Automatisation de l'Acquisition et des Post-traitements en Numérisation 3D

The automation of digitalisation is an indispensable step in the development of 3D measuring, in various fields :- in industry, to accelerate the procedures for control of parts,- in archaeology and biology, for the study of collections of several hundreds even thousand objects (for which the acquisition is for the moment impossible because of necessary time, and thus of the cost). In this thesis, we explain first the various existing systems of acquisition and positioning, by detailing the advantages and the inconveniences of every system. We present then the developed methodology to guide the operator in these choices as well as the tool set up to formalize this methodology. Then we will study the necessity of the automation of the 3D digitalization by illustrating the limits and the constraints of the solutions in place at present. Some examples of application of the methodology are described through various case studies, highlighting the time of intervention of the operator. Then, existing methods for automating the acquisition are described, explaining their limits. Two methods are proposed : the first defines a off-line viewplanning from a reference model while the second calculates the next best position without any a priori information on the object. Both methods allow the complete digitalization of an object without intervention of an operator. To test these methods, a simulation environment and a prototype have been developed. Finally, the results are presented and compared to a manual digitalization.L'automatisation de la numérisation est une étape indispensable au développement de la mesure tridimensionnelle, et ce, dans différents domaines :- en milieu industriel, afin d'accélérer les procédures de contrôle de pièces,- en archéologie et en biologie, pour l'étude de collections de plusieurs centaines voire milliers d'objets (dont l'acquisition est pour le moment impossible en raison du temps nécessaire, et donc du coût).Dans ce mémoire, nous détaillons tout d'abord les différents systèmes d'acquisition et de positionnement existants, en détaillant les avantages et inconvénients de chaque système. Nous présentons ensuite la méthodologie mise en place pour guider l'opérateur dans ces choix ainsi que l'outil d'aide mis en place afin de formaliser cette méthodologie. Puis nous argumenterons de la nécessité de l'automatisation de la numérisation 3D en illustrant les limites et les contraintes des solutions actuellement en place. Des exemples d'application de la méthodologie sont décrits à travers différentes études de cas, mettant en évidence le temps d'intervention de l'opérateur. Ensuite, les méthodes d'automatisation de l'acquisition existantes sont décrites, en expliquant leurs limites face à notre problématique. Deux méthodes sont ensuite proposées : la première définit une planification de vues hors-ligne à partir d'un modèle de référence tandis que la seconde calcule la meilleure position suivante sans aucune information a priori sur l'objet. Ces deux méthodes permettent une numérisation complète d'un objet sans intervention d'un opérateur. Afin de tester ces méthodes, un environnement de simulation a été implémenté, ainsi qu'un prototype. Enfin, les résultats obtenus sont présentés et comparés à une numérisation manuelle

