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Increasing the attractiveness of public transport is a key issue in the endeavours towards more sustainable transport systems. While there is a lot of knowledge on what can be done to increase public transport patronage, there is a lack of empirically based research analysing how to do this in practice. Using a comparative case analysis of six regions in Sweden with the highest increase in passenger volumes for public transport between 2009 and 2015, this paper examines the prerequisites for increasing public transport patronage, with a focus on the governance conditions required to implement such measures. The empirical material consists of semi-structured interviews with public transport planners and strategy documents for the six regions. The findings show that all regions but one employed a similar approach and implemented measures aimed at concentrating resources to corridors where the potential demand was the greatest. Only one region chose a different approach by investing in services in both strong routes and in the peripheral network. However, regardless of approach, the results highlight that there is considerable coherence regarding the governance conditions that enable implementation. Three main conditions were identified, namely political support, well-functioning collaboration between organisations, and public support through citizen dialogue. The results support key findings on collaborative conditions from previous research, including the importance of joint objectives, trust between key individuals, and the need for long time frames in order to develop collaborative capacity.

Removing bus stops is often a prerequisite for introducing faster, more reliable, and more frequent rail or coach services in rural areas. Despite the potentially higher quality of service through trains or coaches, however, the bus-stop removals often become stumbling blocks. It is sometimes feared that the alterations to the public transport network will pose a threat to the possibilities of living in rural areas outside villages. In this study, we investigate how travel by public transport is affected in areas where bus services are substantially reduced in connection with the introduction of rail services with fewer stops. Through an analysis of access trips from rural areas surrounding the train stations, we are able to study the development of public transport patronage in these areas in comparison with a control group with retained rural bus services. A total of 28 villages with surrounding rural areas in southern Sweden are included in the study. Our results reveal a significantly larger patronage increase around new train stations compared to areas where regional bus services are kept, and importantly, the patronage increase does not only occur in the immediate surroundings of the stations. Outside the villages, in the rural areas where public transport services have been cut, the increase is of equal magnitude. Hence, our results oppose the idea of distortion between the villages and their surrounding rural areas, at least in terms of net effect on public transport usage.

There has been a rapid rise in papers modelling the impacts of autonomous vehicles. Drawing on a review of this literature, we analyse and discuss the messages conveyed by these studies from a poli...

Creating efficient public transport systems that attract users is a challenging task in contexts where the control of public transport is divided between various actors. Recent research on public transport has therefore seen increasing focus on issues like coordination, collaboration and steering in complex governance settings. However, more is known about what needs to be done than how to implement the necessary changes. This paper presents a systematic literature review with a focus on developing the understanding on how to improve the conditions for public transport. The reviewed articles are analysed for increasing the understanding of the critical challenges in the planning and implementation of measures to increase public transport travel; the working practices for dealing with problems described in the literature; and the advantages and disadvantages of different working practices. Based on the analysis an analytical framework is developed that can be used to study and evaluate working practices for managing critical challenges. The framework consists of three interconnected factors (i) actors, (ii) institutions (laws and rules that govern the interaction of the actors), and (iii) work processes (phases in the interaction between the actors). Drawing on the results of the systematic review a number of key issues for establishing working practices for dealing with the challenges are emphasized for each of the factors.

Electric buses can improve the environmental performance of public transport. Yet, introducing electric buses brings novel challenges, such as requirements for operational changes, new forms of institutional collaboration, increased investment costs and technological concerns. This paper investigates these challenges and strategies for managing them by comparing experiences of electric bus implementation in English and Swedish cities. The comparative approach enabled us to understand the influence of governance context, organisational practices and relations between stakeholders. The comparison shows that experiences by involved stakeholders are highly context dependant. Financial and regulatory support from the national government, along with passenger demand and route characteristics had significant influence on the implementation. However, the relationship between stakeholders involved and the division of responsibility emerged as central factors to overcome challenges – the most important being the development of functioning collaboration between the stakeholders.

Background The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. Results We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. Conclusions Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.

Nontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern “omics” approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, MmucT, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.

