Using virtual reality to visualize extreme rainfall events derived from climate simulations

Virtual reality (VR) is an emerging and powerful tool to visualize and explore complex scientific data sets in an intuitive, interactive and user-friendly manner. In this study, we explore the usage of VR to create an immersive visualization of hydrological extreme events based on climate simulations. We aim to make use of the added values of VR to promote the communication of scientific results on potential natural hazards to the public. The visualization data are taken from climate simulations within the ClimEx project, which is an international collaboration between research facilities, universities and public water agencies in Bavaria and Quélbec. The project investigates the effects of climate change on meteorological and hydrological extreme events and implications for water management in the two regions. Within this project, an ensemble of 50 transient runs of the regional climate model CRCM5 were run at approximately 11 km spatial resolution for two domains in Europe and North America from 1950 to 2100. As each of these runs is initialized with only slightly altered starting conditions, this ensemble can be interpreted as modelled natural variability. From this data set, we extracted precipitation data regarding one historical flooding event, the Pentecost flood in Southern Germany and Austria in May 1999, as well as precipitation data for two designated future intense rainfall events in the 2060s and 2080s for the same region. Data for these three extreme rainfall events were visualized in VR using a 3D representation of topography of the region of interest as the background. This VR representation was enhanced with satellite images (on top of the topography), points of interest (for easier navigation) and images of the historic Pentecost flood event (for emphazising the impact of the flood event). We will present the necessary steps to create this immersive virtual reality 3D visualization from the raw scientific data and discuss several aspects of the visual design and the adopted user interface

Visualization of climate simulation data in virtual reality using commercial game engines

Due to the size of its customer base the video game industry has long been the best-funded proponent of innovative real-time computer graphics. Many advancements in the field of computer graphics, software and hardware, have become cost-effective due to their use in video games, which in turn funded even further research and breakthroughs. Recent changes in the monetization of commercial game engines made their use in less revenue driven institutions affordable and, hence, possible. This allows us, given suitable hardware, to build and run computationally expensive fully interactive real-time visualizations at a fraction of the cost and time. We can thus investigate and explore the data in our virtual reality application far sooner. Additionally, we are able to spend more time to iteratively refine the user interaction as well as the preprocessing of the raw scientific data. We supply our visualization with the output data of ClimEx’ computational run on the SuperMUC. ClimEx is a research project that studies the effects of climate change on meteorological and hydrological extreme events. It features a multitude of climate-relevant variables and observes the time span between 1950 and 2100. For our use case we chose to compare three different precipitation events. Each event consists of simulated 60 hours of rainfall data anteceding a potential 100-year flood, which is a flood event that has an annual exceedance rate of 1%. The first event draws from historical data and represents the rain leading up to the 1999 Pentecost flood. We compare these data with two computer generated prospective events, which take place in 2060 and 2081, respectively. Since we wish to gain knowledge on strong local extrema as well as the comprehensive overall trend of the attributes, we chose to display the data in virtual reality. The virtually unlimited number of perspectives and points of view simplify investigating and understanding the three-dimensional data. We are also able to place the observer at the center of the data and empower them to interact with and steer the visualization in intuitive ways. By utilizing a tool like virtual reality, we are able to create an immersive, interactive and engaging user experience, which further facilitates the user’s ability to focus on the visual display and extract information from the displayed data. This allows users, especially non-expert users, to grasp the data we present in our visualization with less effort. In our paper we present the necessary steps to create an immersive virtual reality 3D visualization from raw scientific data based on our use case. This entails several aspects of pre-processing, a simple, suitable user interface as well as our solutions to the challenges we encountered

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field