive block update technique by partially re-using the solution from the previous time-step. Comparison with the FLASH internal multigrid gravity solver shows that tree-based methods provide a competitive alternative, particularly for problems with isolated or mixed boundary conditions. We evaluate several multipole acceptance criteria (MACs) and identify a relatively simple approximate partial error MAC which provides high accuracy at low computational cost. The optical depth estimates are found to agree very well with those of the RADMC-3D radiation transport code, with the tree-solver being much faster. Our algorithm is available in the standard release of the FLASH code in version 4.0 and later. [ABSTRACT FROM AUTHOR]

The error in the Solar system ephemeris will lead to dipolar correlations in the residuals of pulsar timing array for widely separated pulsars. In this paper, we utilize such correlated signals, and construct a Bayesian data-analysis framework to detect the unknown mass in the Solar system and to measure the orbital parameters. The algorithm is designed to calculate the waveform of the induced pulsar-timing residuals due to the unmodelled objects following the Keplerian orbits in the Solar system. The algorithm incorporates a Bayesian-analysis suit used to simultaneously analyse the pulsar-timing data of multiple pulsars to search for coherent waveforms, evaluate the detection significance of unknown objects, and to measure their parameters. When the object is not detectable, our algorithm can be used to place upper limits on the mass. The algorithm is verified using simulated data sets, and cross-checked with analytical calculations. We also investigate the capability of future pulsar-timing-array experiments in detecting the unknown objects. We expect that the future pulsar-timing data can limit the unknown massive objects in the Solar system to be lighter than 10-11-10-12 M☉, or measure the mass of Jovian system to a fractional precision of 10-8-10-9. [ABSTRACT FROM AUTHOR]

Motivation: Batch effects are one of the major source of technical variations that affect the measurements in high-throughput studies such as RNA sequencing. It has been well established that batch effects can be caused by different experimental platforms, laboratory conditions, different sources of samples and personnel differences. These differences can confound the outcomes of interest and lead to spurious results. A critical input for batch correction algorithms is the knowledge of batch factors, which in many cases are unknown or inaccurate. Hence, the primary motivation of our paper is to detect hidden batch factors that can be used in standard techniques to accurately capture the relationship between gene expression and other modeled variables of interest. Results: We introduce a new algorithm based on data-adaptive shrinkage and semi-Non-negative Matrix Factorization for the detection of unknown batch effects. We test our algorithm on three different datasets: (i) Sequencing Quality Control, (ii) Topotecan RNA-Seq and (iii) Single-cell RNA sequencing (scRNA-Seq) on Glioblastoma Multiforme. We have demonstrated a superior performance in identifying hidden batch effects as compared to existing algorithms for batch detection in all three datasets. In the Topotecan study, we were able to identify a new batch factor that has been missed by the original study, leading to under-representation of differentially expressed genes. For scRNA-Seq, we demonstrated the power of our method in detecting subtle batch effects. [ABSTRACT FROM AUTHOR]

In this paper, we propose a structural framework for population-based cancer epidemiology and evaluate the performance of double-robust estimators for a binary exposure in cancer mortality. We conduct numerical analyses to study the bias and efficiency of these estimators. Furthermore, we compare 2 different model selection strategies based on 1) Akaike's Information Criterion and the Bayesian Information Criterion and 2) machine learning algorithms, and we illustrate double-robust estimators' performance in a real-world setting. In simulations with correctly specified models and near-positivity violations, all but the naive estimators had relatively good performance. However, the augmented inverse-probability-of-treatment weighting estimator showed the largest relative bias. Under dual model misspecification and near-positivity violations, all double-robust estimators were biased. Nevertheless, the targeted maximum likelihood estimator showed the best bias-variance trade-off, more precise estimates, and appropriate 95% confidence interval coverage, supporting the use of the data-adaptive model selection strategies based on machine learning algorithms. We applied these methods to estimate adjusted 1-year mortality risk differences in 183,426 lung cancer patients diagnosed after admittance to an emergency department versus persons with a nonemergency cancer diagnosis in England (2006-2013). The adjusted mortality risk (for patients diagnosed with lung cancer after admittance to an emergency department) was 16% higher in men and 18% higher in women, suggesting the importance of interventions targeting early detection of lung cancer signs and symptoms. [ABSTRACT FROM AUTHOR]

