Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network

One of the most important and challenging problems in biomedicine and genomics is how to identify the disease genes. In this study, we developed a computational method to identify colorectal cancer-related genes based on (i) the gene expression profiles, and (ii) the shortest path analysis of functional protein association networks. The former has been used to select differentially expressed genes as disease genes for quite a long time, while the latter has been widely used to study the mechanism of diseases. With the existing protein-protein interaction data from STRING (Search Tool for the Retrieval of Interacting Genes), a weighted functional protein association network was constructed. By means of the mRMR (Maximum Relevance Minimum Redundancy) approach, six genes were identified that can distinguish the colorectal tumors and normal adjacent colonic tissues from their gene expression profiles. Meanwhile, according to the shortest path approach, we further found an additional 35 genes, of which some have been reported to be relevant to colorectal cancer and some are very likely to be relevant to it. Interestingly, the genes we identified from both the gene expression profiles and the functional protein association network have more cancer genes than the genes identified from the gene expression profiles alone. Besides, these genes also had greater functional similarity with the reported colorectal cancer genes than the genes identified from the gene expression profiles alone. All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying colorectal cancer genes. It has not escaped our notice that the method can be applied to identify the genes of other diseases as well

Les mécanismes de développement endogène et exogène dans les espaces à faible densité

National audienceIn low-density areas, it appears at least two types of strategic interdependence for development: Firstly between residential and productive economy, secondly between endogenous and exogenous mechanisms. In addition, low density territories benefiting from the influx of residential income may generate new productive activities through several channels: they are often attractive pleasant living environments for new entrepreneurs; residential savings can directly generate innovation by mobilizing new territorial resources. Because of the increasing mobility of actors as constraints (economic or social), resulting in high plasticity of development models of low density areas due to a combination of endogenous and exogenous mechanisms. The chapter is illustrated by the examples of two areas of medium sparsely populated mountain (density of about 10 inhabitants per km2) (Aubrac and Cézallier) and very comparable in terms of local resources and accessibility but recent developments are very mixed.Dans les espaces à faible densité, il se manifeste au moins deux types d'interdépendances stratégiques pour leur développement : d'une part entre économie résidentielle et productive, d'autre part entre mécanismes endogènes et exogènes. De plus, les territoires de faible densité bénéficiant de l'afflux de revenus résidentiels peuvent générer de nouvelles activités productives par plusieurs canaux : ils constituent souvent des cadres de vie agréables attractifs pour des nouveaux entrepreneurs ; des économies résidentielles peuvent générer directement de l'innovation en mobilisant de nouvelles ressources territoriales. En raison de la mobilité croissante des acteurs comme des contraintes (économiques ou sociales), il en résulte une grande plasticité des modèles de développement des zones de faible densité sous l'effet conjugué des mécanismes endogènes et exogènes. Le chapitre est illustré par les exemples de deux zones de moyenne montagne faiblement peuplées (densité de l'ordre de 10 habitants au km2) (l'Aubrac et le Cézallier) et très comparables du point de vue des ressources locales et de l'accessibilité mais dont les évolutions récentes sont très contrastées

A phenomenological investigation of patients’ experiences during direct observation in residency: busting the myth of the fly on the wall

Direct observation (DO) of residents by supervisors is a highly recommended educational tool in postgraduate medical education, yet its uptake is poor. Residents and supervisors report various reasons for not engaging in DO. Some of these relate to their interaction with patients during DO. We do not know the patient perspectives on these interactions, nor, more broadly, what it is like to be a patient in a DO situation. Understanding the patient perspective may lead to a more complete understanding of the dynamics in DO situations, which may benefit patient wellbeing and improve the use of DO as an educational tool. We conducted a phenomenological interview study to investigate the experience of being a patient in a DO situation. Our analysis included multiple rounds of coding and identifying themes, and a final phase of phenomenological reduction to arrive at the essential elements of the experience. Constant reflexivity was at the heart of this process. Our results provide a new perspective on the role of the supervisor in DO situations. Patients were willing to address the resident, but sought moments of contact with, and some participation by, the supervisor. Consequently, conceptions of DO in which the supervisor thinks she is a fly on the wall rather than a part of the interaction, should be critically reviewed. To that end, we propose the concept of participative direct observation in workplace learning, which also acknowledges the observer’s role as participant. Embracing this concept may benefit both patients’ wellbeing and residents’ learning

Clinical impact and cost-consequence analysis of ePlex® blood culture identification panels for the rapid diagnosis of bloodstream infections: a single-center randomized controlled trial

International audienceTo assess clinical impact and perform cost-consequence analysis of the broadest multiplex PCR panels available for the rapid diagnosis of bloodstream infections (BSI). Single-center, randomized controlled trial conducted from June 2019 to February 2021 at a French University hospital with an institutional antimicrobial stewardship program. Primary endpoint was the percentage of patients with optimized antimicrobial treatment 12 h after transmission of positivity and Gram stain results from the first positive BC. This percentage was significantly higher in the multiplex PCR (mPCR) group (90/105 = 85.7% %, CI95% [77.5 ; 91.8] vs. 68/107 = 63.6%, CI95% [53.7 ; 72.6]; p < 10 − 3 ) at interim analysis, resulting in the early termination of the study after the inclusion of 309 patients. For patients not optimized at baseline, the median time to obtain an optimized therapy was much shorter in the mPCR group than in the control group (6.9 h, IQR [2.9; 17.8] vs. 26.4 h, IQR [3.4; 47.5]; p = 0.001). Early optimization of antibiotic therapy resulted in a non-statistically significant decrease in mortality from 12.4 to 8.8% ( p = 0.306), with a trend towards a shorter median length of stay (18 vs. 20 days; p = 0.064) and a non-significant reduction in the average cost per patient of €3,065 ( p = 0.15). mPCR identified all the bacteria present in 88% of the samples. Despite its higher laboratory cost, the use of multiplex PCR for BSI diagnosis leads to early-optimised therapy, seems cost-effective and could reduce mortality and length of stay. Their impact could probably be improved if implemented 24/7

Three-dimensional densitometry imaging of diatom cells using STIM tomography

Scanning transmission ion microscopy tomography (STIM-T) was carried out on diatom cells with the aim of displaying their 3D structure and performing density measurements on their silica skeleton. Two software packages were compared for data reduction: TomoRebuild, based on a simple filtered backprojection algorithm, and DISRA, an iterative program. Silicon carbide microfibres of known density were also analysed as reference specimens. Similar results were obtained with both algorithms, demonstrating the ability of STIM-T to provide density measurements at the cell level without requiring any standard calibration samples. This unique feature stresses the interest of STIM-T to accurately normalise X ray emission micro-tomography data from synchrotron radiation (SXRF: synchrotron radiation X-ray fluorescence) or ion beam sources (PIXE: particle induced X-ray emission). Possible enhancements of the DISRA code are discussed in order to facilitate its use for the reconstruction of future PIXE/STIM tomography data. A "nanoprobe" coupled to a Singletron® accelerator, allowing a spatial resolution of a few tens of nanometers, is going to be built in the coming months at the Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG). This new facility will bring promising applications in imaging and analysis at the sub-cellular level