dsSurvival: Privacy preserving survival models for federated individual patient meta-analysis in DataSHIELD

Objective Achieving sufficient statistical power in a survival analysis usually requires large amounts of data from different sites. Sensitivity of individual-level data, ethical and practical considerations regarding data sharing across institutions could be a potential challenge for achieving this added power. Hence we implemented a federated meta-analysis approach of survival models in DataSHIELD, where only anonymous aggregated data are shared across institutions, while simultaneously allowing for exploratory, interactive modelling. In this case, meta-analysis techniques to combine analysis results from each site are a solution, but a manual analysis workflow hinders exploration. Thus, the aim is to provide a framework for performing meta-analysis of Cox regression models across institutions without manual analysis steps for the data providers. Results We introduce a package ( dsSurvival) which allows privacy preserving meta-analysis of survival models, including the calculation of hazard ratios. Our tool can be of great use in biomedical research where there is a need for building survival models and there are privacy concerns about sharing data.

dsSurvival: Privacy preserving survival models for federated individual patient meta-analysis in DataSHIELD

Achieving sufficient statistical power in a survival analysis usually requires large amounts of data from different sites. Sensitivity of individual-level data, ethical and practical considerations regarding data sharing across institutions could be a potential challenge for achieving this added power. Hence we implemented a federated meta-analysis approach of survival models in DataSHIELD, where only anonymous aggregated data are shared across institutions, while simultaneously allowing for exploratory, interactive modelling. In this case, meta-analysis techniques to combine analysis results from each site are a solution, but a manual analysis workflow hinders exploration. Thus, the aim is to provide a framework for performing meta-analysis of Cox regression models across institutions without manual analysis steps for the data providers. We introduce a package (dsSurvival) which allows privacy preserving meta-analysis of survival models, including the calculation of hazard ratios. Our tool can be of great use in biomedical research where there is a need for building survival models and there are privacy concerns about sharing data. A tutorial in bookdown format with code, diagnostics, plots and synthetic data is available here: https://neelsoumya.github.io/dsSurvivalbookdown/ All code is available from the following repositories: https://github.com/neelsoumya/dsSurvivalClient/ https://github.com/neelsoumya/dsSurvival/

The Contribution of MCDM to SUMP: The Case of Spanish Cities during 2006–2021

Sustainable Urban Mobility Plans (SUMP) are increasingly popular planning tools in cities with environmental issues where numerous actions are usually proposed to reduce pollution from urban transport. However, the diagnosis and implementation of these processes requires broad consensus from all stakeholders and the ability to fit them into urban planning in such a way that it allows the proposals to become realistic actions. In this study, a review of the sustainable urban mobility plans of 47 cities in Spain during the last 15 years has been carried out, analyzing both the diagnosis and proposal of solutions and their subsequent implementation. From the results obtained, a new framework based on a structured hybrid methodology is proposed to aid decision-making for the evaluation of alternatives in the implementation of proposals in SUMP. This hybrid methodology considers experts’ and stakeholders’ opinion and applies two different multi-criteria decision making (MCDM) methods in different phases to present two rankings of best alternatives. From that experience, an analysis based on the MCDM methods called ‘Sequential Interactive Modelling for Urban Systems (SIMUS)’ and weighted sum method (WSM) was applied to a case study of the city of Cartagena, a southeastern middle-size city in Spain. This analytic proposal has been transferred to the practical field in the SUMP of Cartagena, the first instrument of this nature developed after COVID-19 in Spain for a relevant city. The results show how this framework, based on a hybrid methodology, allows the development of complex decision mapping processes using these instruments without obviating the need to generate planning tools that can be transferred from the theoretical framework of urban reality.

Analysis of Policies of Railway Operators Using SWOT Criteria and the SIMUS Method: A Case for the Bulgarian Railway Network

