De la fusion du génie logiciel et d'une bibliothèque à source ouverte pour la modélisation/simulation de processus matériel et logiciel

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Modulation des radeaux lipidiques et des propriétés de fusion des phagosomes par le lipophosphoglycane du parasite intracellulaire Leishmania donovani

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Étude des GTPases potentiellement responsables de la fusion du réticulum endoplasmique

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

The relationship between fusion, suppression, and diplopia in amblyopia

Purpose: Traditionally, it has been thought that no binocular combination occurs in amblyopia. However, there is a growing body of evidence that there are intact binocular mechanisms in amblyopia rendered inactive under normal viewing conditions due to imbalanced monocular inputs. Georgeson and Wallis (2014) recently introduced a novel method to investigate fusion, suppression and diplopia in normal population. We have modified this method to assess binocular interactions in amblyopia. Methods: Ten amblyopic and ten control subjects viewed briefly-presented (200 ms) pairs of dichoptically separated horizontal Gaussian blurred edges. Subjects reported one central edge, one offset edge, or a double edge as the vertical disparity was manipulated. The experiment was conducted at a range of spatial scales (blur widths of 4, 8, 16, and 32 arc min) and contrasts. Our model, based Georgeson and Wallis (2014), converted subjects’ responses into probabilities of fusion, suppression, and diplopia. Results: When the normal participants were presented equal contrast to each eye the probability of fusion gradually decreased with increasing disparity, as the probability of diplopia gradually increased. In only a small proportion of the trials, normal participants experienced suppression. The pattern was consistent across all edge blurs. Interestingly, the majority of amblyopes had a comparable pattern of fusion, i.e. decreasing probability with increasing disparity. However, with increasing disparity the amblyopes tended to suppress the amblyopic eye, experiencing diplopia only in a small proportion of trials particularly at large blurs. Increasing the interocular contrast offset favouring the amblyopic eye normalized the pattern of data in a way similar to normal participants. There were some interesting exceptions: strong suppressors for which our contrast range was inadequate and one case in which diplopia dominated. Conclusions: This task is suitable for assessing binocular interactions in amblyopic participants and providing a way to quantify the relationship between fusion, suppression and diplopia. In agreement with previous studies, our data indicate the presence of binocular mechanisms in amblyopia. A contrast offset favouring the amblyopic eye normalizes the measured binocular interactions in the amblyopic visual system.

De la fusion du génie logiciel et d'une bibliothèque à source ouverte pour la modélisation/simulation de processus matériel et logiciel

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Modulation des radeaux lipidiques et des propriétés de fusion des phagosomes par le lipophosphoglycane du parasite intracellulaire Leishmania donovani

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Étude des GTPases potentiellement responsables de la fusion du réticulum endoplasmique

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

EGFR interacts with the fusion protein of respiratory syncytial virus strain 2-20 and mediates infection and mucin expression.

Respiratory syncytial virus (RSV) is the major cause of viral lower respiratory tract illness in children. In contrast to the RSV prototypic strain A2, clinical isolate RSV 2-20 induces airway mucin expression in mice, a clinically relevant phenotype dependent on the fusion (F) protein of the RSV strain. Epidermal growth factor receptor (EGFR) plays a role in airway mucin expression in other systems; therefore we hypothesized that the RSV 2-20 F protein stimulates EGFR signaling. Infection of cells with chimeric strains RSV A2-2-20F and A2-2-20GF or over-expression of 2-20 F protein resulted in greater phosphorylation of EGFR than infection with RSV A2 or over-expression of A2 F, respectively. Chemical inhibition of EGFR signaling or knockdown of EGFR resulted in diminished infectivity of RSV A2-2-20F but not RSV A2. Over-expression of EGFR enhanced the fusion activity of 2-20 F protein in trans. EGFR co-immunoprecipitated most efficiently with RSV F proteins derived from “mucogenic” strains. RSV 2-20 F and EGFR co-localized in H292 cells, and A2-2-20GF-induced MUC5AC expression was ablated by EGFR inhibitors in these cells. Treatment of BALB/c mice with the EGFR inhibitor erlotinib significantly reduced the amount of RSV A2-2-20F-induced airway mucin expression. Our results demonstrate that RSV F interacts with EGFR in a strain-specific manner, EGFR is a co-factor for infection, and EGFR plays a role in RSV-induced mucin expression, suggesting EGFR is a potential target for RSV disease.

