Uncertainty Quantification and Estimation on Medical Imaging Classification Tasks

This thesis presents an uncertainty quantification (UQ) system on medical classification imaging tasks and its practical use. Deep Neural Networks have shown tremendous success in numerous AI-related fields, for example, object detection, recognition, and health care. However, despite Deep Neural Networks exhibiting remarkable performance, we usually can not guarantee the modelling predictions to be absolutely correct. Therefore, estimation and quantification of uncertainty have become an essential parameter in Deep Learning practical applications, especially in medical imaging. Measuring uncertainty can help with better decision making, early diagnosis, and a variety of tasks. In this thesis, we explore uncertainty quantification (UQ) approaches and propose an uncertainty estimation system for general medical imaging classification tasks. In experiments, we apply the UQ system for three medical imaging databases, including All-IDB2 (an acute lymphoblastic leukemia database), SARS-CoV2 (a coronavirus disease 2019 database) and BreaKHis (a breast cancer histopathological imaging database). Besides, we discuss how to apply UQ methods to obtain more information on the database and its modelling. We can capture the samples with the uncertainty values and predict the most uncertain category. We also discover that we can receive more accurate results than initial modelling results by removing a percentage of data with higher uncertainty results. In summary, we find great potential for UQ research on complex medical classification tasks and consider it to become probably one of the future's essential research directions

Atypical chemoreceptor arrays accommodate high membrane curvature

The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended array. Here, we report an alternative symmetry (P2) of the chemotaxis apparatus that emerges from a strict linear organization of the histidine kinase CheA in Treponema denticola cells, which possesses arrays with the highest native curvature investigated thus far. Using cryo-ET, we reveal that Td chemoreceptor arrays assume an unusual arrangement of the supra-molecular protein assembly that has likely evolved to accommodate the high membrane curvature. The arrays have several atypical features, such as an extended dimerization domain of CheA and a variant CheW-CheR-like fusion protein that is critical for maintaining an ordered chemosensory apparatus. Furthermore, the previously characterized Td oxygen sensor ODP influences CheA ordering. These results suggest a greater diversity of the chemotaxis signaling system than previously thought

CD30 Expression Reveals that Culture Adaptation of Human Embryonic Stem Cells Can Occur Through Differing Routes

Human embryonic stem cells undergo adaptive changes that can increase their growth capacity upon prolonged culture in vitro. This is frequently associated with nonrandom karyotypic changes, commonly involving amplification of genetic material from chromosomes 12, 17, and X. A recent study suggested that the karyotypically abnormal cells can be identified by their expression of CD30, which confers resistance to apoptosis. We have now investigated CD30 expression and apoptosis in karyotypically normal and abnormal sublines of the human ES cell line, H7, but our results were contrary to those previously observed. In this cell line, CD30 expression did not segregate the normal and abnormal cells, and abnormal cells were not protected from apoptosis. These data suggest that culture adaptation can occur through a variety of mechanisms

Implant delivering hydroxychloroquine attenuates vaginal T lymphocyte activation and inflammation

The final publication is available at Elsevier via https://doi.org/10.1016/j.jconrel.2018.03.010 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Evidence suggests that women who are naturally resistant to HIV infection exhibit low baseline immune activation at the female genital tract (FGT). This “immune quiescent” state is associated with lower expression of T-cell activation markers, reduced levels of gene transcription and pro-inflammatory cytokine or chemokine production involved in HIV infection while maintaining an intact immune response against pathogens. Therefore, if this unique immune quiescent state can be pharmacologically induced locally, it will provide an excellent women-oriented strategy against HIV infection To our knowledge, this is the first research article evaluating in vivo, an innovative trackable implant that can provide controlled delivery of hydroxychloroquine (HCQ) to successfully attenuate vaginal T lymphocyte activation and inflammation in a rabbit model as a potential strategy to induce an “immune quiescent” state within the FGT for the prevention of HIV infection. This biocompatible implant can deliver HCQ above therapeutic concentrations in a controlled manner, reduce submucosal immune cell recruitment, improve mucosal epithelium integrity, decrease protein and gene expression of T-cell activation markers, and attenuate the induction of key pro-inflammatory mediators. Our results suggest that microbicides designed to maintain a low level of immune activation at the FGT may offer a promising new strategy for reducing HIV infection.Canadian Institutes of Health Research (CIHR) Operating Grant (MOP110981) CIHR Canadian HIV Vaccine Initiative Grant (OCH-126275) Research Manitoba Graduate Studentship Leslie F. Buggy Graduate Scholarship in Pharmacy from the University of Manitob

Coating of a Novel Antimicrobial Nanoparticle with a Macrophage Membrane for the Selective Entry into Infected Macrophages and Killing of Intracellular Staphylococci