Background: Bayesian predictive probability design, with a binary endpoint, is gaining attention for the phase II trial due to its innovative strategy. To make the Bayesian design more accessible, we elucidate this Bayesian approach with a R package to streamline a statistical plan, so biostatisticians and clinicians can easily integrate the design into clinical trial. Methods: We utilize a Bayesian framework using Bayesian posterior probability and predictive probability to build a R package and develop a statistical plan for the trial design. With pre-defined sample sizes, the approach employs the posterior probability with a threshold to calculate the minimum number of responders needed at end of the study to claim efficacy. Then the predictive probability is applied to evaluate future success at interim stages and form stopping rule at each stage. Results: An R package, ‘BayesianPredictiveFutility’, with associated graphical interface is developed for easy utilization of the trial design. The statistical tool generates a professional statistical plan with comprehensive results including a summary, details of study design, a series of tables and figures from stopping boundary for futility, Bayesian predictive probability, performance [probability of early termination (PET), type I error, and power], PET at each interim analysis, sensitivity analysis for predictive probability, posterior probability, sample size, and beta prior distribution. The statistical plan presents the methodology in a readable language fashion while preserving rigorous statistical arguments. The output formats (Word or PDF) are available to communicate with physicians or to be incorporated in the trial protocol. Two clinical trials in lung cancer are used to demonstrate its usefulness. Conclusions: Bayesian predictive probability method presents a flexible design in clinical trial. The statistical tool brings an added value to broaden the application.

Sensitivity response is a critical parameter that decides the domain of dielectric materials to be implemented as piezocapacitive sensors for low- or high-pressure sensing applications. Here, we have clarified the sensitivity response behavior of three low-cost dielectric materials, two biodegradable paperboards, and one acoustic polymeric foam. The devices are fabricated in the form of a metal–insulator–metal structure, and the capacitive response of the devices is measured using the charge extraction by linearly increasing voltage technique. The sensitivity response curve (ΔC/C o vs. pressure) reveals that the paperboard materials are sensitive enough to detect low-pressure regimes (45 kPa), whereas the acoustic foam is quite promising for high-pressure monitoring (above 150 kPa). Using a multiplexer circuit, we demonstrated the sensitivity response via 2 by 2 matrix structure both as a steady-state and transient response. Our results show that the passive matrix structure interference between different pixels can be minimized after increasing the spacing between electrodes strip. Finally, a full-scale demonstrator (dimension 120 cm × 400 cm) with a 2 × 8 matrix structure laminated under floor tiling has been demonstrated. We show how such a floor sensor utilizing the low-cost substrates can be used to recognize single-stepping, walking, and falling.

Bus priority measures are introduced in cities in order to improve travel time, frequency, and reliability, thereby benefiting the passengers and establishing a more attractive and competitive public transport system. Since first being implemented in Chicago in the late 1930s, bus priority measures are now widely applied across the globe, and a plethora of measures regarding priority in terms of time and space are currently in place. The main challenge for planning and implementing bus priority measures is the conflict over space with other societal purposes and road modes, in particular the car. In addition, the introduction of bus priority is often planned and implemented in a context of institutional complexity, which contributes to making such efforts a challenging task. In this article, political leadership, collaboration, alternative funding schemes, guidelines, and action plans are suggested as important instruments to handle these challenges. (Less)

Microorganisms survive stresses by alternating the expression of genes suitable for surviving the immediate and present danger and eventually adapt to new conditions. Many bacteria have evolved a multiprotein "molecular machinery" designated the "Stressosome" that integrates different stress signals and activates alternative sigma factors for appropriate downstream responses. We and others have identified orthologs of some of the Bacillus subtilis stressosome components, RsbR, RsbS, RsbT and RsbUVW in several mycobacteria and we have previously reported mutual interactions among the stressosome components RsbR, RsbS, RsbT and RsbUVW from Mycobacterium marinum. Here we provide evidence that "STAS" domains of both RsbR and RsbS are important for establishing the interaction and thus critical for stressosome assembly. Fluorescence microscopy further suggested co-localization of RsbR and RsbS in multiprotein complexes visible as co-localized fluorescent foci distributed at scattered locations in the M. marinum cytoplasm; the number, intensity and distribution of such foci changed in cells under stressed conditions. Finally, we provide bioinformatics data that 17 (of 244) mycobacteria, which lack the RsbRST genes, carry homologs of Bacillus cereus genes rsbK and rsbM indicating the existence of alternative σF activation pathways among mycobacteria.

Poly(3,4-ethylenedioxythiophene) doped with the polymer anion poly(styrenesulfonate), PEDOT:PSS, is a common electrochromic material used in the preparation of electrochromic devices (ECDs). In this paper, the PEDOT:PSS doped with a solvent was used both as the electrode and the electrochromic functional layer for fabrication of ECDs on absorptive paper surfaces. The doped PEDOT:PSS dispersion was assessed for the film-forming evenness, sheet resistance and conductivity, and the performance of prepared ECDs for their color contrast and switching dynamics. The ECD performance is discussed in relation to the absorptive characteristics of the substrates. The results indicate that it is feasible to prepare ECDs onto absorptive substrates, despite the partial polymer material imbibition into them. The extent of polymer absorption influences the ECD performance: an increased absorption reduces the color contrast but speeds up the color switching. The electrochemical properties of the used solid electrolyte were found to be crucial for functioning of the ECDs. Insufficient ion transport and associated high resistance led to failure of the devices.