Numerical study of neutron beam divergence in a beam-fusion scenario employing laser driven ions

The most established route to create a laser-based neutron source is by employing laser accelerated, low atomic-number ions in fusion reactions. In addition to the high reaction cross-sections at moderate energies of the projectile ions, the anisotropy in neutron emission is another important feature of beam-fusion reactions. Using a simple numerical model based on neutron generation in a pitcher–catcher scenario, anisotropy in neutron emission was studied for the deuterium–deuterium fusion reaction. Simulation results are consistent with the narrow-divergence ( ∼ 70 ° full width at half maximum) neutron beam recently served in an experiment employing multi-MeV deuteron beams of narrow divergence (up to 30° FWHM, depending on the ion energy) accelerated by a sub-petawatt laser pulse from thin deuterated plastic foils via the Target Normal Sheath Acceleration mechanism. By varying the input ion beam parameters, simulations show that a further improvement in the neutron beam directionality (i.e. reduction in the beam divergence) can be obtained by increasing the projectile ion beam temperature and cut-off energy, as expected from interactions employing higher power lasers at upcoming facilities.

High volume fabrication of laser targets using MEMS techniques

The latest techniques for the fabrication of high power laser targets, using processes developed for the manufacture of Micro-Electro-Mechanical System (MEMS) devices are discussed. These laser targets are designed to meet the needs of the increased shot numbers that are available in the latest design of laser facilities. Traditionally laser targets have been fabricated using conventional machining or coarse etching processes and have been produced in quantities of 10s to low 100s. Such targets can be used for high complexity experiments such as Inertial Fusion Energy (IFE) studies and can have many complex components that need assembling and characterisation with high precision. Using the techniques that are common to MEMS devices and integrating these with an existing target fabrication capability we are able to manufacture and deliver targets to these systems. It also enables us to manufacture novel targets that have not been possible using other techniques. In addition, developments in the positioning systems that are required to deliver these targets to the laser focus are also required and a system to deliver the target to a focus of an F2 beam at 0.1Hz is discussed.

Primary pulmonary myxoid sarcoma with EWSR1-CREB1 fusion: a new tumor entity.

We present clinicopathologic data on 10 pulmonary myxoid sarcomas, which are defined by distinctive histomorphologic features and characterized by a recurrent fusion gene, that appear to represent a distinct tumor entity at this site. The patients [7 female, 3 male; aged 27 to 67 y (mean, 45 y)] presented with local or systemic symptoms (n=5), symptoms from cerebral metastasis (1), or incidentally (2). Follow-up of 6 patients showed that 1 with brain metastasis died shortly after primary tumor resection, 1 developed a renal metastasis but is alive and well, and 4 are disease free after 1 to 15 years. All tumors involved pulmonary parenchyma, with a predominant endobronchial component in 8 and ranged from 1.5 to 4 cm. Microscopically, they were lobulated and composed of cords of polygonal, spindle, or stellate cells within myxoid stroma, morphologically reminiscent of extraskeletal myxoid chondrosarcoma. Four cases showed no or minimal atypia, 6 showed focal pleomorphism, and 5 had necrosis. Mitotic indices varied, with most tumors not exceeding 5/10 high-power fields. Tumors were immunoreactive for only vimentin and weakly focal for epithelial membrane antigen. Of 9 tumors, 7 were shown to harbor a specific EWSR1-CREB1 fusion by reverse transcription-polymerase chain reaction and direct sequencing, with 7 of 10 showing EWSR1 rearrangement by fluorescence in situ hybridization. This gene fusion has been described previously in 2 histologically and behaviorally different sarcomas: clear cell sarcoma-like tumors of the gastrointestinal tract and angiomatoid fibrous histiocytomas; however, this is a novel finding in tumors with the morphology we describe and that occur in the pulmonary region.

