ABSTRACT
The third-generation sequencing technology, PacBio, has shown an ability to sequence the HIV virus amplicons in their full length. The long read of PaBio offers a distinct advantage to comprehensively understand the virus evolution complexity at quasispecies level (i.e. maintaining linkage information of variants) comparing to the short reads from Illumina shotgun sequencing. However, due to the highnoise nature of the PacBio reads, it is still a challenge to build accurate contigs at high sensitivity. Most of previously developed NGS assembly tools work with the assumption that the input reads are fairly accurate, which is largely true for the data derived from Sanger or Illumina technologies. When applying these tools on PacBio high-noise reads, they are largely driven by noise rather than true signal eventually leading to poor results in most cases. In this study, we propose the de novo assembly procedure, which comprises a positivefocused strategy, and linkage-frequency noise reduction so that it is more suitable for PacBio high-noise reads. We further tested the unique de novo assembly procedure on HIV PacBio benchmark data and clinical samples, which accurately assembled dominant and minor populations of HIV quasispecies as expected. The improved de novo assembly procedure shows potential ability to promote PacBio technology in the field of HIV drug-resistance clinical detection, as well as in broad HIV phylogenetic studies.
ABSTRACT
The University Hospitals of Geneva initiated their latest strategic plan by consulting widely with employees and patients. Nine main avenues were defined as priority projects for the institution. The project « More time for patients ¼ aims at simplifying clinical and administrative processes using tools from Lean management and Design Thinking. Its objectives are to redefine the organization of the healthcare-related tasks in order to optimize the time spent with patients and relatives, increase patients' involvement and shared decision making, and improve both the communication with patients, as well as the interdisciplinary collaboration, with patients always at the heart of care.
Les HUG ont initié leur dernier plan stratégique en consultant largement les collaborateurs et les patients. Neuf axes principaux ont été alors définis comme prioritaires pour l'avenir de l'institution, constituant les projets Vision 20/20. Le projet intitulé « Plus de temps pour les patients ¼ vise à optimiser le temps de présence avec les patients et les proches, à augmenter l'implication du patient dans sa prise en charge et à améliorer la communication entre les soignants et les patients, ainsi que la collaboration interdisciplinaire en gardant le patient au cÅur de la démarche. Ces objectifs nécessitent la redéfinition de l'organisation des tâches médico-soignantes avec une forte implication des acteurs de terrain, et la simplification des processus cliniques et administratifs.
Subject(s)
Communication , Decision Making , Hospitals, University , HumansABSTRACT
OBJECTIVES: To determine whether the items on the Time Out and the Sign Out of the Surgical Safety Checklist are properly checked by operating room (OR) staff and to explore whether the number of checked items is influenced by the severity of the intervention and the use of the checklist as a memory tool during the Time Out and the Sign Out periods. METHODS: From March to July 2010, data were collected during elective surgery at the Geneva University Hospitals, Switzerland. The main outcome was to assess whether each item of the Time Out and the Sign Out checklists have been checked, that is, 'confirmed' by at least one member of the team and 'validated' by at least one other member of the team. The secondary outcome was the number of validated items during the Time Out and the Sign Out. RESULTS: Time Outs (N=80) and Sign Outs (N=81) were conducted quasi systematically (99%). Items were mostly confirmed during the Time Out (range 100-72%) but less often during the Sign Out (range 86-19%). Validation of the items was far from optimal: only 13% of Time Outs and 3% of Sign Outs were properly checked (all items validated). During the Time Out, the validation process was significantly improved among the highest risk interventions (29% validation vs 15% among interventions at lower risk). During the Sign Out, a similar effect was observed (19% and 8%, respectively). A small but significant benefit was observed when using a printed checklist as a memory tool during the Sign Out, the proportion of interventions with almost all validated items being higher compared with those without the memory tool (20% and 0%, respectively). CONCLUSIONS: Training on the proper completion of the checklist must be provided to OR teams. The severity of the interventions influenced the number of items properly checked.
