High-Content Analysis of Breast Cancer Using Single-Cell Deep Transfer Learning

High-content analysis has revolutionized cancer drug discovery by identifying substances that alter the phenotype of a cell, which prevents tumor growth and metastasis. The high-resolution biofluorescence images from assays allow precise quantitative measures enabling the distinction of small molecules of a host cell from a tumor. In this work, we are particularly interested in the application of deep neural networks (DNNs), a cutting-edge machine learning method, to the classification of compounds in chemical mechanisms of action (MOAs). Compound classification has been performed using image-based profiling methods sometimes combined with feature reduction methods such as principal component analysis or factor analysis. In this article, we map the input features of each cell to a particular MOA class without using any treatment-level profiles or feature reduction methods. To the best of our knowledge, this is the first application of DNN in this domain, leveraging single-cell information. Furthermore, we use deep transfer learning (DTL) to alleviate the intensive and computational demanding effort of searching the huge parameter's space of a DNN. Results show that using this approach, we obtain a 30% speedup and a 2% accuracy improvement.

Segmentectomia Pulmonar Anatómica por Videotoracoscopia: Experiência Inicial de um Centro

The use of minimally invasive surgery for the treatment of lung cancer has been growing worldwide. Between May 2008 and November 2012, we performed 24 videothoracoscopic anatomical lung resections in our department. This includes 22 lobectomies and 2 anatomic segmentectomies, which is known to be a more complex surgery, since it demands a finer dissection of sub-lobar structures. We report the clinical cases of two patients who underwent anatomic segmentectomies. The first one was a 63 year old woman, smoker and with a history of breast cancer 20 years earlier. An incidental 9 mm node was found in the lingula. The patient underwent an anatomic lingulectomy and the frozen section was suggestive of a primary lung cancer. Therefore, we proceeded to a full lymphadenectomy. The final pathology evaluation showed a typical carcinoid tumour (pT1aN0). The second patient was a 50 year old woman, a smoker and with a heavy family history of lung cancer. In a screening CT scan a 8 mm ground glass opacity was identified in the left lower lobe (segment VI). After a VATS wedge resection of the node the frozen section evaluation was compatible with adenocarcinoma. We then proceeded to an anatomic segmentectomy with lymphadenectomy. The definitive pathology evaluation confirmed that it was a pT1a N0 bronchioloalveolar adenocarcinoma. The patients now have 5 and 2 months of follow up respectivelly and neither of them has signs of recurrence and the surgical incision showed a good aesthetic result. Anatomic segmentectomy is the indicated surgery especially in patients with low grade tumours, in early stage lung cancers or in patients without pulmonary function for a lobar resection, and it can be done safely using VATS.

Breast Cancer Presents With a Paraneoplastic Neurologic Syndrome

BACKGROUND: Paraneoplastic neurologic syndromes (PNS) pose quite an uncommon neurological complication, affecting less than 1% of patients with breast cancer. Nearly one third of these patients lack detectable onconeural antibodies (ONAs), and improvement in neurologic deficits with concomitant cancer treatments is achieved in less than 30% of cases. CASE PRESENTATION: A 42-year-old, premenopausal woman presented with facial paralysis on the central left side accompanied by a left tongue deviation, an upward vertical nystagmus, moderate spastic paraparesis, dystonic posturing of the left foot, lower limb hyperreflexia and bilateral extensor plantar reflex. After ruling out all other potential neurologic causes, PNS was suspected but no ONAs were found. A PET-CT scan detected increased metabolism in the right breast, as well as an ipsilateral thoracic interpectoral adenopathy. Core biopsy confirmed the presence of an infiltrating duct carcinoma. After breast surgery, the neurologic symptoms disappeared. One week later, the patient was readmitted to the hospital with a bilateral fatigable eyelid ptosis, and two weeks later, there was a noticeable improvement in eyelid ptosis, accompanied by a rapid and progressive development of lower spastic paraparesis. She started adjuvant treatment with chemotherapy with marked clinical and neurological improvement, and by the end of radiotherapy, there were no signs of neurologic impairment. CONCLUSION: This case study highlights the importance of a high level of vigilance for the detection of PNS, even when ONAs are not detected, as the rapid identification and treatment of the underlying tumor offers the best chance for a full recovery.

Pathology of complete atrioventricular block in chronic chagas' myocarditis

Sclero-atrophy, fibrosis, vascular ectasia, phlebosclerosis and mild non-specific chronic inflammatory changes were observed in variable location and proportion involving the atrioventricular conducting tissue of the heart in five human cases of chronic Chagas' myocarditis associated with complete atrioventricular block. One case presented complete destruction of the A-V conduction system. In three cases the lesions were disseminated all along the conducting tissue but did not cause anywhere a complete disruption in the continuity of the system. The distal portion of the bundle branches were the most damaged sector of the system, exceptfor the fasciculi of the posterior division of the left bundle branch which were relatively preserved. One case exhibited bilateral sclero-atrophy of the bundle branches as the main change; and another showed early and mild fibrocalcific damage of the penetrating portion of the His bundle. The A-V node appeared as the least involved part of the conducting system in the cases studied. Demonstration of the lesions in this series of cases seems important because: a) it reveals that complete atrioventriculr block in chronic Chagas' disease results from disseminated lesions and not from focal disruptive change as has been commonly observed in cases of other etiologies; b) it shows that chronic inflammation can produce at the end variable and widespread vascular, degenerative andfibrotic alterations within the conducting tissue of the heart, which may lead to its total destruction.

