AI in Medical Imaging Informatics: Current Challenges and Future Directions

This paper reviews state-of-the-art research solutions across the spectrum of medical imaging informatics, discusses clinical translation, and provides future directions for advancing clinical practice. More specifically, it summarizes advances in medical imaging acquisition technologies for different modalities, highlighting the necessity for efficient medical data management strategies in the context of AI in big healthcare data analytics. It then provides a synopsis of contemporary and emerging algorithmic methods for disease classification and organ/ tissue segmentation, focusing on AI and deep learning architectures that have already become the de facto approach. The clinical benefits of in-silico modelling advances linked with evolving 3D reconstruction and visualization applications are further documented. Concluding, integrative analytics approaches driven by associate research branches highlighted in this study promise to revolutionize imaging informatics as known today across the healthcare continuum for both radiology and digital pathology applications. The latter, is projected to enable informed, more accurate diagnosis, timely prognosis, and effective treatment planning, underpinning precision medicine

A Learning Health System for Radiation Oncology

The proposed research aims to address the challenges faced by clinical data science researchers in radiation oncology accessing, integrating, and analyzing heterogeneous data from various sources. The research presents a scalable intelligent infrastructure, called the Health Information Gateway and Exchange (HINGE), which captures and structures data from multiple sources into a knowledge base with semantically interlinked entities. This infrastructure enables researchers to mine novel associations and gather relevant knowledge for personalized clinical outcomes. The dissertation discusses the design framework and implementation of HINGE, which abstracts structured data from treatment planning systems, treatment management systems, and electronic health records. It utilizes disease-specific smart templates for capturing clinical information in a discrete manner. HINGE performs data extraction, aggregation, and quality and outcome assessment functions automatically, connecting seamlessly with local IT/medical infrastructure. Furthermore, the research presents a knowledge graph-based approach to map radiotherapy data to an ontology-based data repository using FAIR (Findable, Accessible, Interoperable, Reusable) concepts. This approach ensures that the data is easily discoverable and accessible for clinical decision support systems. The dissertation explores the ETL (Extract, Transform, Load) process, data model frameworks, ontologies, and provides a real-world clinical use case for this data mapping. To improve the efficiency of retrieving information from large clinical datasets, a search engine based on ontology-based keyword searching and synonym-based term matching tool was developed. The hierarchical nature of ontologies is leveraged to retrieve patient records based on parent and children classes. Additionally, patient similarity analysis is conducted using vector embedding models (Word2Vec, Doc2Vec, GloVe, and FastText) to identify similar patients based on text corpus creation methods. Results from the analysis using these models are presented. The implementation of a learning health system for predicting radiation pneumonitis following stereotactic body radiotherapy is also discussed. 3D convolutional neural networks (CNNs) are utilized with radiographic and dosimetric datasets to predict the likelihood of radiation pneumonitis. DenseNet-121 and ResNet-50 models are employed for this study, along with integrated gradient techniques to identify salient regions within the input 3D image dataset. The predictive performance of the 3D CNN models is evaluated based on clinical outcomes. Overall, the proposed Learning Health System provides a comprehensive solution for capturing, integrating, and analyzing heterogeneous data in a knowledge base. It offers researchers the ability to extract valuable insights and associations from diverse sources, ultimately leading to improved clinical outcomes. This work can serve as a model for implementing LHS in other medical specialties, advancing personalized and data-driven medicine

Efficient Decision Support Systems

This series is directed to diverse managerial professionals who are leading the transformation of individual domains by using expert information and domain knowledge to drive decision support systems (DSSs). The series offers a broad range of subjects addressed in specific areas such as health care, business management, banking, agriculture, environmental improvement, natural resource and spatial management, aviation administration, and hybrid applications of information technology aimed to interdisciplinary issues. This book series is composed of three volumes: Volume 1 consists of general concepts and methodology of DSSs; Volume 2 consists of applications of DSSs in the biomedical domain; Volume 3 consists of hybrid applications of DSSs in multidisciplinary domains. The book is shaped decision support strategies in the new infrastructure that assists the readers in full use of the creative technology to manipulate input data and to transform information into useful decisions for decision makers