Automatisation de l'acquisition et des post-traitements en numérisation 3D

L'automatisation de la numérisation est une étape indispensable au développement de la mesure tridimensionnelle, et ce, dans différents domaines : en milieu industriel, afin d'accélérer les procédures de contrôle de pièces, en archéologie et en biologie, pour l'étude de collections de plusieurs centaines voire milliers d objets. Dans ce mémoire, nous détaillons tout d abord les différents systèmes d acquisition et de positionnement existants, en détaillant les avantages et inconvénients de chaque système. Nous présentons ensuite la méthodologie mise en place pour guider l opérateur dans ces choix ainsi que l outil d aide mis en place afin de formaliser cette méthodologie. Puis nous argumenterons de la nécessité de l automatisation de la numérisation 3D en illustrant les limites et les contraintes des solutions actuellement en place. Des exemples d application de la méthodologie sont décrits à travers différentes études de cas, mettant en évidence le temps d intervention de l opérateur. Ensuite, les méthodes d automatisation de l acquisition existantes sont décrites, en expliquant leurs limites face à notre problématique. Deux méthodes sont ensuite proposées : la première définit une planification de vues hors-ligne à partir d un modèle de référence tandis que la seconde calcule la meilleure position suivante sans aucune information a priori sur l objet. Ces deux méthodes permettent une numérisation complète d un objet sans intervention d un opérateur. Afin de tester ces méthodes, un environnement de simulation a été implémenté, ainsi qu un prototype. Enfin, les résultats obtenus sont présentés et comparés à une numérisation manuelle.The automation of digitalisation is an indispensable step in the development of 3D measuring, in various fields : in industry, to accelerate the procedures for control of parts, in archaeology and biology, for the study of collections of several hundreds even thousand objects. In this thesis, we explain first the various existing systems of acquisition and positioning, by detailing the advantages and the inconveniences of every system. We present then the developed methodology to guide the operator in these choices as well as the tool set up to formalize this methodology. Then we will study the necessity of the automation of the 3D digitalization by illustrating the limits and the constraints of the solutions in place at present. Some examples of application of the methodology are described through various case studies, highlighting the time of intervention of the operator. Then, existing methods for automating the acquisition are described, explaining their limits. Two methods are proposed : the first defines a off-line viewplanning from a reference model while the second calculates the next best position without any a priori information on the object. Both methods allow the complete digitalization of an object without intervention of an operator. To test these methods, a simulation environment and a prototype have been developed. Finally, the results are presented and compared to a manual digitalization.DIJON-BU Sciences Economie (212312102) / SudocSudocFranceF

Method for semi-automated microscopy of filtration-enriched circulating tumor cells

BACKGROUND: Circulating tumor cell (CTC)-filtration methods capture high numbers of CTCs in non-small-cell lung cancer (NSCLC) and metastatic prostate cancer (mPCa) patients, and hold promise as a non-invasive technique for treatment selection and disease monitoring. However filters have drawbacks that make the automation of microscopy challenging. We report the semi-automated microscopy method we developed to analyze filtration-enriched CTCs from NSCLC and mPCa patients. METHODS: Spiked cell lines in normal blood and CTCs were enriched by ISET (isolation by size of epithelial tumor cells). Fluorescent staining was carried out using epithelial (pan-cytokeratins, EpCAM), mesenchymal (vimentin, N-cadherin), leukocyte (CD45) markers and DAPI. Cytomorphological staining was carried out with Mayer-Hemalun or Diff-Quik. ALK-, ROS1-, ERG-rearrangement were detected by filter-adapted-FISH (FA-FISH). Microscopy was carried out using an Ariol scanner. RESULTS: Two combined assays were developed. The first assay sequentially combined four-color fluorescent staining, scanning, automated selection of CD45(−) cells, cytomorphological staining, then scanning and analysis of CD45(−) cell phenotypical and cytomorphological characteristics. CD45(−) cell selection was based on DAPI and CD45 intensity, and a nuclear area >55 μm(2). The second assay sequentially combined fluorescent staining, automated selection of CD45(−) cells, FISH scanning on CD45(−) cells, then analysis of CD45(−) cell FISH signals. Specific scanning parameters were developed to deal with the uneven surface of filters and CTC characteristics. Thirty z-stacks spaced 0.6 μm apart were defined as the optimal setting, scanning 82 %, 91 %, and 95 % of CTCs in ALK-, ROS1-, and ERG-rearranged patients respectively. A multi-exposure protocol consisting of three separate exposure times for green and red fluorochromes was optimized to analyze the intensity, size and thickness of FISH signals. CONCLUSIONS: The semi-automated microscopy method reported here increases the feasibility and reliability of filtration-enriched CTC assays and can help progress towards their validation and translation to the clinic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-016-2461-4) contains supplementary material, which is available to authorized users

Prognostic Value of the Lung Immune Prognosis Index Score for Patients Treated with Immune Checkpoint Inhibitors for Advanced or Metastatic Urinary Tract Carcinoma