In zero energy houses, heating load would be reduced sharply during winter, as its building envelope is highly insulated. The normal compressor is triggered by a low load operation leading to more frequent on-off cycling. This paper presents a novel control algorithm named fan intermittent operation, for the indoor unit of room air conditioner removing the compressor on-off cycling under low load condition and to provide stable warm air to satisfy the task of local domain with extremely low compressor frequency. Based on periodic variation control of condensing temperature, a 5% energy saving rate can be established under the winter condition simulation. [ABSTRACT FROM AUTHOR]

Machine Learning (ML) techniques now are ubiquitous tools to extract structural information from data collections. With the increasing volume of data, large-scaleML applications require an efficient implementation to accelerate the performance. Existing systems parallelize algorithms through either data parallelism or model parallelism. But data parallelism cannot obtain good statistical efficiency due to the conflicting updates to parameters while the performance is damaged by global barriers in model parallel methods. In this paper, we propose a new system, named Angel, to facilitate the development of large-scale ML applications in production environment. By allowing concurrent updates to model across different groups and scheduling the updates in each group, Angel can achieve a good balance between hardware efficiency and statistical efficiency. Besides, Angel reduces the network latency by overlapping the parameter pulling and update computing and also utilizes the sparseness of data to avoid the pulling of unnecessary parameters. We also enhance the usability of Angel by providing a set of efficient tools to integrate with application pipelines and provisioning efficient fault tolerance mechanisms.We conduct extensive experiments to demonstrate the superiority of Angel. [ABSTRACT FROM AUTHOR]

Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text has been accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to classical indexes, e.g. suffix trees and suffix arrays, while requiring less space. For genomic data, a well-known family of compressed full-text indexes, called FM-indexes, presents unmatched performance in practice. One major drawback of FMindexes is that their locating operations, which report all occurrence positions of patterns in a given text, are not efficient, especially for the patterns with many occurrences. Results: In this paper, we introduce a novel locating algorithm, FMtree, to fast retrieve all occurrence positions of any pattern via FM-indexes. When searching for a pattern over a given text, FMtree organizes the search space of the locating operation into a conceptual multiway tree. As a result, multiple occurrence positions of this pattern can be retrieved simultaneously by traversing the multiway tree. Compared with existing locating algorithms, our tree-based algorithm reduces large numbers of redundant operations and presents better data locality. Experimental results show that FMtree is usually one order of magnitude faster than the state-of-the-art algorithms, and still memory-efficient. Availability and implementation: FMtree is freely available at https://github.com/chhylp123/ FMtree. [ABSTRACT FROM AUTHOR]

Laplace domain waveform inversion (WI) is one of the most effective algorithms to generate an initial velocity model. Because of its bandwidth independence with respect to the source wavelet, this method can yield reasonable initial models without low-frequency components in the seismic data. However, the conventional Laplace domainWI algorithm has an accuracy problem from its simultaneous consideration of the first arrival traveltime and apparent amplitude in the Laplace domain wavefield. This simultaneous consideration creates undesirable cross-correlation terms between the residual of the traveltime and the partial derivatives of the apparent amplitude in the gradient directions and between the residual of the apparent amplitude and the partial derivatives of the traveltime in the gradient directions. In this paper, we introduce a new objective function that uses a shifted Laplace domain wavefield to solve the problem of Laplace domain WI. Information that is associated with the traveltime and apparent amplitude can be separately inverted by using this shifted Laplace domain WI. This separation of the information can suppress the undesirable cross-correlation terms between the residual of the traveltime and the partial derivatives of apparent amplitude and between the residual of the apparent amplitude and the partial derivatives of the traveltime in the gradient directions. We can effectively perform shifted Laplace domain modelling by using the damped monochromatic wave equation. We verify the accuracy of this shifted Laplace domain modelling scheme by comparing the shifted Laplace-transformed result from a synthetic seismogram to a wavefield that is modelled in the shifted Laplace domain. We perform a contribution analysis to demonstrate that the shifted Laplace domain wavefield is essential to improve the accuracy of the inverted results. Finally, we confirm the robustness of the shifted Laplace domain WI algorithm by testing it against a BP model. [ABSTRACT FROM AUTHOR]