Medical Robotics

The first generation of surgical robots are already being installed in a number of operating rooms around the world. Robotics is being introduced to medicine because it allows for unprecedented control and precision of surgical instruments in minimally invasive procedures. So far, robots have been used to position an endoscope, perform gallbladder surgery and correct gastroesophogeal reflux and heartburn. The ultimate goal of the robotic surgery field is to design a robot that can be used to perform closed-chest, beating-heart surgery. The use of robotics in surgery will expand over the next decades without any doubt. Minimally Invasive Surgery (MIS) is a revolutionary approach in surgery. In MIS, the operation is performed with instruments and viewing equipment inserted into the body through small incisions created by the surgeon, in contrast to open surgery with large incisions. This minimizes surgical trauma and damage to healthy tissue, resulting in shorter patient recovery time. The aim of this book is to provide an overview of the state-of-art, to present new ideas, original results and practical experiences in this expanding area. Nevertheless, many chapters in the book concern advanced research on this growing area. The book provides critical analysis of clinical trials, assessment of the benefits and risks of the application of these technologies. This book is certainly a small sample of the research activity on Medical Robotics going on around the globe as you read it, but it surely covers a good deal of what has been done in the field recently, and as such it works as a valuable source for researchers interested in the involved subjects, whether they are currently “medical roboticists” or not

Measuring primate gene expression evolution using high throughput transcriptomics and massively parallel reporter assays

A key question in biology is how one genome sequence can lead to the great cellular diversity present in multicellular organisms. Enabled by he sequencing revolution, RNA sequencing (RNA-seq) has emerged as a central tool to measure transcriptome-wide gene expression levels. More recently, single cell RNA-seq was introduced and is becoming a feasible alternative to the more established bulk sequencing. While many different methods have been proposed, a thorough optimisation of established protocols can lead to improvements in robustness, sensitivity, scalability and cost effectiveness. Towards this goal, I have contributed to optimizing the single cell RNA-seq method "Single Cell RNA Barcoding and sequencing" (SCRB-seq) and publishing an improved version that uses optimized reaction conditions and molecular crowding (mcSCRB-seq). mcSCRB-seq achieves higher sensitivity at lower cost per cell and shows the highest RNA capture rate when compared with other published methods. We next sought the direct comparison to other scRNA-seq protocols within the Human Cell Atlas (HCA) benchmarking effort. Here we used mcSCRB-seq to profile a common reference sample that included heterogeneous cell populations from different sources. Transfer of the acquired knowledge on single cell RNA sequencing methods to bulk RNA-seq, led to the development of the prime-seq protocol. A sensitive, robust and cost-efficient bulk RNA-seq protocol that can be performed in any molecular biology laboratory. We compared the data generated, using the prime-seq protocol to the gold standard method TruSeq, using power simulations and found that the statistical power to detect differentially expressed genes is comparable, at 40-fold lower cost. While gene expression is an informative phenotype, the regulation that leads to the different phenotypes is still poorly understood. A state-of-the-art method to measure the activity of cis-regulatory elements (CRE) in a high throughput fashion are Massively Parallel Reporter Assays (MPRA). These assays can be used to measure the activity of thousands of cis-Regulatory Elements (CRE) in parallel. A good way to decode the genotype to phenotype conundrum is using evolutionary information. Cross-species comparisons of closely related species can help understand how particular diverging phenotypes emerged and how conserved gene regulatory programs are encoded in the genome. A very useful tool to perform comparative studies are cell lines, particularly induced Pluripotent Stem Cells (iPSCs). iPSCs can be reprogrammed from different primary somatic cells and are per definition pluripotent, meaning they can be differentiated into cells of all three germlayers. A main challenge for primate research is to obtain primary cells. To this end I contributed to establishing a protocol to generate iPSCs from a non-invasive source of primary cells, namely urine. By using prime-seq we characterized the primary Urine Derived Stem Cells (UDSCs) and the reprogrammed iPSCs. Finally, I used an MPRA to measure activity of putative regulatory elements of the gene TRNP1 across the mammalian phylogeny. We found co-evolution of one particular CRE with brain folding in old world monkeys. To validate the finding we looked for transcription factor binding sites within the identified CRE and intersected the list with transcription factors confirmed to be expressed in the cellular system using prime-seq. In addition we found that changes in the protein coding sequence of TRNP1 and neural stem cell proliferation induced by TRNP1 orthologs correlate with brain size. In summary, within my doctorate I developed methods that enable measuring gene expression and gene regulation in a comparative genomics setting. I further applied these methods in a cross mammalian study of the regulatory sequences of the gene TRNP1 and its association with brain phenotypes