Biodemes and zymodemes of Trypanosoma cruzi strains: correlations with clinical data and experimental pathology

With the objective of establishing biological and biochemical characteristics of a significant number of Trypanosoma cruzi strains from different geographical areas, 138 strains isolated from naturally infected humans, triatomine or vertebrate hosts were studied; 120 were isolated from different areas of Brazil and 18 from other South and Central American countries. Inocula from triatomine or culture forms were injected into suckling Swiss mice, followed by passages into mice 10 to 12 g. Biological characters and histopathological study permitted the inclusion of the strains into three Types or biodemes: I, II, III. Isoenzymic analysis confirmed a correspondence between the biodemes and zymodemes : Type I and Z2b, Type II and Z2, Type III and Z1. Results showed the ubiquitary distribution of the several types of strains. The predominance of the same Type and zymodeme in one geographical area was confirmed : Type II strains among the human cases from eastern Bahia and east of Goiás; Type III strains from humans of north Brazil and Central America and from silvatic vectors or vertebrates from other geographical areas. The biological types of strains correlate with different histopathological lesions considering cardiac involvement and neuronal lesions. These findings suggest that the biological behavior together with isoenzymes patterns and pathological pictures in the vertebrate host can be an important tool for establishing correlations between strains behavior and clinico-pathological manifestations of Chagas' disease in different geographical areas.

Severe digestive pathology associated with chronic Chaga's disease in Ecuador: report of two cases

DNA extracted from peripheral blood of two Ecuadorian patients showing severe digestive pathology was amplified by the polymerase chain reaction using a Trypanosoma cruzi specific oligonucleotide primers derived from the primary sequence of a cDNA encoding for a 24 kDa excretory/secretory protein. The positive PCR results together with the clinical findings confirmed that both patients had a digestive pathology due to Chagas' disease. This pathology could be more frequent than previously described in the chagasic endemic regions of Andean countries.

A comparison between digital breast tomosynthesis and mammography: dosimetric and image quality characterization of clinical system

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Hepatic pathology in Capillaria hepatica infected mice

Septal fibrosis of the liver regularly develops in rats infected with Capillaria hepatica. To find out whether such fibrosis also occurs in mice, 20 animals were submitted to infection with either 100 or 300 embryonated eggs and histologically examined after several periods of time, from 30 to 110 days afterwards. Results showed that mice developed acute, severe, diffuse and focal hepatic lesions that were soon modulated to focal areas of fibrosis containing eggs and worm remnants, despite the fact that a few worms remained alive, at least up to 110 days after inoculation. Areas of perisinusoidal fibrosis appeared in the proximity and around focal parasitic lesions, but clear-cut septal fibrosis was not observed. Why septal fibrosis forms in rats, but not in mice during C. hepatica infection, only further studies can clarify. Mice seem to show better host/parasite relationship than rats in regard to C. hepatica infection.

Pseudoneoplastic lesion of the breast caused by Schistosoma mansoni

A case of a pseudoneoplastic lesion of the breast clinically and sonographically suggestive of a fibroadenoma is reported. Excisional biopsy revealed the nodule was an inflammatory process consequent to infection by Schistosoma mansoni.

Optimization of breast tomosynthesis image reconstruction using parallel computing

Breast cancer is the most common cancer among women, being a major public health problem. Worldwide, X-ray mammography is the current gold-standard for medical imaging of breast cancer. However, it has associated some well-known limitations. The false-negative rates, up to 66% in symptomatic women, and the false-positive rates, up to 60%, are a continued source of concern and debate. These drawbacks prompt the development of other imaging techniques for breast cancer detection, in which Digital Breast Tomosynthesis (DBT) is included. DBT is a 3D radiographic technique that reduces the obscuring effect of tissue overlap and appears to address both issues of false-negative and false-positive rates. The 3D images in DBT are only achieved through image reconstruction methods. These methods play an important role in a clinical setting since there is a need to implement a reconstruction process that is both accurate and fast. This dissertation deals with the optimization of iterative algorithms, with parallel computing through an implementation on Graphics Processing Units (GPUs) to make the 3D reconstruction faster using Compute Unified Device Architecture (CUDA). Iterative algorithms have shown to produce the highest quality DBT images, but since they are computationally intensive, their clinical use is currently rejected. These algorithms have the potential to reduce patient dose in DBT scans. A method of integrating CUDA in Interactive Data Language (IDL) is proposed in order to accelerate the DBT image reconstructions. This method has never been attempted before for DBT. In this work the system matrix calculation, the most computationally expensive part of iterative algorithms, is accelerated. A speedup of 1.6 is achieved proving the fact that GPUs can accelerate the IDL implementation.