Adaptive Optics Lucky Imager (AOLI) is a state-of-the-art instrument that combines adaptive optics (AO) and lucky imaging (LI) with the objective of obtaining diffraction-limited images in visible wavelength at mid- and big-size ground-based telescopes. The key innovation of AOLI is the development and use of the new Two Pupil Plane Positions Wavefront Sensor (TP3-WFS). The TP3-WFS, working in visible band, represents an advance over classical wavefront sensors such as the Shack-Hartmann WFS because it can theoretically use fainter natural reference stars, which would ultimately provide better sky coverages to AO instruments using this newer sensor. This paper describes the software, algorithms and procedures that enabled AOLI to become the first astronomical instrument performing real-time AO corrections in a telescope with this new type of WFS, including the first control-related results at the William Herschel Telescope. [ABSTRACT FROM AUTHOR]

Distributed networks of health-care data sources are increasingly being utilized to conduct pharmacoepidemio-logic database studies. Such networks may contain data that are not physically pooled but instead are distributed horizontally (separate patients within each data source) or vertically (separate measures within each data source) in order to preserve patient privacy. While multivariable methods for the analysis of horizontally distributed data are frequently employed, few practical approaches have been put forth to deal with vertically distributed healthcare databases. In this paper, we propose 2 propensity score-based approaches to vertically distributed data analysis and test their performance using 5 example studies. We found that these approaches produced point estimates close to what could be achieved without partitioning. We further found a performance benefit (i.e., lower mean squared error) for sequentially passing a propensity score through each data domain (called the "sequential approach") as compared with fitting separate domain-specific propensity scores (called the "parallel approach"). These results were validated in a small simulation study. This proof-of-concept study suggests a new multivariable analysis approach to vertically distributed health-care databases that is practical, preserves patient privacy, and warrants further investigation for use in clinical research applications that rely on health-care databases. [ABSTRACT FROM AUTHOR]

In this paper, we examine patterns of self-reported diagnosis of noncommunicable diseases (NCDs) and prevalences of algorithm/measured test-based, undiagnosed, and untreated NCDs in China, Ghana, India, Mexico, Russia, and South Africa. Nationally representative samples of older adults aged ≥50 years were analyzed from wave 1 of the World Health Organization's Study on Global Ageing and Adult Health (2007-2010; n = 34,149). Analyses focused on 6 conditions: angina, arthritis, asthma, chronic lung disease, depression, and hypertension. Outcomes for these NCDs were: 1) self-reported disease, 2) algorithm/measured test-based disease, 3) undiagnosed disease, and 4) untreated disease. Algorithm/measured test-based prevalence of NCDs was much higher than self-reported prevalence in all 6 countries, indicating underestimation of NCD prevalence in low- and middle-income countries. Undiagnosed prevalence of NCDs was highest for hypertension, ranging from 19.7% (95% confidence interval (CI): 18.1, 21.3) in India to 49.6% (95% CI: 46.2, 53.0) in South Africa. The proportion untreated among all diseases was highest for depression, ranging from 69.5% (95% CI: 57.1, 81.9) in South Africa to 93.2% (95% CI: 90.1, 95.7) in India. Higher levels of education and wealth significantly reduced the odds of an undiagnosed condition and untreated morbidity. A high prevalence of undiagnosed NCDs and an even higher proportion of untreated NCDs highlights the inadequacies in diagnosis and management of NCDs in local health-care systems. [ABSTRACT FROM AUTHOR]

In 2012, the US Census Bureau posed a challenge under the America COMPETES Act, an act designed to improve the competitiveness of the United States by investing in innovation through research and development. The Census Bureau contracted Kaggle.com to host and manage a worldwide competition to develop the best statistical model to predict 2010 Census mail return rates. The Census Bureau provided competitors with a block group-level database consisting of housing, demographic, and socioeconomic variables derived from the 2010 Census, five-year American Community Survey estimates, and 2010 Census operational data. The Census Bureau then challenged teams to use these data (and other publicly available data) to construct the models. One goal of the challenge was to leverage winning models as inputs to a new model-based hard-to-count (HTC) score, a metric to stratify and target geographic areas according to propensity to self-respond in sample surveys and censuses. All contest winners employed data-mining and machine-learning techniques to predict mail-return rates. This made the models relatively hard to interpret (when compared with the Census Bureau’s original HTC score) and impossible to directly translate to a new HTC score. Nonetheless, the winning models contained insights toward building a new model-based score using variables from the database. This paper describes the original algorithm-based HTC score, insights gained from the Census Return Rate Challenge, and the model underlying a new HTC score. [ABSTRACT FROM AUTHOR]

