A dynamic model for the evolution of protein structure

Protein domains are three-dimensional arrangements of atomic structure that are recurrent in the proteomes of organisms. Since the three-dimensional structure of a protein determines its function, it is the fold, much more than the underlying protein sequence and underlying chemistry, that is evolutionarily conserved. We are interested in probing the history of life with these domain structures and glimpsing qualitative changes over time by studying a dynamic model of protein evolution. Using standard phylogenetic methods and a census of protein domain structure in hundreds of genomes, we have reconstructed phylogenetic trees of protein domains, defined using the Structural Classification of Proteins (SCOP), where the nodes are folds or fold superfamilies (FSFs), the character vector for each node is a list of abundances of said fold or FSF across a range of species that spans all three superkingdoms of life, and the character states are linearly polarized by abundance; higher abundance within and among species equates to older structures and determines tree structure. Here we explore at what rate fold or FSF variants and new folds or FSFs appear in evolution. We also explore what collective model of proteome evolution explains such rates. Briefly, what are the dynamics of change? A set of birth-death differential equations was selected to capture the change of interest, with one set for folds and another for FSFs. The models assume that at any given moment there are a certain number of different folds or FSFs, with various abundances, and as each fold or FSF diversifies there are slight changes in the folds or FSFs, producing fold or FSF variants. Eventually as the variants continue to diversify and change as well, a new fold or FSF is born. Thus, there are two rate parameters in each model: the growth rate of fold or FSF variants and the rate of appearance of new folds or FSFs. The model governs the rate change of the average total abundance of a fold or FSF with time. It is fit to the tree so only those fold or FSF transitions actually present in the tree are assumed possible in the equations. It assumes a global perspective: the total abundance of a fold or FSF is that of the fold or FSF across all species, not within one organism. This perspective is used to properly discount terms of horizontal transfer in a birth-death model since such a transfer contributes no new folds or FSFs to the net abundance across all organisms. Our model determines 1) that there is a tight connection between the history of folds and FSFs, 2) that the corresponding transition probabilities to new variants of a fold experienced a sharp increase just as the transition probabilities to new folds experienced a steep decline and 3) that this simultaneous sharp increase and decline is explainable by and consistent with the combinatorial explosion of structural domains, referring to the period of high combination and rearrangement of domains and distribution of these new combinations in novel lineages, and the rise of organismal diversification. Our simulations suggest a picture of the past in which exploration of protein structure space proceeds much like that of a budding field of knowledge: first, coarse grain discoveries are made, followed by fine-grain elaboration of each once the coarse-grain discoveries have been exhausted

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Road traffic open data in Sweden: Availability and commercial exploitation - A research study on the state of open transportation data in Sweden

This chapter includes a description of how the study was conducted. In order to explore the possibilities for private companies to use open data, an extensive literature review was conducted. Furthermore, this helped to get familiarized with the subject of open data and understand how it is utilized today by public companies. While researching different methods for data analytics that are being used in transportation, it was found that predictive analytics was one of the most prominent methods as it can be used in numerous ways in order to improve predictions and planning within organizations. The use of predictive analytics in transportation includes predicting delays and traffic conditions which were found to be appropriate areas of analytics with regards to the types of open data that are commonly available. Hence, these will be the areas of transport analytics that will be focused on in this study. In order to analyze the full potential of open transport data, both as a means of improving existing businesses as well as to allow for new business opportunities to originate, the methodology had to be considered accordingly. To scope out opportunities for improvement of business activities, research projects were reviewed where a number of types of open transport-related data were used to predict future outcomes of traffic conditions and events in public transportation that could have potential impacts on how daily activities within transportation organizations are performed. The projects were chosen based on the potential accessibility that the data used for the analysis has in Swedish open data sources, in order to make sure that corresponding solutions to the problems are feasible to perform in Sweden. Furthermore, in order to analyze the potential for new businesses to arise from available open data, several existing companies that have gained their success through the use of such data were studied to gain an insight into how value can be extracted from it. To analyze the accessibility of relevant open data in Sweden, Trafiklab, and Trafikverket, two open data sources for transportation-related data have been used. These were chosen in a screening method of the biggest open data sources that offer a large amount of data publicly in Sweden.Incomin