Utility of sarcoma-specific fusion gene analysis in paraffin-embedded material for routine diagnosis at a specialist centre.

AIMS: Diagnosis of soft tissue sarcomas can be difficult. It can be aided by detection of specific genetic aberrations in many cases. This study assessed the utility of a molecular genetics/cytogenetics service as part of the routine diagnostic service at the Royal Marsden Hospital. METHODS: A retrospective audit was performed over a 15-month period to evaluate the diagnostic usefulness for soft tissue sarcomas with translocations of fluorescence in situ hybridisation (FISH) and reverse-transcriptase PCR (RT-PCR) in paraffin-embedded (PE) material. Results were compared with histology, and evaluated. RESULTS: Molecular investigations were performed on PE material in 158 samples (total 194 RT-PCR and 174 FISH tests), of which 85 were referral cases. Synovial sarcoma, Ewing sarcoma and low-grade fibromyxoid sarcoma were the most commonly tested tumours. Myxoid liposarcoma showed the best histological and molecular concordance, and alveolar rhabdomyosarcoma showed the best agreement between methods. FISH had a higher sensitivity for detecting tumours (73%, compared with 59% for RT-PCR) with a better success rate than RT-PCR, although the latter was specific in identifying the partner gene for each fusion. In particular, referral blocks in which methods of tissue fixation and processing were not certain resulted in higher RT-PCR failure rates. CONCLUSIONS: FISH and RT-PCR on PE tissue are practical and effective ancillary tools in the diagnosis of soft tissue sarcomas. They are useful in confirming doubtful histological diagnoses and excluding malignant diagnoses. PCR is less sensitive than FISH, and the use of both techniques is optimal for maximising the detection rate of translocation-positive sarcomas.

Meningeal alveolar soft part sarcoma confirmed by characteristic ASPCR1-TFE3 fusion

Sarcoma metastatic to the brain is uncommon and rarely occurs as the initial manifestation of tumor. Alveolar soft part sarcoma (ASPS) is a rare but well-studied subtype of sarcoma. A 39-year-old man presented with seizures due to a left temporal meningeal-enhancing lesion with striking brain edema on MRI. The patient underwent neurosurgical resection for suspected meningioma. Histology showed large tumor cells clustering and forming small nests, in places with pseudoalveolar pattern. Diastase-resistant periodic acid-Schiff revealed very rare granular and rod-like cytoplasmic inclusions. Immunohistochemistry showed convincing positivity only with vimentin and smooth muscle actin. The histological features were strongly suggestive of ASPS. At the molecular level RT-PCR and sequencing analysis demonstrated ASPCR1-TFE3 fusion confirming the histological diagnosis of ASPS. There was no evidence of primary extracranial tumor by physical examination and on chest and abdominal CT scan 11 months after presentation. ASPS typically arise from the soft tissues of the extremities and develop multiple metastatic deposits usually with a long clinical course. This case may represent primary meningeal ASPS although metastatic deposit from an undiscovered primary site cannot be entirely excluded.

Low frequency of the TEL/AML1 fusion gene in acute lymphoblastic leukaemia in Spain.

We report on a series of Spanish patients with acute lymphoblastic leukaemia in whom the t(12;21) [TEL/AML1] translocation could not be identified with two sensitive techniques: reverse transcript-polymerase chain reaction (RT-PCR) and fluorescence in-situ hybridization (FISH). 101 cases were analysed: 38 children (29 B-cell precursor; nine T-cell precursor) and 63 adults (48 B-cell precursor; 15 T-cell precursor). Specific RT-PCR to amplify the TEL/AML1 fusion transcript was negative in all 101 cases. Moreover, all 38 paediatric samples were also negative by interphase FISH analysis for the presence of the TEL/AML1 fusion. These results suggest the existence of geographic/race variations in the genotype of acute lymphoblastic leukaemia (ALL).