Internalization of Staphylococcus aureus by macrophages can inactivate bacterial killing mechanisms, allowing intracellular residence and dissemination of infection. Concurrently, these staphylococci can evade antibiotics that are frequently unable to pass mammalian cell membranes. A binary, amphiphilic conjugate composed of triclosan and ciprofloxacin is synthesized that self-assemble through micelle formation into antimicrobial nanoparticles (ANPs). These novel ANPs are stabilized through encapsulation in macrophage membranes, providing membrane-encapsulated, antimicrobial-conjugated NPs (Me-ANPs) with similar protein activity, Toll-like receptor expression and negative surface charge as their precursor murine macrophage/human monocyte cell lines. The combination of Toll-like receptors and negative surface charge allows uptake of Me-ANPs by infected macrophages/monocytes through positively charged, lysozyme-rich membrane scars created during staphylococcal engulfment. Me-ANPs are not engulfed by more negatively charged sterile cells possessing less lysozyme at their surface. The Me-ANPs kill staphylococci internalized in macrophages in vitro. Me-ANPs likewise kill staphylococci more effectively than ANPs without membrane-encapsulation or clinically used ciprofloxacin in a mouse peritoneal infection model. Similarly, organ infections in mice created by dissemination of infected macrophages through circulation in the blood are better eradicated by Me-ANPs than by ciprofloxacin. These unique antimicrobial properties of macrophage-monocyte Me-ANPs provide a promising direction for human clinical application to combat persistent infections

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

CRISPR-Cas9 is a versatile genome editing technology for studying the functions of genetic elements. To broadly enable the application of Cas9 in vivo, we established a Cre-dependent Cas9 knockin mouse. We demonstrated in vivo as well as ex vivo genome editing using adeno-associated virus (AAV)-, lentivirus-, or particle-mediated delivery of guide RNA in neurons, immune cells, and endothelial cells. Using these mice, we simultaneously modeled the dynamics of KRAS, p53, and LKB1, the top three significantly mutated genes in lung adenocarcinoma. Delivery of a single AAV vector in the lung generated loss-of-function mutations in p53 and Lkb1, as well as homology-directed repair-mediated Kras[superscript G12D] mutations, leading to macroscopic tumors of adenocarcinoma pathology. Together, these results suggest that Cas9 mice empower a wide range of biological and disease modeling applications.National Science Foundation (U.S.). Graduate Research Fellowship (Grant 1122374)Damon Runyon Cancer Research Foundation (Fellowship DRG-2117-12)Massachusetts Institute of Technology. Simons Center for the Social Brain (Postdoctoral Fellowship)European Molecular Biology Organization (Fellowship)Foundation for Polish Science (Fellowship)American Society for Engineering Education. National Defense Science and Engineering Graduate FellowshipNational Science Foundation (U.S.). Graduate Research FellowshipMassachusetts Institute of Technology (Presidential Graduate Fellowship)Human Frontier Science Program (Strasbourg, France) (Postdoctoral Fellowship)National Human Genome Research Institute (U.S.) (CEGS P50 HG006193)Howard Hughes Medical InstituteKlarman Cell ObservatoryNational Cancer Institute (U.S.) (Center of Cancer Nanotechnology Excellence Grant U54CA151884)National Institutes of Health (U.S.) (Controlled Release Grant EB000244)National Heart, Lung, and Blood Institute (Program of Excellence in Nanotechnology (PEN) Award Contract HHSN268201000045C)Massachusetts Institute of Technology (Poitras Gift 1631119)Stanley CenterSimons Foundation (6927482)Nancy Lurie Marks Family Foundation (6928117)United States. Public Health Service (National Institutes of Health (U.S.) R01-CA133404)David H. Koch Institute for Integrative Cancer Research at MIT (Marie D. and Pierre Casimir-Lambert Fund)MIT Skoltech InitiativeNational Cancer Institute (U.S.) (Koch Institute Support (Core) Grant P30-CA14051)National Institute of Mental Health (U.S.) (Director’s Pioneer Award DP1-MH100706)National Institute of Neurological Disorders and Stroke (U.S.) (Transformative R01 Grant R01-NS 07312401)National Science Foundation (U.S.) (Waterman Award)W. M. Keck FoundationKinship Foundation. Searle Scholars ProgramKlingenstein FoundationVallee FoundationMerkin Foundatio

Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism

Motivation: Despite being often perceived as the main contributors to cell fate and physiology, genes alone cannot predict cellular phenotype. During the process of gene expression, 95% of human genes can code for multiple proteins due to alternative splicing. While most splice variants of a gene carry the same function, variants within some key genes can have remarkably different roles. To bridge the gap between genotype and phenotype, condition- and tissue-specific models of metabolism have been constructed. However, current metabolic models only include information at the gene level. Consequently, as recently acknowledged by the scientific community, common situations where changes in splice-isoform expression levels alter the metabolic outcome cannot be modeled. Results: We here propose GEMsplice, the first method for the incorporation of splice-isoform expression data into genome-scale metabolic models. Using GEMsplice, we make full use of RNA-Seq quantitative expression profiles to predict, for the first time, the effects of splice isoform-level changes in the metabolism of 1455 patients with 31 different breast cancer types. We validate GEMsplice by generating cancer-versus-normal predictions on metabolic pathways, and by comparing with gene-level approaches and available literature on pathways affected by breast cancer. GEMsplice is freely available for academic use at https://github.com/GEMsplice/GEMsplice_code. Compared to state-of-the-art methods, we anticipate that GEMsplice will enable for the first time computational analyses at transcript level with splice-isoform resolution

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research