Increased power generation in supercapacitive microbial fuel cell stack using Fe-N-C cathode catalyst

The anode and cathode electrodes of a microbial fuel cell (MFC) stack, composed of 28 single MFCs, were used as the negative and positive electrodes, respectively of an internal self-charged supercapacitor. Particularly, carbon veil was used as the negative electrode and activated carbon with a Fe-based catalyst as the positive electrode. The red-ox reactions on the anode and cathode, self-charged these electrodes creating an internal electrochemical double layer capacitor. Galvanostatic discharges were performed at different current and time pulses. Supercapacitive-MFC (SC-MFC) was also tested at four different solution conductivities. SC-MFC had an equivalent series resistance (ESR) decreasing from 6.00 Ω to 3.42 Ω in four solutions with conductivity between 2.5 mScm−1 and 40 mScm−1. The ohmic resistance of the positive electrode corresponded to 75–80% of the overall ESR. The highest performance was achieved with a solution conductivity of 40 mS cm−1 and this was due to the positive electrode potential enhancement for the utilization of Fe-based catalysts. Maximum power was 36.9mW (36.9Wm−3) that decreased with increasing pulse time. SC-MFC was subjected to 4520 cycles (8 days) with a pulse time of 5 s (ipulse 55 mA) and a self-recharging time of 150 s showing robust reproducibility

Towards Customer-Centricity in the Aftermarket A Case Study of Customer-Centricity in an Aftermarket Logistics Organisation

Customer-centricity is increasingly stipulated as a fundamental strategic goal in corporations across several industries worldwide. However, many organisations still experience difficulties in achieving customer-centricity in practice. Furthermore, there is limited research that investigates in-depth how a traditionally product-centric organisation within the aftermarket context should work to become customer-centric. Thus, this thesis project aims to address this research gap by exploring what is required from an aftermarket logistics organisation within the automotive industry to realise the shift from product-centricity. The case organisation recently commenced an initiative to achieve customer-centricity due to intensified competition, the digital transformation within the industry, and increasingly sophisticated customer requirements. The research was based on a qualitative case study with an abductive approach to theory development, comprising focus groups, semi-structured and unstructured interviews with managers and employees from the case organisation, as well as representatives from two benchmarking organisations. Moreover, the empirical data was analysed iteratively and thematically to deduce the key areas related to the research questions. A frame of reference was developed to support this analysis, encompassing the following areas: background to the aftermarket context, definition of customer-centricity, hindrances to achieving customercentricity, and basic capabilities supporting efforts to implement customer-centricity. This thesis project concluded that the product-centric aftermarket logistics organisation faces several hindrances when seeking to achieve customer-centricity. Some of the main identified hindrances were the following: ambiguity around who the customer is in the aftermarket, lack of senior management commitment among the actors in the aftermarket supply chain, power dynamics that somewhat restrict the case organisation from having deeper interactions with the customers, unclear roles and responsibilities related to the customer experience, lack of digital systems for efficient sharing of customer data, and lack of metrics assessing individual customers’ overall experience. Furthermore, it was concluded that the product-centric aftermarket organisation should, in parallel, take specific measures to address the hindrances while developing basic capabilities. These measures include, e.g., assigning roles with end-toend responsibilities accountable for the customer experience, and installing IoT devices to capture detailed end-customer data. The capabilities investigated in this study are the following: capture the voice-of-the-customer, customer-centric performance measurement, create value according to the service logic, and deliver high service quality

N-acetylglucosamine Regulates Virulence Properties in Microbial Pathogens

There is growing evidence that the sugar N-acetylglucosamine (GlcNAc) plays diverse roles in cell signaling pathways that impact the virulence properties of microbes and host cells. GlcNAc is already well known as a ubiquitous structural component at the cell surface that forms part of bacterial cell wall peptidoglycan, cell wall chitin in fungi and parasites, and extracellular matrix glycosaminoglycans of animal cells. Chitin and peptidoglycan have been previously linked to cell signaling as they can stimulate responses in plant and animal host cells [1–3]. Recent studies now indicate that GlcNAc released from these polymers can also activate cell signaling via several different mechanisms [4–6]. The role of these new GlcNAc signaling pathways in the regulation of virulence factors will be the focus of this review