Advanced continuous-discrete model for joint time-use expenditure and mode choice estimation

This paper presents the joint time use, expenditure and mode choice model, based on the theoretical Framework of Jara-Díazand Gueva (2003), for the first time estimated in Panel Setting while using Survey edexpenditure data. This extended estimation takes into account multiple trips per individual, as well as mode availability. The model was es-timated using the novel dataset gathered in Austria in 2015. It includes individual-specific Information on time-use, expenditures and mode choice. As a result, we calculate the value of leisure (VoL), travel time savings (VTTS) and time as signed to travel (VTAT), that are rel-evant inputs to appraisals of transport policies. We also show that, at least fort he Austrian working population, the omission of expenditures in the model might result in a significant overestimation of the value of leisure (16.83%); the VoL (9.29€/h) was estimated to be considerably lower than the wage rate (12.14€/h) and the VTTS varies strongly between the modes (9.98€/h for car, 3.91€/h for public transport, 9.25€/h for bike and 17.53€/h for walk). The joint estimation framework produced positive estimates of VTAT (5.38€/h) only for public transport, reflecting the favorable public transport conditions in Austria

New consistency index based on inertial operating speed

The occurrence of road crashes depends on several factors, with design consistency (i.e., conformance of highway geometry to drivers' expectations) being one of the most important. A new consistency model for evaluating the performance of tangent-to-curve transitions on two-lane rural roads was developed. This model was based on the inertial consistency index (ICI) defined for each transition. The ICI was calculated at the beginning point of the curve as the difference between the average operating speed on the previous 1-km road segment (inertial operating speed) and the actual operating speed at this point. For the calibration of the ICI and its thresholds, 88 road segments, which included 1,686 tangent-to-curve transitions, were studied. The relationship between those results and the crash rate associated with each transition was analyzed. The results showed that the higher the ICI was, the higher the crash rate; thus, the probability of accidents increased. Similar results were obtained from the study of the relationship between the ICI and the weighted average crash rate of the corresponding group of transitions. A graphical and statistical analysis established that road consistency might be considered good when the ICI was lower than 10 km/h, poor when the ICI was higher than 20 km/h, and fair otherwise. A validation process that considered 20 road segments was performed. The ICI values obtained were highly correlated to the number of crashes that had occurred at the analyzed transitions. Thus, the ICI and its consistency thresholds resulted in a new approach for evaluation of consistency.The authors thank the Center for Studies and Experimentation of Public Works of the Spanish Ministry of Public Works, which partially subsidized the data collection, for obtaining the empirical operating speed profiles used in the validation process. The authors also thank the General Directorate of Public Works of the Infrastructure and Transportation Department of the Valencian government, the Valencian Province Council, and the General Directorate of Traffic of the Ministry of the Interior of the Government of Spain for their cooperation in data gathering.García García, A.; Llopis Castelló, D.; Camacho Torregrosa, FJ.; Pérez Zuriaga, AM. (2013). New consistency index based on inertial operating speed. Transportation Research Record. (2391):105-112. doi:10.3141/2391-10S1051122391Ng, J. C. ., & Sayed, T. (2004). Effect of geometric design consistency on road safety. Canadian Journal of Civil Engineering, 31(2), 218-227. doi:10.1139/l03-090Gibreel, G. M., Easa, S. M., Hassan, Y., & El-Dimeery, I. A. (1999). State of the Art of Highway Geometric Design Consistency. Journal of Transportation Engineering, 125(4), 305-313. doi:10.1061/(asce)0733-947x(1999)125:4(305)Hassan, Y. (2004). Highway Design Consistency: Refining the State of Knowledge and Practice. Transportation Research Record: Journal of the Transportation Research Board, 1881(1), 63-71. doi:10.3141/1881-08Polus, A., & Mattar-Habib, C. (2004). New Consistency Model for Rural Highways and Its Relationship to Safety. Journal of Transportation Engineering, 130(3), 286-293. doi:10.1061/(asce)0733-947x(2004)130:3(286)Cafiso, S., Di Graziano, A., Di Silvestro, G., La Cava, G., & Persaud, B. (2010). Development of comprehensive accident models for two-lane rural highways using exposure, geometry, consistency and context variables. Accident Analysis & Prevention, 42(4), 1072-1079. doi:10.1016/j.aap.2009.12.015Zuriaga, A. M. P., García, A. G., Torregrosa, F. J. C., & D’Attoma, P. (2010). Modeling Operating Speed and Deceleration on Two-Lane Rural Roads with Global Positioning System Data. Transportation Research Record: Journal of the Transportation Research Board, 2171(1), 11-20. doi:10.3141/2171-0