Transimpedance amplifier for early detection of breast cancer

Breast cancer is the most common type of cancer worldwide. The effectiveness of its treatment depends on early stage detection, as well as on the accuracy of its diagnosis. Recently, diagnosis techniques have been submitted to relevant breakthroughs with the upcoming of Magnetic Resonance Imaging, Ultrasound Sonograms and Positron Emission Tomography (PET) scans, among others. The work presented here is focused on studying the application of a PET system to a Positron Emission Mammography (PEM) system. A PET/PEM system works under the principle that a scintillating crystal will detect a gamma-ray pulse, originated at the cancerous cells, converting it into a correspondent visible light pulse. The latter must then be converted into an electrical current pulse by means of a Photo- -Sensitive Device (PSD). After the PSD there must be a Transimpedance Amplifier (TIA) in order to convert the current pulse into a suitable output voltage, in a time period lower than 40 ns. In this Thesis, the PSD considered is a Silicon Photo-Multiplier (SiPM). The usage of this recently developed type of PSD is impracticable with the conventional TIA topologies, as it will be proven. Therefore, the usage of the Regulated Common-Gate (RCG) topology will be studied in the design of the amplifier. There will be also presented two RCG variations, comprising a noise response improvement and differential operation of the circuit. The mentioned topology will also be tested in a Radio-Frequency front-end, showing the versatility of the RCG. A study comprising a low-voltage self-biasing feedback TIA will also be shown. The proposed circuits will be simulated with standard CMOS technology (UMC 130 nm), using a 1.2 V power supply. A power consumption of 0.34 mW with a signal-to-noise ratio of 43 dB was achieved.

Assessment of Notch1 ligands production - key protein targets in breast cancer

Cell-to-cell communication is required for many biological processes in development and adult life. One of the most common systems utilized by a wide range of eukaryotes is the Notch signalling pathway. Four Notch receptors and five ligands have been identified in mammals that interact via their extracellular domains leading to transcription activation. Studies have shown that the Notch ligands expression is undetectable in normal breast tissues, but moderate to high expression has been detected in breast cancer. Thus, any of the Notch1 ligands can be studied as possible therapeutic targets for breast cancer. To study Notch pathway proteins there is the need to obtain stable protein solutions. E. coli is the host of excellence for recombinant proteins for the ease of use, fast growth and high cell densities. However, the expression of mammalian proteins in such systems may overwhelm the bacterial cellular machinery, which does not possess the ability for post-translational modifications, or dedicated compartments for protein synthesis. Mammalian cells are therefore preferred, despite their technical and financial increased demands. We aim to determine the best expression and purification conditions for the different ligand protein constructs, to develop specific function-blocking antibodies using the Phage Display technology. Moreover, we propose to crystallize the Notch1 ligands alone and in complex with the phage display selected antibodies, unveiling molecular details. hJag2DE3 and hDll1DE6 proteins were purified from refolded inclusion bodies or mammalian cell culture supernatants, respectively, and purity was confirmed by SDS-PAGE (>95%). Protein produced in mammalian cells showed to be more stable, apparently with the physiological disulfide pattern, contrary to what was observed in the refolded protein. Several nano-scale crystallization experiments were set up in 96-well plates, but no positive result was obtained. We will continue to pursue for the best expression for the Notch ligand constructs in both expression systems.

Microwave imaging of the axilla to aid breast cancer diagnosis

Breast cancer is the most common type of cancer among women all over the world. An important issue that is not commonly addressed in breast cancer imaging literature is the importance of imaging the underarm region—where up to 80% of breast cancer cells can metastasise to. The first axillary lymph nodes to receive drainage from the primary tumour in the breast are called Sentinel Node. If cancer cells are found in the Sentinel Node, there is an increased risk of metastatic breast cancer which makes this evaluation crucial to decide what follow-up exams and therapy to follow. However, non-invasive detection of cancer cells in the lymph nodes is often inconclusive, leading to the surgical removal of too many nodes which causes adverse side-effects for patients. Microwave Imaging is one of the most promising non-invasive imaging modalities for breast cancer early screening and monitoring. This novel study tests the feasibility of imaging the axilla region by means of the simulation of an Ultra-Wideband Microwave Imaging system. Simulations of such system are completed in several 2D underarm models that mimic the axilla. Initial imaging results are obtained by means of processing the simulated backscattered signals by eliminating artefacts caused by the skin and beamforming the processed signals in order to time-align all the signals recorded at each antenna. In this dissertation several image formation algorithms are implemented and compared by visual inspection of the resulting images and through a range of performance metrics, such as Signal-to-Clutter Ratio and FullWidth Half Maximum calculations. The results in this study showed that Microwave Imaging is a promising technique that might allow to identify the presence and location of metastasised cancer cells in axillary lymph nodes, enabling the non-invasive evaluation of breast cancer staging.