Few prognostic factors have been identified in patients with metastatic urothelial carcinoma (mUC) treated with immune checkpoint inhibitors (ICIs). The Lung Immune Prognostic Index (LIPI) was associated with clinical outcomes for ICIs in several tumor types. We aim to assess the value of the LIPI in patients with mUC treated with ICIs. A retrospective ICI cohort and a validation cohort (SAUL cohort) included, respectively, patients with mUC treated with ICI in 8 European centers (any line) and patients treated with atezolizumab in a second or further line. A chemotherapy-only cohort was also analyzed. The LIPI score was based on 2 factors, derived neutrophils/(leukocytes minus neutrophils) ratio (dNLR) > 3 and lactate dehydrogenase > upper limit of normal, and defined 3 prognostic groups. The association of LIPI with progression-free survival (PFS) and overall survival (OS) was assessed. In the ICI and SAUL cohorts, 137 and 541 patients were respectively analyzed. In the ICI cohort, mPFS and mOS were 3.6 mo (95% CI; 2.6–6.0) and 13.8 mo (95% CI; 11.5–23.2) whereas in the SAUL cohort the mPFS and mOS were 2.2 mo (95% CI; 2.1–2.3) and 8.7 mo (95% CI; 7.8–9.9) respectively. The LIPI classified the population of these cohorts in good (56%; 52%), intermediate (35%; 36%) and poor (9%; 12%) prognostic groups (values for the ICI and SAUL cohorts respectively). Poor LIPI was associated with a poorer OS in both cohorts: hazard ratio (HR) for the ICI cohort = 2.69 (95% CI; 1.24–5.84, p = 0.035); HR = 2. 89 for the SAUL cohort (CI 95%: 1.93–4.32, p < 0.0001). Similar results were found in the chemo cohort. The LIPI score allows to identify different subgroups in patients with good prognostis according to the Bellmunt score criteria, with a subset of patients with poorer outcomes having an mOS of 3.7 mo compared to the good and intermediate LIPI subgroups with mOS of 17.9 and 7.4 mo, respectively. The LIPI score was associated with survival in mUC patients treated by ICIs. Future prospective studies will be required to test the combination of Bellmunt score and the LIPI score as a more accurate prognosis tool

Oncological Outcomes of Distal Ureterectomy for High-Risk Urothelial Carcinoma: A Multicenter Study by The French Bladder Cancer Committee

International audienceUpper urinary tract urothelial carcinoma (UTUC) is an uncommon disease and its gold-standard treatment is radical nephroureterectomy (RNU). Distal ureterectomy (DU) might be an alternative for tumors of the distal ureter but its indications remain unclear. Here, we aimed to evaluate the oncological outcomes of DU for UTUC of the pelvic ureter. We performed a multicenter retrospective analysis of patients with UTUC who underwent DU. The primary endpoint was 5-year cancer-specific survival (CSS), followed by overall survival (OS), intravesical recurrence-free (IVR) and homolateral urinary tract recurrence-free (HUR) survivals as secondary endpoints. Univariate and multivariate Cox regressions were performed to assess factors associated with outcomes. 155 patients were included, 91% of which were high-risk. 5-year CSS was 84.4%, OS was 71.9%, IVR-free survival was 43.6% and HUR-free survival was 74.4%. Multifocality, high grade and tumor size were the most significant predictors of survival endpoints. Of note, neither hydronephrosis nor pre-operative diagnostic ureteroscopy/JJ stent were associated with any of the endpoints. Perioperative morbidity was minimal. In conclusion, DU stands as a possible alternative to RNU for UTUC of the pelvic ureter. Close monitoring is mandatory due to the high risk of recurrence in the remaining urinary tract

Circulating tumor DNA landscape and prognostic impact of acquired resistance to targeted therapies in cancer patients: a national center for precision medicine (PRISM) study