Highly collaborative scientists are often called on to extend their expertise to different types of projects and to expand the scope and scale of projects well beyond their previous experience. For a large-scale project involving "big data" to be successful, several different aspects of the research plan need to be developed and tested, which include but are not limited to the experimental design, sample collection, sample preparation, metadata recording, technical capability, data acquisition, approaches for data analysis, methods for integration of different data types, recruitment of additional expertise as needed to guide the project, and strategies for clear communication throughout the project. To capture this process, we describe an example project in proteogenomics that built on our collective expertise and experience. Key steps included definition of hypotheses, identification of an appropriate clinical cohort, pilot projects to assess feasibility, refinement of experimental designs, and extensive discussions involving the research team throughout the process. The goal of this chapter is to provide the reader with a set of guidelines to support development of other large-scale multiomics projects.

Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the "M"- and the "Aronson"-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.

In planning for a future sustainable transport system, it is important to consider the likely effects of e-commerce. This paper analyses the understanding of impacts of e-commerce on urban planning as expressed in planning practice in a number of Swedish municipalities. Knowledge claims concerning the potential effects of e-commerce are studied through an analysis of planning documents and supplementing interviews. These knowledge claims in planning practice are contrasted with the findings presented and discussed in the research literature. The results indicate that the current understanding of e-commerce in Swedish planning practice is limited and that it is primarily viewed as an opportunity to address transport system issues by reducing passenger transport. However, the overview of the literature shows that e-commerce has so far only had limited effects on prevailing mobility habits and that freight transport has increased in parallel with increased e-commerce. Furthermore, e-commerce challenges city centres as commercial areas. Thus, from a planning perspective e-commerce should not be regarded as an easy solution for an unsustainable transport sector. To harness its potential benefits, there is a need to develop pro-active planning strategies that address the potential impacts of e-commerce.

The purpose is to analyse and explain factors determining whether conventional trade with stores or e-commerce with home delivery is more energy-efficient. The findings from previous studies are compared in order to identify more general patterns of energy consumption, describe which energy consumption factors (product waste and product returns, buildings, packaging, passenger transport and freight transport) are considered and what assumptions are made. In this comparison, we analyse product characteristics and product classes, discuss the energy factors with the greatest impact and the contextual impact of each factor on the energy consumption. The paper is based on a structured literature review and a content analysis, which helped us to synthesise current knowledge and explain consistent and inconsistent findings across individual studies of energy consumption in conventional sales channels versus e-commerce channels. Our literature search identified 11 studies, with 16 cases, that compared the energy efficiency. The results show the following: 1) The net effect of energy consumption was in the majority of the cases positive for the e-commerce channel, 2) The proportion of unsold products and product returns seem to have a major impact on the energy efficiency of different sales channels, 3) Buildings had only a minor effect on the energy consumption difference. It was slightly lower in the home delivery systems, 4) Packaging contributed considerably to the energy consumption difference for some products. The e-commerce channel consumed generally more energy from packaging, but indirect effects (e.g. volume efficiency) were not considered, and 5) The total energy consumption from transportation was greater in the conventional supply chains, as the additional energy in passenger transport generally outweighed the increased energy in freight transport in e-commerce. The paper points out directions for future research and discusses implications for research, policy-making and practice.

The report presents an international literature review on Transit Oriented Development (TOD) research carried out in order to frame the research problem and gaps for a research project that is to be carried out largely in the Swedish context. The literature searches of peer-reviewed articles, literature reviews, and conference papers were carried out in the bibliographic databases Google Scholar, Scopus and Web of Science based on keywords selected by the project team. The report presents definitions of TOD, the application of the TOD concept in semiperipheral,peripheral and rural areas, the role of the private sector in delivering TOD, aswell as best practice examples, including enabling processual planning factors, barriers and outcomes. It then identifies research gaps that are related to the above topics. Based on the findings of the literature review, the report suggests an outline for future research.