Atmospheric turbulence presents a fundamental challenge to Fourier phase recovery in optical interferometry. Typical reconstruction algorithms employ Bayesian inference techniques which rely on prior knowledge of the scene under observation. In contrast, redundant spacing calibration (RSC) algorithms employ redundancy in the baselines of the interferometric array to directly expose the contribution of turbulence, thereby enabling phase recovery for targets of arbitrary and unknown complexity. Traditionally RSC algorithms have been applied directly to single-exposure measurements, which are reliable only at high photon flux in general. In scenarios of low photon flux, such as those arising in the observation of dim objects in space, one must instead rely on time-averaged, atmosphere-invariant quantities such as the bispectrum. In this paper, we develop a novel RSC-based algorithm for prior-less phase recovery in which we generalize the bispectrum to higher order atmosphere-invariants (nspectra) for improved sensitivity. We provide a strategy for selection of a high-signal-to-noise ratio set of n-spectra using the graph-theoretic notion of the minimum cycle basis. We also discuss a key property of this set (wrap-invariance), which then enables reliable application of standard linear estimation techniques to recover the Fourier phases from the 2π-wrapped n-spectra phases. For validation, we analyse the expected shot-noise-limited performance of our algorithm for both pairwise and Fizeau interferometric architectures, and corroborate this analysis with simulation results showing performance near an atmosphere-oracle Cramer-Rao bound. Lastly, we apply techniques from the field of compressed sensing to perform image reconstruction from the estimated complex visibilities. [ABSTRACT FROM AUTHOR]

Geophysical parameters of the deep Earth's interior can be evaluated through the resonance effects associated with the core and inner-core wobbles on the forced nutations of the Earth's figure axis, as observed by very long baseline interferometry (VLBI), or on the diurnal tidal waves, retrieved from the time-varying surface gravity recorded by superconducting gravimeters (SGs). In this paper, we inverse for the rotational mode parameters from both techniques to retrieve geophysical parameters of the deep Earth. We analyse surface gravity data from 15 SG stations and VLBI delays accumulated over the last 35 yr. We show existing correlations between several basic Earth parameters and then decide to inverse for the rotational modes parameters. We employ a Bayesian inversion based on the Metropolis-Hastings algorithm with a Markov-chain Monte Carlo method. We obtain estimates of the free core nutation resonant period and quality factor that are consistent for both techniques. We also attempt an inversion for the free inner-core nutation (FICN) resonant period from gravity data. The most probable solution gives a period close to the annual prograde term (or S1 tide). However the 95 per cent confidence interval extends the possible values between roughly 28 and 725 d for gravity, and from 362 to 414 d from nutation data, depending on the prior bounds. The precisions of the estimated long-period nutation and respective small diurnal tidal constituents are hence not accurate enough for a correct determination of the FICN complex frequency. [ABSTRACT FROM AUTHOR]

This paper evaluates an efficient implementation to multiply the inverse of a numerator relationship matrix for genotyped animals (A22-1) by a vector (q). The computation is required for solving mixed model equations in single-step genomic BLUP (ssGBLUP) with the preconditioned conjugate gradient (PCG). The inverse can be decomposed into sparse matrices that are blocks of the sparse inverse of a numerator relationship matrix (A-1) including genotyped animals and their ancestors. The elements of A-1 were rapidly calculated with the Henderson's rule and stored as sparse matrices in memory. Implementation of A22-1 q was by a series of sparse matrix–vector multiplications. Diagonal elements of A22-1, which were required as preconditioners in PCG, were approximated with a Monte Carlo method using 1,000 samples. The efficient implementation of A22-1 q was compared with explicit inversion of A22 with 3 data sets including about 15,000, 81,000, and 570,000 genotyped animals selected from populations with 213,000, 8.2 million, and 10.7 million pedigree animals, respectively. The explicit inversion required 1.8 GB, 49 GB, and 2,415 GB (estimated) of memory, respectively, and 42 s, 56 min, and 13.5 d (estimated), respectively, for the computations. The efficient implementation required <1 MB, 2.9 GB, and 2.3 GB of memory, respectively, and <1 sec, 3 min, and 5 min, respectively, for setting up. Only <1 sec was required for the multiplication in each PCG iteration for any data sets. When the equations in ssGBLUP are solved with the PCG algorithm, A22-1 is no longer a limiting factor in the computations. [ABSTRACT FROM AUTHOR]

