Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness

cited By 2Bacterial microbiota play a critical role in mediating local and systemic immunity, and shifts in these microbial communities have been linked to impaired outcomes in critical illness. Emerging data indicate that other intestinal organisms, including bacteriophages, viruses of eukaryotes, fungi, and protozoa, are closely interlinked with the bacterial microbiota and their host, yet their collective role during antibiotic perturbation and critical illness remains to be elucidated. We employed multi-omics factor analysis (MOFA) to systematically integrate the bacterial (16S rRNA), fungal (intergenic transcribed spacer 1 rRNA), and viral (virus discovery next generation sequencing) components of the intestinal microbiota of 33 critically ill patients with and without sepsis and 13 healthy volunteers. In addition, we quantified the absolute abundances of bacteria and fungi using 16S and 18S rRNA PCRs and characterized the short-chain fatty acids (SCFAs) butyrate, acetate, and propionate using nuclear magnetic resonance spectroscopy. We observe that a loss of the anaerobic intestinal environment is directly correlated with an overgrowth of aerobic pathobionts and their corresponding bacteriophages as well as an absolute enrichment of opportunistic yeasts capable of causing invasive disease. We also observed a strong depletion of SCFAs in both disease states, which was associated with an increased absolute abundance of fungi with respect to bacteria. Therefore, these findings illustrate the complexity of transkingdom changes following disruption of the intestinal bacterial microbiome. IMPORTANCE While numerous studies have characterized antibiotic-induced disruptions of the bacterial microbiome, few studies describe how these disruptions impact the composition of other kingdoms such as viruses, fungi, and protozoa. To address this knowledge gap, we employed MOFA to systematically integrate viral, fungal, and bacterial sequence data from critically ill patients (with and without sepsis) and healthy volunteers, both prior to and following exposure to broad-spectrum antibiotics. In doing so, we show that modulation of the bacterial component of the microbiome has implications extending beyond this kingdom alone, enabling the overgrowth of potentially invasive fungi and viruses. While numerous preclinical studies have described similar findings in vitro, we confirm these observations in humans using an integrative analytic approach. These findings underscore the potential value of multi-omics data integration tools in interrogating how different components of the microbiota contribute to disease states. In addition, our findings suggest that there is value in further studying potential adjunctive therapies using anaerobic bacteria or SCFAs to reduce fungal expansion after antibiotic exposure, which could ultimately lead to improved outcomes in the intensive care unit (ICU).Peer reviewe

Evaluation of Pseudo-Haptic Interactions with Soft Objects in Virtual Environments

This paper proposes a pseudo-haptic feedback method conveying simulated soft surface stiffness information through a visual interface. The method exploits a combination of two feedback techniques, namely visual feedback of soft surface deformation and control of the indenter avatar speed, to convey stiffness information of a simulated surface of a soft object in virtual environments. The proposed method was effective in distinguishing different sizes of virtual hard nodules integrated into the simulated soft bodies. To further improve the interactive experience, the approach was extended creating a multi-point pseudo-haptic feedback system. A comparison with regards to (a) nodule detection sensitivity and (b) elapsed time as performance indicators in hard nodule detection experiments to a tablet computer incorporating vibration feedback was conducted. The multi-point pseudo-haptic interaction is shown to be more time-efficient than the single-point pseudo-haptic interaction. It is noted that multi-point pseudo-haptic feedback performs similarly well when compared to a vibration-based feedback method based on both performance measures elapsed time and nodule detection sensitivity. This proves that the proposed method can be used to convey detailed haptic information for virtual environmental tasks, even subtle ones, using either a computer mouse or a pressure sensitive device as an input device. This pseudo-haptic feedback method provides an opportunity for low-cost simulation of objects with soft surfaces and hard inclusions, as, for example, occurring in ever more realistic video games with increasing emphasis on interaction with the physical environment and minimally invasive surgery in the form of soft tissue organs with embedded cancer nodules. Hence, the method can be used in many low-budget applications where haptic sensation is required, such as surgeon training or video games, either using desktop computers or portable devices, showing reasonably high fidelity in conveying stiffness perception to the user

Interaction for Immersive Analytics

International audienceIn this chapter, we briefly review the development of natural user interfaces and discuss their role in providing human-computer interaction that is immersive in various ways. Then we examine some opportunities for how these technologies might be used to better support data analysis tasks. Specifically, we review and suggest some interaction design guidelines for immersive analytics. We also review some hardware setups for data visualization that are already archetypal. Finally, we look at some emerging system designs that suggest future directions

Visual feedback for grasping in virtual reality environments for an interface to instruct digital human models

Digital Human Models (DHMs) are widely used in big industry whereas they are not used in small and medium-sized enterprises. One of the main reasons is the complexity and usability. Engineers need a notable amount of training to be able to use DHM software. The authors suggest a new interactive Virtual Reality (VR) interface to instruct DHMs. Within this VR environment, engineers can naturally interact with virtual objects using their hands. These interactions are used as an instruction for DHMs. To support the software user best it is necessary to provide feedback to be able to grasp the virtual object most efficiently. In this work we present a user study in which we investigate which visual feedback leads to the best performance for grasping virtual objects. The results show that users are supported most when additional Hand Color Feedback is provided in the VR environment

TouchGlass: Raycasting from a Glass Surface to Point at Physical Objects in Public Exhibits

Part 3: Interaction in Public SpacesInternational audiencePhysical objects such as natural items or fine art pieces are often placed behind glass cases to protect them from dust and damage. Generally, interacting with such objects is indirect, based for example on an adjacent touch interface detracting users’ attention from the object. In this paper, we explore whether the glass case could be used as an input surface to point and select distant physical objects. With such an approach, the glass case offers a physical delimiter for interaction to avoid unintended activations. We explore this innovative approach through a two steps approach. First, we carry an informative study with 46 participants to validate the most appropriate “walk-up and use” technique. Our results show that using a ray orthogonal to the glass surface is the most natural approach in a public setting. Next, we further explore this orthogonal raycasting technique and conduct a target acquisition experiment to evaluate the impact on target selection performance of the target size, target distance, presence of spatial references and user’s head position with regards to the glass case. Results reveal that using the glass as touch surface allows to easily select targets as small as 3 cm up to 35 cm away from the glass. From these results, we provide a set of guidelines to design interactive exhibits using a touch glass case