A web-based framework for visualization, annotation, and automatic exploitation of high-resolution bioimages using tree-based machine learning methods

CYTOMIN

A rich internet application for remote visualization, collaborative annotation, and automated analysis of large-scale biomages

WIST3 Cytomine 101707

Focus EMU, February 22, 2005

Une opinion rédigée et transmise à la Première ministre et aux Ministresprésidents régionaux par un collectif de signataires

The Cerenkov effect revisited: from swimming ducks to zero modes in gravitational analogs

We present an interdisciplinary review of the generalized Cerenkov emission of radiation from uniformly moving sources in the different contexts of classical electromagnetism, superfluid hydrodynamics, and classical hydrodynamics. The details of each specific physical systems enter our theory via the dispersion law of the excitations. A geometrical recipe to obtain the emission patterns in both real and wavevector space from the geometrical shape of the dispersion law is discussed and applied to a number of cases of current experimental interest. Some consequences of these emission processes onto the stability of condensed-matter analogs of gravitational systems are finally illustrated.Comment: Lecture Notes at the IX SIGRAV School on "Analogue Gravity" in Como, Italy from May 16th-21th, 201

Drying nano particles solution on an oscillating tip at an air liquid interface: what we can learn, what we can do

Evaporation of fluid at micro and nanometer scale may be used to self-assemble nanometre-sized particles in suspension. Evaporating process can be used to gently control flow in micro and nanofluidics, thus providing a potential mean to design a fine pattern onto a surface or to functionalize a nanoprobe tip. In this paper, we present an original experimental approach to explore this open and rather virgin domain. We use an oscillating tip at an air liquid interface with a controlled dipping depth of the tip within the range of the micrometer. Also, very small dipping depths of a few ten nanometers were achieved with multi walls carbon nanotubes glued at the tip apex. The liquid is an aqueous solution of functionalized nanoparticles diluted in water. Evaporation of water is the driving force determining the arrangement of nanoparticles on the tip. The results show various nanoparticles deposition patterns, from which the deposits can be classified in two categories. The type of deposit is shown to be strongly dependent on whether or not the triple line is pinned and of the peptide coating of the gold nanoparticle. In order to assess the classification, companion dynamical studies of nanomeniscus and related dissipation processes involved with thinning effects are presented

Utilization of mechanical power and associations with clinical outcomes in brain injured patients: a secondary analysis of the extubation strategies in neuro-intensive care unit patients and associations with outcome (ENIO) trial

Background: There is insufficient evidence to guide ventilatory targets in acute brain injury (ABI). Recent studies have shown associations between mechanical power (MP) and mortality in critical care populations. We aimed to describe MP in ventilated patients with ABI, and evaluate associations between MP and clinical outcomes. Methods: In this preplanned, secondary analysis of a prospective, multi-center, observational cohort study (ENIO, NCT03400904), we included adult patients with ABI (Glasgow Coma Scale ≤ 12 before intubation) who required mechanical ventilation (MV) ≥ 24 h. Using multivariable log binomial regressions, we separately assessed associations between MP on hospital day (HD)1, HD3, HD7 and clinical outcomes: hospital mortality, need for reintubation, tracheostomy placement, and development of acute respiratory distress syndrome (ARDS). Results: We included 1217 patients (mean age 51.2 years [SD 18.1], 66% male, mean body mass index [BMI] 26.3 [SD 5.18]) hospitalized at 62 intensive care units in 18 countries. Hospital mortality was 11% (n = 139), 44% (n = 536) were extubated by HD7 of which 20% (107/536) required reintubation, 28% (n = 340) underwent tracheostomy placement, and 9% (n = 114) developed ARDS. The median MP on HD1, HD3, and HD7 was 11.9 J/min [IQR 9.2-15.1], 13 J/min [IQR 10-17], and 14 J/min [IQR 11-20], respectively. MP was overall higher in patients with ARDS, especially those with higher ARDS severity. After controlling for same-day pressure of arterial oxygen/fraction of inspired oxygen (P/F ratio), BMI, and neurological severity, MP at HD1, HD3, and HD7 was independently associated with hospital mortality, reintubation and tracheostomy placement. The adjusted relative risk (aRR) was greater at higher MP, and strongest for: mortality on HD1 (compared to the HD1 median MP 11.9 J/min, aRR at 17 J/min was 1.22, 95% CI 1.14-1.30) and HD3 (1.38, 95% CI 1.23-1.53), reintubation on HD1 (1.64; 95% CI 1.57-1.72), and tracheostomy on HD7 (1.53; 95%CI 1.18-1.99). MP was associated with the development of moderate-severe ARDS on HD1 (2.07; 95% CI 1.56-2.78) and HD3 (1.76; 95% CI 1.41-2.22). Conclusions: Exposure to high MP during the first week of MV is associated with poor clinical outcomes in ABI, independent of P/F ratio and neurological severity. Potential benefits of optimizing ventilator settings to limit MP warrant further investigation

A Machine Learning Approach for Material Detection in Hyperspectral Images

peer reviewedIn this paper we propose a machine learning approach for the detection of gaseous traces in thermal infra red hyperspectral images. It exploits both spectral and spatial information by extracting subcubes and by using extremely randomized trees with multiple outputs as a classifier. Promising results are shown on a dataset of more than 60 hypercubes.HAWKEYE SST4-CT-2005-51616

A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning

peer reviewedWe present a novel methodology combining web-based software development practices, machine learning, and spatial databases for computer-aided quantification of regions of interest (ROIs) in large-scale imaging data. We describe our main methodological choices, and then illustrate the benefits of the approach (workload reduction, improved precision, scalability, and traceability) on hundreds of whole-slide images of biological tissue slices in cancer research.CYTOMIN

A rich internet application for remote visualization and collaborative annotation of digital slide images in histology and cytology

This work proposes a new web-based tool to ease collaborative projects in digital histology and cytology.WIST3 Cytomine 101707

Development of a core outcome set for ventilation trials in neurocritical care patients with acute brain injury: protocol for a Delphi consensus study of international stakeholders.

INTRODUCTION: There is little consensus and high heterogeneity on the optimal set of relevant clinical outcomes in research studies regarding extubation in neurocritical care patients with brain injury undergoing mechanical ventilation. The aims of this study are to: (1) develop a core outcome set (COS) and (2) reach consensus on a hierarchical composite endpoint for such studies. METHODS AND ANALYSIS: The study will include a broadly representative, international panel of stakeholders with research and clinical expertise in this field and will involve four stages: (1) a scoping review to generate an initial list of outcomes represented in the literature, (2) an investigator meeting to review the outcomes for inclusion in the Delphi surveys, (3) four rounds of online Delphi consensus-building surveys and (4) online consensus meetings to finalise the COS and hierarchical composite endpoint. ETHICS AND DISSEMINATION: This study received ethical approval from the French Society of Anesthesia and Critical Care Medicine Institutional Review Board (SFAR CERAR-IRB 00010254-2023-029). The study results will be disseminated through communication to stakeholders, publication in a peer-reviewed journal, and presentations at conferences. TRIAL REGISTRATION NUMBER: This study is registered with the Core Outcome Measures in Effectiveness Trials (COMET) Initiative