Several models in data analysis are estimated by minimizing the objective function defined as the residual sum of squares between the model and the data. A necessary and sufficient condition for the existence of a least squares estimator is that the objective function attains its infimum at a unique point. It is shown that the objective function for Parafac-2 need not attain its infimum, and that of DEDICOM, constrained Parafac-2, and, under a weak assumption, SCA and Dynamals do attain their infimum. Furthermore, the sequence of parameter vectors, generated by an alternating least squares algorithm, converges if it decreases the objective function to its infimum which is attained at one or finitely many points.
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To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.
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BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python.RESULTS: The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS.CONCLUSIONS: pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.
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Criminal expertise plays a crucial role in the choices offenders make when committing a crime, including their modus operandi. However, our knowledge about criminal decision making online remains limited. Drawing on insights from cyber security, we conceptualize the cybercrime commission process as the sequence of phases of the cyber kill chain that offenders go through. We assume that offenders who follow the sequence consecutively use the most efficient hacking method. Building upon the expertise paradigm, we hypothesize that participants with greater hacking experience and IT skills undertake more efficient hacks. To test this hypothesis, we analyzed data from 69 computer security and software engineering students who were invited to hack a vulnerable website in a computer lab equipped with monitoring software, which allowed to collect objective behavioral measures. Additionally, we collected individual measures regarding hacking expertise through an online questionnaire. After quantitatively measuring efficiency using sequence analysis, a regression model showed that the expertise paradigm may also apply to hackers. We discuss the implications of our novel research for the study of offender decision-making processes more broadly.
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Discussions on policy and management initiatives to facilitate individuals throughout working careers take place without sufficient insight into how career paths are changing, how these changes are related to a modernization of life course biographies, and whether this leads to increased labour market transitions. This paper asks how new, flexible labour market patterns can best be analyzed using an empirical, quantitative approach. The data used are from the career module of the Panel Study of Belgian Households (PSBH). This module, completed by almost 4500 respondents consists of retrospective questions tracing lengthy and even entire working life histories. To establish any changes in career patterns over such extended periods of time, we compare two evolving methodologies: Optimal Matching Analysis (OMA) and Latent Class Regression Analysis (LCA). The analyses demonstrate that both methods show promising potential in discerning working life typologies and analyzing sequence trajectories. However, particularities of the methods demonstrate that not all research questions are suitable for each method. The OMA methodology is appropriate when the analysis concentrates on the labour market statuses and is well equipped to make clear and interpretable differentiations if there is relative stability in career paths during the period of observation but not if careers become less stable. Latent Class has the strength of adopting covariates in the clustering allowing for more historically connected types than the other methodology. The clustering is denser and the technique allows for more detailed model fitting controls than OMA. However, when incorporating covariates in a typology, the possibilities of using the typology in later, causal, analyses is somewhat reduced.
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Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
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Just what and how eight experienced teachers in four coaching dyads learned during a 1-year reciprocal peer coaching trajectory was examined in the present study. The learning processes were mapped by providing a detailed description of reported learning activities, reported learning outcomes, and the relations between these two. The sequences of learning activities associated with a particular type of learning outcome were next selected, coded, and analyzed using a variety of quantitative methods. The different activity sequences undertaken by the teachers during a reciprocal peer coaching trajectory were found to trigger different aspects of their professional development.
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Dynamic body feedback is used in dance movement therapy (DMT), with the aim to facilitate emotional expression and a change of emotional state through movement and dance for individuals with psychosocial or psychiatric complaints. It has been demonstrated that moving in a specific way can evoke and regulate related emotions. The current study aimed to investigate the effects of executing a unique set of kinetic movement elements on an individual mover’s experience of happiness. A specific sequence consisting of movement elements that recent studies have related to the feeling of happiness was created and used in a series of conditions. To achieve a more realistic reflection of DMT practice, the study incorporated the interpersonal dimension between the dance movement therapist (DMTh) and the client, and the impact of this interbodily feedback on the emotional state of the client. This quantitative study was conducted in a within-subject design. Five male and 20 female participants (mean age = 20.72) participated in three conditions: a solo executed movement sequence, a movement sequence executed with a DMTh who attuned and mirrored the movements, and a solo executed movement sequence not associated with feelings of happiness. Participants were only informed about the movements and not the feelings that may be provoked by these movements. The effects on individuals were measured using the Positive and Negative Affect Schedule and visual analog scales. Results showed that a specific movement sequence based on movement elements associated with happiness executed with a DMTh can significantly enhance the corresponding affective state. An additional finding of this study indicated that facilitating expressed emotion through movement elements that are not associated with happiness can enhance feelings such as empowerment, pride, and determination, which are experienced as part of positive affect. The results show the impact of specific fullbody movement elements on the emotional state and the support outcome of DMT on emotion regulation.
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Estimation of the factor model by unweighted least squares (ULS) is distribution free, yields consistent estimates, and is computationally fast if the Minimum Residuals (MinRes) algorithm is employed. MinRes algorithms produce a converging sequence of monotonically decreasing ULS function values. Various suggestions for algorithms of the MinRes type are made for confirmatory as well as for exploratory factor analysis. These suggestions include the implementation of inequality constraints and the prevention of Heywood cases. A simulation study, comparing the bootstrap standard deviations for the parameters with the standard errors from maximum likelihood, indicates that these are virtually equal when the score vectors are sampled from the normal distribution. Two empirical examples demonstrate the usefulness of constrained exploratory and confirmatory factor analysis by ULS used in conjunction with the bootstrap method.
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Decisions and business rules are essential Components of an organization. Combined, these components form a basis for securing the implementation of new laws, regulations and internal policies into processes, work instructions and information systems. To ensure proper implementation, business rule types must be taken into account, as the functions per type may be different. The current body of knowledge on decision and business rule management offers some insights into different types of business rules, however, these types are often presented as a secondary focus of a contribution or set in stone without proper evidence supporting these claims. This study therefore aims to explore the different business rule types utilized in the body of knowledge as well as practice. This will form a basis to determine possible overlap and inconsistencies and aid in establishing the functional differences between the defined business rule types. By applying a literature review, semi-structured interviews and secondary data analysis, we observed that the current body of knowledge shows serious diffusion with regards to business rule types, the same holds for practice. Therefore, future research should focus to research these differences in detail with the aim to harmonize the proliferation of business rule types.
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