The creation of an efficient public transport system increasingly requires collaboration between independent organizations. Institutional reforms in Europe have created governance situations where collaboration between organizations is a critical issue, and examples include the integration of transport and land-use planning and the planning of large public transport projects. The organizational context of public transport, with several formal, discrete organizations that need to collaborate, raises questions about how functioning collaborations can be accomplished. This paper examines how to create functioning collaboration between organizations in the public transport sector. We depart from a theory of collaboration as a stepwise trust-building process, and we present results from a comparative case study of collaboration in two Swedish public transport projects. The results show some of the prerequisites that must be in place in order for the collaboration to work, but also the boundaries of what collaborative approaches can bring about. Conditions such as honest, open, and inclusive dialog between stakeholders and resources in the form of finance, knowledge, mandate, and leadership are important. While there is no guarantee that this will lead to differences in interests being resolved, the results indicate that it improves the chances of finding compromises that all of the involved stakeholders can accept, especially if favorable conditions for collaboration are established at an early stage of the planning process. Building on these findings, we suggest some practical recommendations for improving collaboration in future public transport projects. These practical recommendations are aimed at improving the handling of unavoidable conflicts in collaboration in a constructive way.

Undifferentiated embryonal sarcoma of the liver (UESL) is a rare and aggressive malignancy. Though the molecular underpinnings of this cancer have been largely unexplored, recurrent chromosomal breakpoints affecting a noncoding region on chr19q13, which includes the chromosome 19 microRNA cluster (C19MC), have been reported in several cases. We performed comprehensive molecular profiling on samples from 14 patients diagnosed with UESL. Congruent with prior reports, we identified structural variants in chr19q13 in 10 of 13 evaluable tumors. From whole transcriptome sequencing, we observed striking expressional activity of the entire C19MC region. Concordantly, in 7 of 7 samples undergoing miRNAseq, we observed hyperexpression of the miRNAs within this cluster to levels >100 fold compared to matched normal tissue or a non-C19MC amplified cancer cell line. Concurrent TP53 mutation or copy number loss was identified in all evaluable tumors with evidence of C19MC overexpression. We find that C19MC miRNAs exhibit significant negative correlation to TP53 regulatory miRNAs and K-Ras regulatory miRNAs. Using RNA-seq we identified that pathways relevant to cellular differentiation as well as mRNA translation machinery are transcriptionally enriched in UESL. In summary, utilizing a combination of next-generation sequencing and high-density arrays we identify the combination of C19MC hyperexpression via chromosomal structural event with TP53 mutation or loss as highly recurrent genomic features of UESL., Author summary We perform the most comprehensive molecular analysis to date of undifferentiated embryonal sarcoma of the liver, utilizing whole exome sequencing, RNA sequencing, miRNA sequencing, and SNP arrays. We find that UESL tumors harbor aberrant transcriptional start sites within C19MC region that is driven by structural rearrangement, leading to extreme overexpression of C19MC miRNAs. We further find that C19MC miRNAs negatively correlate with TP53 and K-Ras regulatory miRNAs. UESL also harbors highly recurrent TP53 mutation or copy number loss. Therefore, we provide for the first time a genomic landscape of UESL and describe cellular consequences of the discovered foundational genomic changes.

The aim of this report is to contribute to develop knowledge about what the developments in positioning and smartphone technology bring to the table for the public transport sector. The overarching question in the report is: can new technology improve demand-responsive transport (DRT)? The cases analysed in this report were selected using a number of criteria to delimit the sample and distinguish the cases from “traditional” DRT and from ride-hailing services. A total of 35 different services were identified that met the criteria for what this report refers to as on-demand public transport. The identified cases are located in nine different countries and 23 different cities or regions, and includes services that have been or are operating in major urban areas, smaller towns, suburbs, semi-rural and rural areas. Nine services, most of which are subsidised by the public sector, have been analysed in more detail. The comparison of the cases reveal differences and similarities concerning aspects such as vehicles and fleet sizes, and service partnerships. Different variants are also described regarding operational policies of the services. This includes origin-destination policies, areas covered by the services, where to pick up and drop off passengers, operating hours, booking method, time of booking, payment and pricing. For the nine cases that are the focus of the report a comparison of patronage, productivity and production costs are also made. A main conclusion from this part of the study is that so far there is scant evidence that new technology improves the productivity of DRT. This suggests that new technology is no panacea for fixing the problems of DRT and the study shows that thus far, at least, on-demand public transport hardly represents a transport revolution.

This paper explores the mental-models of Swedish planners in order to understand the extent to which they support the ideals of sustainable transport. Focussing on three critical challenges: forecast-led versus vision-led planning; tackling congestion; and, public acceptability; the findings, drawn from in-depth interviews, demonstrate mostly advanced thinking. However, implementation can be at odds with these mental models, highlighting important lessons for other cities. There is a disconnect between the objectives of reducing car use and the continuation of investments in increasing road capacity, and a difficulty in transitioning from forecast-led planning to back-casting. Political controversies and public acceptability for measures to decrease car use are an added challenge.