Excellentia Eminentia Effectio

"In these pages you will learn about the fascinating research endeavors that each of our faculty members is undertaking. We have divided their research into the broad categories of health, sustainability, information, and systems. While we recognize the imperfect nature of categorizing research that, by its very nature may be interdisciplinary or transdisciplinary, we nonetheless believe it will be helpful as a way to see the depth and breadth of our research endeavors within each grouping. As you read the profiles on these pages, I know you will begin to appreciate that, taken as a whole, the research spectrum at Columbia Engineering is exceptional and that, as our professors go about their work, they are at the cusp of making breakthroughs that will have a major impact on the way we live our lives today and tomorrow.

Shape analysis of the human brain.

Autism is a complex developmental disability that has dramatically increased in prevalence, having a decisive impact on the health and behavior of children. Methods used to detect and recommend therapies have been much debated in the medical community because of the subjective nature of diagnosing autism. In order to provide an alternative method for understanding autism, the current work has developed a 3-dimensional state-of-the-art shape based analysis of the human brain to aid in creating more accurate diagnostic assessments and guided risk analyses for individuals with neurological conditions, such as autism. Methods: The aim of this work was to assess whether the shape of the human brain can be used as a reliable source of information for determining whether an individual will be diagnosed with autism. The study was conducted using multi-center databases of magnetic resonance images of the human brain. The subjects in the databases were analyzed using a series of algorithms consisting of bias correction, skull stripping, multi-label brain segmentation, 3-dimensional mesh construction, spherical harmonic decomposition, registration, and classification. The software algorithms were developed as an original contribution of this dissertation in collaboration with the BioImaging Laboratory at the University of Louisville Speed School of Engineering. The classification of each subject was used to construct diagnoses and therapeutic risk assessments for each patient. Results: A reliable metric for making neurological diagnoses and constructing therapeutic risk assessment for individuals has been identified. The metric was explored in populations of individuals having autism spectrum disorders, dyslexia, Alzheimers disease, and lung cancer. Conclusion: Currently, the clinical applicability and benefits of the proposed software approach are being discussed by the broader community of doctors, therapists, and parents for use in improving current methods by which autism spectrum disorders are diagnosed and understood

Special oils for halal and safe cosmetics

Three types of non conventional oils were extracted, analyzed and tested for toxicity. Date palm kernel oil (DPKO), mango kernel oil (MKO) and Ramputan seed oil (RSO). Oil content for tow cultivars of dates Deglect Noor and Moshkan was 9.67% and 7.30%, respectively. The three varieties of mango were found to contain about 10% oil in average. The red yellow types of Ramputan were found to have 11 and 14% oil, respectively. The phenolic compounds in DPKO, MKO and RSO were 0.98, 0.88 and 0.78 mg/ml Gallic acid equivalent, respectively. Oils were analyzed for their fatty acid composition and they are rich in oleic acid C18:1 and showed the presence of (dodecanoic acid) lauric acid C12:0, which reported to appear some antimicrobial activities. All extracted oils, DPKO, MKO and RSO showed no toxic effect using prime shrimp bioassay. Since these oils are stable, melt at skin temperature, have good lubricity and are great source of essential fatty acids; they could be used as highly moisturizing, cleansing and nourishing oils because of high oleic acid content. They are ideal for use in such halal cosmetics such as Science, Engineering and Technology 75 skin care and massage, hair-care, soap and shampoo products