In Search of Patient Zero: Visual Analytics of Pathogen Transmission Pathways in Hospitals

Pathogen outbreaks (i.e., outbreaks of bacteria and viruses) in hospitals can cause high mortality rates and increase costs for hospitals significantly. An outbreak is generally noticed when the number of infected patients rises above an endemic level or the usual prevalence of a pathogen in a defined population. Reconstructing transmission pathways back to the source of an outbreak -- the patient zero or index patient -- requires the analysis of microbiological data and patient contacts. This is often manually completed by infection control experts. We present a novel visual analytics approach to support the analysis of transmission pathways, patient contacts, the progression of the outbreak, and patient timelines during hospitalization. Infection control experts applied our solution to a real outbreak of Klebsiella pneumoniae in a large German hospital. Using our system, our experts were able to scale the analysis of transmission pathways to longer time intervals (i.e., several years of data instead of days) and across a larger number of wards. Also, the system is able to reduce the analysis time from days to hours. In our final study, feedback from twenty-five experts from seven German hospitals provides evidence that our solution brings significant benefits for analyzing outbreaks

The nature of iron-oxygen vacancy defect centers in PbTiO3

The iron(III) center in ferroelectric PbTiO3 together with an oxygen vacancy forms a charged defect associate, oriented along the crystallographic c-axis. Its microscopic structure has been analyzed in detail comparing results from a semi-empirical Newman superposition model analysis based on finestructure data and from calculations using density functional theory. Both methods give evidence for a substitution of Fe3+ for Ti4+ as an acceptor center. The position of the iron ion in the ferroelectric phase is found to be similar to the B-site in the paraelectric phase. Partial charge compensation is locally provided by a directly coordinated oxygen vacancy. Using high-resolution synchrotron powder diffraction, it was verified that lead titanate remains tetragonal down to 12 K, exhibiting a c/a-ratio of 1.0721.Comment: 11 pages, 5 figures, accepted in Phys. Rev.

Is virtual reality effective to teach prevention of surgical site infections in the operating room? study protocol for a randomised controlled multicentre trial entitled VIP Room study

INTRODUCTION: Some surgical site infections (SSI) could be prevented by following adequate infection prevention and control (IPC) measures. Poor compliance with IPC measures often occurs due to knowledge gaps and insufficient education of healthcare professionals. The education and training of SSI preventive measures does not usually take place in the operating room (OR), due to safety, and organisational and logistic issues. The proposed study aims to compare virtual reality (VR) as a tool for medical students to learn the SSI prevention measures and adequate behaviours (eg, limit movements…) in the OR, to conventional teaching. METHODS AND ANALYSIS: This protocol describes a randomised controlled multicentre trial comparing an educational intervention based on VR simulation to routine education. This multicentre study will be performed in three universities: Grenoble Alpes University (France), Imperial College London (UK) and University of Heidelberg (Germany). Third-year medical students of each university will be randomised in two groups. The students randomised in the intervention group will follow VR teaching. The students randomised in the control group will follow a conventional education programme. Primary outcome will be the difference between scores obtained at the IPC exam at the end of the year between the two groups. The written exam will be the same in the three countries. Secondary outcomes will be satisfaction and students' progression for the VR group. The data will be analysed with intention-to-treat and per protocol. ETHICS AND DISSEMINATION: This study has been approved by the Medical Education Ethics Committee of the London Imperial College (MEEC1920-172), by the Ethical Committee for the Research of Grenoble Alpes University (CER Grenoble Alpes-Avis-2019-099-24-2) and by the Ethics Committee of the Medical Faculty of Heidelberg University (S-765/2019). Results will be published in peer-reviewed medical journals, communicated to participants, general public and all relevant stakeholders

Inositol Hexakisphosphate-Induced Autoprocessing of Large Bacterial Protein Toxins

Large bacterial protein toxins autotranslocate functional effector domains to the eukaryotic cell cytosol, resulting in alterations to cellular functions that ultimately benefit the infecting pathogen. Among these toxins, the clostridial glucosylating toxins (CGTs) produced by Gram-positive bacteria and the multifunctional-autoprocessing RTX (MARTX) toxins of Gram-negative bacteria have distinct mechanisms for effector translocation, but a shared mechanism of post-translocation autoprocessing that releases these functional domains from the large holotoxins. These toxins carry an embedded cysteine protease domain (CPD) that is activated for autoprocessing by binding inositol hexakisphosphate (InsP6), a molecule found exclusively in eukaryotic cells. Thus, InsP6-induced autoprocessing represents a unique mechanism for toxin effector delivery specifically within the target cell. This review summarizes recent studies of the structural and molecular events for activation of autoprocessing for both CGT and MARTX toxins, demonstrating both similar and potentially distinct aspects of autoprocessing among the toxins that utilize this method of activation and effector delivery

Functional Conservation of Cis-Regulatory Elements of Heat-Shock Genes over Long Evolutionary Distances

Transcriptional control of gene regulation is an intricate process that requires precise orchestration of a number of molecular components. Studying its evolution can serve as a useful model for understanding how complex molecular machines evolve. One way to investigate evolution of transcriptional regulation is to test the functions of cis-elements from one species in a distant relative. Previous results suggested that few, if any, tissue-specific promoters from Drosophila are faithfully expressed in C. elegans. Here we show that, in contrast, promoters of fly and human heat-shock genes are upregulated in C. elegans upon exposure to heat. Inducibility under conditions of heat shock may represent a relatively simple “on-off” response, whereas complex expression patterns require integration of multiple signals. Our results suggest that simpler aspects of regulatory logic may be retained over longer periods of evolutionary time, while more complex ones may be diverging more rapidly

COVIDiSTRESS Global Survey dataset on psychological and behavioural consequences of the COVID-19 outbreak

This N = 173,426 social science dataset was collected through the collaborative COVIDiSTRESS Global Survey – an open science effort to improve understanding of the human experiences of the 2020 COVID-19 pandemic between 30th March and 30th May, 2020. The dataset allows a cross-cultural study of psychological and behavioural responses to the Coronavirus pandemic and associated government measures like cancellation of public functions and stay at home orders implemented in many countries. The dataset contains demographic background variables as well as measures of Asian Disease Problem, perceived stress (PSS-10), availability of social provisions (SPS-10), trust in various authorities, trust in governmental measures to contain the virus (OECD trust), personality traits (BFF-15), information behaviours, agreement with the level of government intervention, and compliance with preventive measures, along with a rich pool of exploratory variables and written experiences. A global consortium from 39 countries and regions worked together to build and translate a survey with variables of shared interests, and recruited participants in 47 languages and dialects. Raw plus cleaned data and dynamic visualizations are available

Eleven strategies for making reproducible research and open science training the norm at research institutions

Reproducible research and open science practices have the potential to accelerate scientific progress by allowing others to reuse research outputs, and by promoting rigorous research that is more likely to yield trustworthy results. However, these practices are uncommon in many fields, so there is a clear need for training that helps and encourages researchers to integrate reproducible research and open science practices into their daily work. Here, we outline eleven strategies for making training in these practices the norm at research institutions. The strategies, which emerged from a virtual brainstorming event organized in collaboration with the German Reproducibility Network, are concentrated in three areas: (i) adapting research assessment criteria and program requirements; (ii) training; (iii) building communities. We provide a brief overview of each strategy, offer tips for implementation, and provide links to resources. We also highlight the importance of allocating resources and monitoring impact. Our goal is to encourage researchers - in their roles as scientists, supervisors, mentors, instructors, and members of curriculum, hiring or evaluation committees - to think creatively about the many ways they can promote reproducible research and open science practices in their institutions