Microanatomy of the trophosome region of Paracatenula cf. polyhymnia (Catenulida, Platyhelminthes) and its intracellular symbionts

Marine catenulid platyhelminths of the genus Paracatenula lack mouth, pharynx and gut. They live in a symbiosis with intracellular bacteria which are restricted to the body region posterior to the brain. The symbiont-housing cells (bacteriocytes) collectively form the trophosome tissue, which functionally replaces the digestive tract. It constitutes the largest part of the body and is the most important synapomorphy of this group. While some other features of the Paracatenula anatomy have already been analyzed, an in-depth analysis of the trophosome region was missing. Here, we identify and characterize the composition of the trophosome and its surrounding tissue by analyzing series of ultra-thin cross-sections of the species Paracatenula cf. polyhymnia. For the first time, a protonephridium is detected in a Paracatenula species, but it is morphologically reduced and most likely not functional. Cells containing needle-like inclusions in the reference species Paracatenula polyhymnia Sterrer and Rieger, 1974 were thought to be sperm, and the inclusions interpreted as the sperm nucleus. Our analysis of similar cells and their inclusions by EDX and Raman microspectroscopy documents an inorganic spicule consisting of a unique magnesium–phosphate compound. Furthermore, we identify the neoblast stem cells located underneath the epidermis. Except for the modifications due to the symbiotic lifestyle and the enigmatic spicule cells, the organization of Paracatenula cf. polyhymnia conforms to that of the Catenulida in all studied aspects. Therefore, this species represents an excellent model system for further studies of host adaptation to an obligate symbiotic lifestyle

BeadArray Expression Analysis Using Bioconductor

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered

The Substrate-Bound Crystal Structure of a Baeyer–Villiger Monooxygenase Exhibits a Criegee-like Conformation

The Baeyer\u2013Villiger monooxygenases (BVMOs) are a family of bacterial flavoproteins that catalyze the synthetically useful Baeyer\u2013Villiger oxidation reaction. This involves the conversion of ketones into esters or cyclic ketones into lactones by introducing an oxygen atom adjacent to the carbonyl group. The BVMOs offer exquisite regio- and enantiospecificity while acting on a wide range of substrates. They use only NADPH and oxygen as cosubstrates, and produce only NADP+ and water as byproducts, making them environmentally attractive for industrial purposes. Here, we report the first crystal structure of a BVMO, cyclohexanone monooxygenase (CHMO) from Rhodococcus sp. HI-31 in complex with its substrate, cyclohexanone, as well as NADP+ and FAD, to 2.4 \uc5 resolution. This structure shows a drastic rotation of the NADP+ cofactor in comparison to previously reported NADP+-bound structures, as the nicotinamide moiety is no longer positioned above the flavin ring. Instead, the substrate, cyclohexanone, is found at this location, in an appropriate position for the formation of the Criegee intermediate. The rotation of NADP+ permits the substrate to gain access to the reactive flavin peroxyanion intermediate while preventing it from diffusing out of the active site. The structure thus reveals the conformation of the enzyme during the key catalytic step. CHMO is proposed to undergo a series of conformational changes to gradually move the substrate from the solvent, via binding in a solvent excluded pocket that dictates the enzyme\u2019s chemospecificity, to a location above the flavin\u2013peroxide adduct where catalysis occurs.Peer reviewed: YesNRC publication: Ye

Prototypes for Content-Based Image Retrieval in Clinical Practice

Content-based image retrieval (CBIR) has been proposed as key technology for computer-aided diagnostics (CAD). This paper reviews the state of the art and future challenges in CBIR for CAD applied to clinical practice

Visualization of proteomics data using R and bioconductor.

Data visualization plays a key role in high-throughput biology. It is an essential tool for data exploration allowing to shed light on data structure and patterns of interest. Visualization is also of paramount importance as a form of communicating data to a broad audience. Here, we provided a short overview of the application of the R software to the visualization of proteomics data. We present a summary of R's plotting systems and how they are used to visualize and understand raw and processed MS-based proteomics data.LG was supported by the European Union 7th Framework Program (PRIME-XS project, grant agreement number 262067) and a BBSRC Strategic Longer and Larger grant (Award BB/L002817/1). LMB was supported by a BBSRC Tools and Resources Development Fund (Award BB/K00137X/1). TN was supported by a ERASMUS Placement scholarship.This is the final published version of the article. It was originally published in Proteomics (PROTEOMICS Special Issue: Proteomics Data Visualisation Volume 15, Issue 8, pages 1375–1389, April 2015. DOI: 10.1002/pmic.201400392). The final version is available at http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400392/abstract