Enabling inference for context-dependent models of mutation by bounding the propagation of dependency

Although the rates at which positions in the genome mutate are known to depend not only on the nucleotide to be mutated, but also on neighboring nucleotides, it remains challenging to do phylogenetic inference using models of context-dependent mutation. In these models, the effects of one mutation may in principle propagate to faraway locations, making it difficult to compute exact likelihoods. This paper shows how to use bounds on the propagation of dependency to compute likelihoods of mutation of a given segment of genome by marginalizing over sufficiently long flanking sequence. This can be used for maximum likelihood or Bayesian inference. Protocols examining residuals and iterative model refinement are also discussed. Tools for efficiently working with these models are provided in an R package, that could be used in other applications. The method is used to examine context dependence of mutations since the common ancestor of humans and chimpanzee.

The effect of ICT connectivity on individual work productivity: Investigating the influence of ICT self-discipline

<p>Information and Communication Technologies (ICTs) in the workplace are increasingly connecting employees. This ICT connectivity has mixed effects on individuals' work productivity and it raises ongoing concern in literature and in the media. The goal of this research was to investigate ICT self-discipline in this context to better explain the effect of ICT connectivity on individual work productivity. A review of existing literature on ICTs in the workplace took place, drawing from the disciplines of Information Systems (IS), Communications, Psychology and Organisational Studies. The literature review assisted with the development of a conceptual research model, which was subsequently used to guide this research. The conceptual research model was validated and refined through the qualitative phase of this research. This phase used semi-structured interviews to expand views on the research phenomena. The updated research model was further validated during the model refinement phase of this research. This phase consisted of two focus groups. Collectively, the literature review, the qualitative phase and the model refinement phase assisted in transforming the updated research model into a testable form. The quantitative phase of this research consolidated key themes from relevant literature and findings from the two prior research phases to develop a survey instrument. An online survey was conducted to test the research model and address the research goal. The statistical analysis of the survey data provided useful results. First, the indicator and construct validity showed that the survey instrument was reliable and it accurately reflected the investigated phenomena. Second, the hypothesis testing showed support for the research model when tested in different contexts. The findings from this phase helped address the research goal. Overall, findings from this research indicated that job requirement for ICT connectivity influences an individual's level of ICT connectivity for work, ICT connectivity positively impacts individual work productivity and ICT self-discipline positively influences individual work productivity. Additionally, ICT self-discipline can positively moderate the effect of ICT connectivity on individual work productivity for employees with low-interdependent jobs and/or working in large/multi-national firms. Further, ICT self-discipline can negatively moderate the effect of ICT connectivity on individual work productivity for employees with high-interdependent jobs and/or working in small firms. Thus, for enhanced productivity, it is important to assess an employee‘s work settings prior to determining how strictly to impose ICT self-discipline. This research addresses concerns on the effects of ICTs raised in the literature and in the media. The research drew from IS and Psychology literature to develop the notion of ICT self-discipline – an individual‘s ability to regulate their behaviors towards ICTs. The research investigated how this notion could enhance the effect of ICTs on individual work productivity. Further, a model towards theory explaining productive ICT connectivity for work is contributed. This model goes beyond existing theories in IS and contributes knowledge to the literature on IS, Communications, Psychology and Organisational Studies. Finally, this study informs practice by providing employees with insights on how to deal with communication through ICTs to ensure they are continuously productive at work.</p>

The effect of ICT connectivity on individual work productivity: Investigating the influence of ICT self-discipline

<p>Information and Communication Technologies (ICTs) in the workplace are increasingly connecting employees. This ICT connectivity has mixed effects on individuals' work productivity and it raises ongoing concern in literature and in the media. The goal of this research was to investigate ICT self-discipline in this context to better explain the effect of ICT connectivity on individual work productivity. A review of existing literature on ICTs in the workplace took place, drawing from the disciplines of Information Systems (IS), Communications, Psychology and Organisational Studies. The literature review assisted with the development of a conceptual research model, which was subsequently used to guide this research. The conceptual research model was validated and refined through the qualitative phase of this research. This phase used semi-structured interviews to expand views on the research phenomena. The updated research model was further validated during the model refinement phase of this research. This phase consisted of two focus groups. Collectively, the literature review, the qualitative phase and the model refinement phase assisted in transforming the updated research model into a testable form. The quantitative phase of this research consolidated key themes from relevant literature and findings from the two prior research phases to develop a survey instrument. An online survey was conducted to test the research model and address the research goal. The statistical analysis of the survey data provided useful results. First, the indicator and construct validity showed that the survey instrument was reliable and it accurately reflected the investigated phenomena. Second, the hypothesis testing showed support for the research model when tested in different contexts. The findings from this phase helped address the research goal. Overall, findings from this research indicated that job requirement for ICT connectivity influences an individual's level of ICT connectivity for work, ICT connectivity positively impacts individual work productivity and ICT self-discipline positively influences individual work productivity. Additionally, ICT self-discipline can positively moderate the effect of ICT connectivity on individual work productivity for employees with low-interdependent jobs and/or working in large/multi-national firms. Further, ICT self-discipline can negatively moderate the effect of ICT connectivity on individual work productivity for employees with high-interdependent jobs and/or working in small firms. Thus, for enhanced productivity, it is important to assess an employee‘s work settings prior to determining how strictly to impose ICT self-discipline. This research addresses concerns on the effects of ICTs raised in the literature and in the media. The research drew from IS and Psychology literature to develop the notion of ICT self-discipline – an individual‘s ability to regulate their behaviors towards ICTs. The research investigated how this notion could enhance the effect of ICTs on individual work productivity. Further, a model towards theory explaining productive ICT connectivity for work is contributed. This model goes beyond existing theories in IS and contributes knowledge to the literature on IS, Communications, Psychology and Organisational Studies. Finally, this study informs practice by providing employees with insights on how to deal with communication through ICTs to ensure they are continuously productive at work.</p>

Cryo-EM single-particle structure refinement and map calculation using Servalcat

In 2020, cryo-EM single-particle analysis achieved true atomic resolution thanks to technological developments in hardware and software. The number of high-resolution reconstructions continues to grow, increasing the importance of the accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted F o − F c difference map, which is derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The F o − F c map helps in the visualization of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in the electron-density maps produced by X-ray crystallography, and some H atoms are even visible at ∼1.8 Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If point-group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with the appropriate symmetry constraints.