We present Spin-SILC, a new foreground component separation method that accurately extracts the cosmic microwave background (CMB) polarization E and B modes from raw multifrequency Stokes Q and U measurements of the microwave sky. Spin-SILC is an internal linear combination method that uses spin wavelets to analyse the spin-2 polarization signal P = Q + iU. The wavelets are additionally directional (non-axisymmetric). This allows different morphologies of signals to be separated and therefore the cleaning algorithm is localized using an additional domain of information. The advantage of spin wavelets over standard scalar wavelets is to simultaneously and self-consistently probe scales and directions in the polarization signal P = Q + iU and in the underlying E and B modes, therefore providing the ability to perform component separation and E-B decomposition concurrently for the first time. We test Spin-SILC on full-mission Planck simulations and data and show the capacity to correctly recover the underlying cosmological E and B modes. We also demonstrate a strong consistency of our CMB maps with those derived from existing component separation methods. Spin-SILC can be combined with the pseudo- and pure E-B spin wavelet estimators presented in a companion paper to reliably extract the cosmological signal in the presence of complicated sky cuts and noise. Therefore, it will provide a computationally efficient method to accurately extract the CMB E and B modes for future polarization experiments. [ABSTRACT FROM AUTHOR]

Motivation Biclustering is an unsupervised technique of simultaneous clustering of rows and columns of input matrix. With multiple biclustering algorithms proposed, UniBic remains one of the most accurate methods developed so far. Results In this paper we introduce a Bioconductor package called runibic with parallel implementation of UniBic. For the convenience the algorithm was reimplemented, parallelized and wrapped within an R package called runibic. The package includes: (i) a couple of times faster parallel version of the original sequential algorithm, (ii) much more efficient memory management, (iii) modularity which allows to build new methods on top of the provided one and (iv) integration with the modern Bioconductor packages such as SummarizedExperiment, ExpressionSet and biclust. Availability and implementation The package is implemented in R and is available from Bioconductor (starting from version 3.6) at the following URL http://bioconductor.org/packages/runibic with installation instructions and tutorial. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

ABSTRACT A companion paper presents an algorithm for estimating the actions of orbits in axisymmetric potentials. This algorithm is fast enough for it to be feasible to fit automatically a parametrized distribution function to observational data for the solar neighbourhood. We explore the predictive power of these models and the extent to which global models are constrained by data confined to the solar cylinder. We adopt a gravitational potential that is generated by three discs (gas and both thin and thick stellar discs), a bulge and a dark halo, and fit the thin-disc component of the distribution function to the solar-neighbourhood velocity distribution from the Geneva-Copenhagen survey. We find that the disc's vertical density profile is in good agreement with data at z ≲ 500 pc. The thick-disc component of the distribution function is then used to extend the fit to data from Gilmore & Reid for z ≲ 2.5 kpc. The resulting model predicts excellent fits to the profile of the vertical velocity dispersion σ z( z) from the RAVE survey and to the distribution of vφ velocity components at | z| ∼ 1 kpc from the Sloan Digital Sky Survey. The ability of this model to predict successfully data that were not used in the fitting process suggests that the adopted gravitational potential (which is close to a maximum-disc potential) is close to the true one. We show that if another plausible potential is used, the predicted values of σ z are too large. The models imply that in contrast to the thin disc, the thick disc has to be hotter vertically than radially, a prediction that it will be possible to test in the near future. When the model parameters are adjusted in an unconstrained manner, there is a tendency to produce models that predict unexpected radial variations in quantities such as scale height. This finding suggests that to constrain these models adequately one needs data that extends significantly beyond the solar cylinder. The models presented in this paper might prove useful to the interpretation of data for external galaxies that have been taken with an integral field unit. [ABSTRACT FROM AUTHOR]

SUMMARY In this paper, we introduce the so-called symplectic discrete singular convolution differentiator (SDSCD) method for structure-preserving modelling of elastic waves. In the method presented, physical space is discretized by the DSCD, whereas an explicit third-order symplectic scheme is used for the time discretization. This approach uses optimization and truncation to form a localized operator. This preserves the fine structure of the wavefield in complex media and avoids non-causal interaction when parameter discontinuities are present in the medium. Theoretically, the approach presented is a structure-preserving algorithm. Also, some numerical experiments are shown in this paper. Elastic wavefield modelling experiments on a laterally heterogeneous medium with high parameter contrasts demonstrate the superior performance of the SDSCD for suppression of numerical dispersion. Long-term computational experiments exhibit the remarkable capability of the approach presented for long-time simulations. Promising numerical results suggest the SDSCD is suitable for high-precision and long-time numerical simulations, as it has structure-preserving property and it can suppress effectively numerical dispersion when coarse grids are used. [ABSTRACT FROM AUTHOR]