Abstract Background Despite the effectiveness of the various targeted therapies currently approved for solid tumors, acquired resistance remains a persistent problem that limits the ultimate effectiveness of these treatments. Polyclonal resistance to targeted therapy has been described in multiple solid tumors through high-throughput analysis of multiple tumor tissue samples from a single patient. However, biopsies at the time of acquired resistance to targeted agents may not always be feasible and may not capture the genetic heterogeneity that could exist within a patient. Methods We analyzed circulating tumor DNA (ctDNA) with a large next-generation sequencing panel to characterize the landscape of secondary resistance mechanisms in two independent prospective cohorts of patients (STING: n = 626; BIP: n = 437) with solid tumors who were treated with various types of targeted therapies: tyrosine kinase inhibitors, monoclonal antibodies and hormonal therapies. Results Emerging alterations involved in secondary resistance were observed in the plasma of up 34% of patients regardless of the type of targeted therapy. Alterations were polyclonal in up to 14% of patients. Emerging ctDNA alterations were associated with significantly shorter overall survival for patients with some tumor types. Conclusion This comprehensive landscape of genomic aberrations indicates that genetic alterations involved in secondary resistance to targeted therapy occur frequently and suggests that the detection of such alterations before disease progression may guide personalized treatment and improve patient outcome

Resistance to Selective FGFR Inhibitors in FGFR-Driven Urothelial Cancer

International audienceSeveral fibroblast growth factor receptor (FGFR) inhibitors are approved or in clinical development for the treatment of FGFR-driven urothelial cancer, and molecular mechanisms of resistance leading to patient relapses have not been fully explored. We identified 21 patients with FGFR-driven urothelial cancer treated with selective FGFR inhibitors and analyzed postprogression tissue and/or circulating tumor DNA (ctDNA). We detected single mutations in the FGFR tyrosine kinase domain in seven (33%) patients (FGFR3 N540K, V553L/M, V555L/M, E587Q; FGFR2 L551F) and multiple mutations in one (5%) case (FGFR3 N540K, V555L, and L608V). Using Ba/F3 cells, we defined their spectrum of resist-ance/sensitivity to multiple selective FGFR inhibitors. Eleven (52%) patients harbored alterations in the PI3K–mTOR pathway (n = 4 TSC1/2, n = 4 PIK3CA, n = 1 TSC1 and PIK3CA, n = 1 NF2, n = 1 PTEN). In patientderived models, erdafitinib was synergistic with pictilisib in the presence of PIK3CA E545K, whereas erdafitinib–gefitinib combination was able to overcome bypass resistance mediated by EGFR activation. SIGNIFICANCE: In the largest study on the topic thus far, we detected a high frequency of FGFR kinase domain mutations responsible for resistance to FGFR inhibitors in urothelial cancer. Off-target resistance mechanisms involved primarily the PI3K–mTOR pathway. Our findings provide preclinical evidence sustaining combinatorial treatment strategies to overcome bypass resistance

Integrative Pan-Cancer Genomic and Transcriptomic Analyses of Refractory Metastatic Cancer

International audienceMetastatic relapse after treatment is the leading cause of cancer mortality, and known resistance mechanisms are missing for most treatments administered to patients. To bridge this gap, we analyze a pan-cancer cohort (META-PRISM) of 1,031 refractory metastatic tumors profiled via whole-exome and transcriptome sequencing. META-PRISM tumors, particularly prostate, bladder, and pancreatic types, displayed the most transformed genomes compared with primary untreated tumors. Standard-of-care resistance biomarkers were identified only in lung and colon cancers-9.6% of META-PRISM tumors, indicating that too few resistance mechanisms have received clinical validation. In contrast, we verified the enrichment of multiple investigational and hypothetical resistance mechanisms in treated compared with nontreated patients, thereby confirming their putative role in treatment resistance. Additionally, we demonstrated that molecular markers improve 6-month survival prediction, particularly in patients with advanced breast cancer. Our analysis establishes the utility of the META-PRISM cohort for investigating resistance mechanisms and performing predictive analyses in cancer. SIGNIFICANCE: This study highlights the paucity of standard-of-care markers that explain treatment resistance and the promise of investigational and hypothetical markers awaiting further validation. It also demonstrates the utility of molecular profiling in advanced-stage cancers, particularly breast cancer, to improve the survival prediction and assess eligibility to phase I clinical trials. This article is highlighted in the In This Issue feature, p. 1027