This study is useful for railway operators as it enables them to verify their decisions against the results of the application of the techniques of strategic planning and multi-criteria analysis. It gives railway stakeholders concise, objective and unbiased information so that they can then make decisions and also allows them to determine the strengths and sensitivity, of the best solution found. This paper presents a methodology for the assessment of the policies of railway operators using Strengths–Weakness–Opportunities–Threats (SWOT) criteria and the Sequential Interactive Modelling for Urban Systems (SIMUS) method. The methodology of the research consists of two stages. In the first stage, the alternatives of the policies for the railway operator are formulated; the criteria in the SWOT group are defined; and the values of the criteria are determined for each of the alternatives. In the second stage, the SIMUS method is applied to rank the alternatives and assess the criteria in the SWOT groups. The criteria are interpreted as objectives and linear optimizations are performed. A comparison between the desired values for each objective of the SWOT criteria and the optimum values of the objective functions obtained by SIMUS was made. The methodology was applied to the Bulgarian railway network. Three policies for railway operation were studied. The total number of 17 railway policies criteria in the SWOT group were defined and assessed—three strengths criteria, seven weaknesses criteria, three opportunities criteria and four threats criteria. The results indicated that the best strategy is A3 (some reconstruction of the railway infrastructure and new rolling stock on some lines), with the highest score of 3.76, followed by A2 (new rolling stock on some lines), with a score of 2.71. The status-quo strategy (A1) has a very low score of 0.43, that the current situation or status-quo cannot be supported. The weights of both strengths and opportunities are both of the same importance with a weight of 0.180. It was found out that the clusters Weakness and Threats are dominant with weights of 0.4 and 0.24 respectively. The results show that the weights are all practically the same, about 0.06, and therefore, no discrimination by importance is possible. The methodology makes it possible to consider the alternatives simultaneously, and in this way, the results will reflect the effect of one criterion on all others, and permit us to quantify the differences between expected and real results.

CSynth: an interactive modelling and visualization tool for 3D chromatin structure

Motivation The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools. Results We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualize models of any chromosome conformation capture (3C) data. Unlike other modelling systems, CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues/cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and a public engagement tool. Availabilityand implementation CSynth is web based and available to use at https://csynth.org. Supplementary information Supplementary data are available at Bioinformatics online.

Coupling the Parallel Ice Sheet Model with the Modular Ocean Model via an Antarctic ice-shelf cavity module

<p>Ocean-ice shelf interactions are the main drivers for the current mass loss from the Antarctic Ice Sheet. Recent studies have shown that increased continental meltwater input can enhance discharge through ice-ocean feedbacks. This raises the need for interactive modelling between ocean and ice-sheet systems to assess the consequences of additional freshwater input on the Antarctic region and beyond. While high-resolution simulations (1/4 degree or greater) can resolve detailed interactions between the ocean and ice shelf, the computational costs make them applicable only for regional studies or decadal to centennial time scales. In this study we present a framework for coupling a coarse resolution ocean model (MOM) to the Parallel Ice Sheet Model (PISM) via the Potsdam Ice-shelf Cavity mOdel (PICO). The intermediate model PICO approximates the overturning circulation in ice shelf cavities and includes ice-ocean boundary layer physics. We present this offline coupling approach and discuss the fluxes exchanged between the distinct model runs as well as energy and mass conservation. Using this flexible and computationally efficient framework, feedbacks between the ice and ocean can be analysed on a global spatial scale and paleoclimate time-scales.</p><p> </p>

Multi-Criteria Evaluation of Railway Network Performance in Countries of the TEN-T Orient–East Med Corridor

Railway networks have different levels of development, which affects the overall transport process and integrated sustainable development. This paper presents a methodology to assess and classify the railway network performance along the Trans-European Transport Network (TEN-T) core network corridor. The Orient–East Med corridor (OEM) has been examined. Twenty-two infrastructural, economic and technological criteria for assessment of railway transport have been proposed. The countries were ranked used multi-criteria decision making (MCDM), by applying the Sequential Interactive Modelling for Urban Systems (SIMUS). A sensitivity analysis was performed regarding each objective, and then, their allowable range of variation was determined without modifying the whole ranking of countries. The criteria weights have been determined on the basis of the output of using the SIMUS method. It was found that the main criteria for ranking the countries are: length of the connecting railway lines of the corridor in the country, length of the railway lines in the country, number of intermodal terminals, gross domestic product (GDP) per capita, passengers transport performance, freight transport performance for the railway network, corridor freight usage intensity. It was found that the railway transport in the area of the OEM corridor located in Central Europe is better developed than in the Southeast European area. A cluster analysis was performed to classify countries into groups to verify the results. The results show that the eight countries included in the OEM corridor can be classified into three groups. The methodology could be used to make decisions about transport planning and improvement of the connectivity and sustainability of the railway transport, considering their development.