ABSTRACT In a companion paper, we have presented an algorithm for simulating two-fluid gas and dust mixtures in smoothed particle hydrodynamics (SPH). In this paper, we develop an implicit timestepping method that preserves the exact conservation of the both linear and angular momenta in the underlying SPH algorithm, but unlike previous schemes, allows the iterations to converge to arbitrary accuracy and is suited to the treatment of non-linear drag regimes. The algorithm presented in Paper I is also extended to deal with realistic astrophysical drag regimes, including both linear and non-linear Epstein and Stokes drag. The scheme is benchmarked against the test suite presented in Paper I, including (i) the analytic solutions of the dustybox problem and (ii) solutions of the dustywave, dustyshock, dustysedov and dustydisc obtained with explicit timestepping. We find that the implicit method is 1-10 times faster than the explicit temporal integration when the ratio r between the timestep and the drag stopping time is 1 ≲ r≲ 1000. [ABSTRACT FROM AUTHOR]

ABSTRACT We present a new cluster-detection algorithm designed for the Panoramic Survey Telescope and Rapid Response System (Pan-STARRS) survey but with generic application to any multiband data. The method makes no prior assumptions about the properties of clusters other than (i) the similarity in colour of cluster galaxies (the 'red sequence'); and (ii) an enhanced projected surface density. The detector has three main steps: (i) it identifies cluster members by photometrically filtering the input catalogue to isolate galaxies in colour-magnitude space; (ii) a Voronoi diagram identifies regions of high surface density; and (iii) galaxies are grouped into clusters with a Friends-of-Friends technique. Where multiple colours are available, we require systems to exhibit sequences in two colours. In this paper, we present the algorithm and demonstrate it on two data sets. The first is a 7-deg2 sample of the deep Sloan Digital Sky Survey (SDSS) equatorial stripe (Stripe 82), from which we detect 97 clusters with z≤ 0.6. Benefitting from deeper data, we are 100 per cent complete in the maxBCG optically selected cluster catalogue (based on shallower single-epoch SDSS data) and find an additional 78 previously unidentified clusters. The second data set is a mock Medium Deep Survey Pan-STARRS catalogue, based on the Λ cold dark matter (ΛCDM) model and a semi-analytic galaxy formation recipe. Knowledge of galaxy-halo memberships in the mock catalogue allows for the quantification of algorithm performance. We detect 305 mock clusters in haloes with mass >1013 h−1 M⊙ at z≲ 0.6 and determine a spurious detection rate of <1 per cent, consistent with tests on the Stripe 82 catalogue. The detector performs well in the recovery of model ΛCDM clusters. At the median redshift of the catalogue, the algorithm achieves >75 per cent completeness down to halo masses of 1013.4 h−1 M⊙ and recovers >75 per cent of the total stellar mass of clusters in haloes down to 1013.8 h−1 M⊙. A companion paper presents the complete cluster catalogue over the full 270-deg2 Stripe 82 catalogue. [ABSTRACT FROM AUTHOR]

Changes in women’s menstrual bleeding patterns precede the onset of menopause. In this paper, the authors identify population subgroups based on menstrual characteristics of the menopausal transition experience. Using the TREMIN data set (1943–1979), the authors apply a Bayesian change-point model with 8 parameters for each woman that summarize change in menstrual bleeding patterns during the menopausal transition. The authors then use estimates from this model to classify menstrual patterns into subgroups using a K-medoids algorithm. They identify 6 subgroups of women whose transition experience can be distinguished by age at onset, variability of the menstrual cycle, and duration of the early transition. These results suggest that for most women, mean and variance change points are well aligned with proposed bleeding markers of the menopausal transition, but for some women they are not clearly associated. Increasing understanding of population differences in the transition experience may lead to new insights into ovarian aging. Because of age inclusion criteria, most longitudinal studies of the menopausal transition probably include only a subset of the 6 subgroups of women identified in this paper, suggesting a potential bias in the understanding of both the menopausal transition and the linkage between the transition and chronic disease. [ABSTRACT FROM PUBLISHER]

The dynamical ages and some other physical parameters of the opposite lobes of 20 subjectively selected giant radio galaxies (GRGs), as well as of their environment, are estimated using the algorithm of Machalski et al. These data, supplemented with the relevant data determined for another 10 GRGs in Paper III, are used to analyse the aspects of the apparent length and luminosity asymmetries in the lobes in view of their dynamical evolution. As in Paper III, the fits give slightly different dynamical ages and other model parameters for the opposite lobes modelled independently of each other. Therefore, demanding similar values of the jet power and the radio core density for the same source, a self-consistent age solution for the opposite lobes is considered, which results in different density profiles along the lobes and different initial energy distributions of the emitting particles at their heads. The analysis shows the following. (i) The age of the longer lobe, fitted independently, tends to be younger than that for the shorter lobe. This contradicts with the axial expansion expected in a symmetrical environment (a halo) surrounding the source and strongly supports the self-consistent solution with different ambient density profiles along the opposite lobes. In the frame of the latter solution, the difference between the ages of the opposite lobes almost always diminishes, compared to that found with the independent fits, not exceeding a factor of ∼1.25. (ii) There is a clear correlation between the age ratio and the difference in radio spectra: longer lobes with a steeper spectrum in most cases are older; however, longer lobes having a flatter spectrum are mostly younger. The age difference is always larger than that expected from the unknown inclination of the jets' axis to the observer's line of sight and a pure kinematic effect. (iii) The slope of the injected (initial) radio spectrum, , has a narrow distribution around a value of 0.5. Its value tends to be lower in the longer lobe than in the shorter lobe. The difference between the values of in the opposite lobes is very low; a standard deviation of ∼0.02 from the mean is found. This difference increases about three times in the self-consistent solution, but always within the relatively narrow range of 0.46-0.62. (iv) There is a strong correlation between the difference in values of β (the exponent describing the external density profile) for the opposite lobes and the ratio of their volume. This is much stronger than a dependence of on the ratio of the lobes' length. This likely suggests that the environment of the GRGs is non-uniform or clumpy. [ABSTRACT FROM AUTHOR]

We complete the development and description of a thermodynamic method for the computation of phase equilibria and physical properties of multiphase mantle assemblages. Our previous paper focused on the computation of physical properties. In this paper, our focus shifts to the phase equilibria. We further develop our theory to specify the ideal and excess contributions to solution properties and derive properties of multiphase assemblages. We discuss our global inversion strategy for determining the values of the free parameters in our theory and compare inverted parameter values with expectations based on scaling arguments. Comparisons between our method and experimental phase equilibria data encompass the pressure-temperature regime of Earth's mantle. Finally, we present applications of our method that illustrate how it may be used to explore the origins of mantle structure and mantle dynamics. Continuing rapid advances in experimental and theoretical petrology and mineral physics have motivated an expansion of the scope of our model via the addition of several new phases, and of the soda component: an appendix lists all parameters in our model and references to the experimental and theoretical studies that constrain them. Our algorithm for global minimization of the Gibbs free energy is embodied in a code called HeFESTo, and is detailed in a second appendix. [ABSTRACT FROM AUTHOR]

Motivation: Data compression is crucial in effective handling of genomic data. Among several recently published algorithms, ERGC seems to be surprisingly good, easily beating all of the competitors. Results: We evaluated ERGC and the previously proposed algorithms GDC and iDoComp, which are the ones used in the original paper for comparison, on a wide data set including 12 assemblies of human genome (instead of only four of them in the original paper). ERGC wins only when one of the genomes (referential or target) contains mixed-cased letters (which is the case for only the two Korean genomes). In all other cases ERGC is on average an order of magnitude worse than GDC and iDoComp. [ABSTRACT FROM AUTHOR]

This paper presents a new algorithm,trimor, to analyse multi-order spectra of triple systems. The algorithm is an extension oftricor, the three-dimensional correlation technique that derives the radial velocities of triple stellar systems from single-order spectra. The combined correlation derived from many orders enables the detection and the measurement of radial velocities of faint tertiary companions. The paper appliedtrimor to the already available spectra of HD 188753, a well-known triple system, yielding the radial velocities of the faintest star in the system. This rendered the close pair of the triple system a double-lined spectroscopic binary, which led to a precise mass ratio and an estimate of its inclination. The close-pair inclination is very close to the inclination of the wide orbit, consistent with the assertion that this triple system has a close to coplanar configuration. [ABSTRACT FROM AUTHOR]