Data Science Commons^™

Brain Antigens Stimulate Proliferation Of T Lymphocytes With A Pathogenic Phenotype In Multiple Sclerosis Patients, Assaf Gottlieb, Hoai Phuong T Pham, John William Lindsey

Faculty, Staff and Student Publications

A method to stimulate T lymphocytes with a broad range of brain antigens would facilitate identification of the autoantigens for multiple sclerosis and enable definition of the pathogenic mechanisms important for multiple sclerosis. In a previous work, we found that the obvious approach of culturing leukocytes with homogenized brain tissue does not work because the brain homogenate suppresses antigen-specific lymphocyte proliferation. We now report a method that substantially reduces the suppressive activity. We used this non-suppressive brain homogenate to stimulate leukocytes from multiple sclerosis patients and controls. We also stimulated with common viruses for comparison. We measured proliferation, selected the …

Electron Transfer Dynamics And Electrocatalytic Oxygen Evolution Activities Of The Co3o4 Nanoparticles Attached To Indium Tin Oxide By Self-Assembled Monolayers, Xuan Liu, Qianhong Tian, Yvpei Li, Zixiang Zhou, Jinlian Wang, Shuling Liu, Chao Wang

Faculty, Staff and Student Publications

The Co3O4 nanoparticle-modified indium tin oxide-coated glass slide (ITO) electrodes are successfully prepared using dicarboxylic acid as the self-assembled monolayer through a surface esterification reaction. The ITO-SAM-Co3O4 (SAM = dicarboxylic acid) are active to electrochemically catalyze oxygen evolution reaction (OER) in acid. The most active assembly, with Co loading at 3.31 × 10-8 mol cm-2, exhibits 374 mV onset overpotential and 497 mV overpotential to reach 1 mA cm-2 OER current in 0.1 M HClO4. The electron transfer rate constant (k) is acquired using Laviron's approach, and the results show that k is not affected by the carbon …

Processing Binding Data Using An Open-Source Workflow, Errol L G Samuel, Secondra L Holmes, Damian W Young

Faculty, Staff and Students Publications

The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There …

Machine Learning Approach To Distinguish Ulcerative Colitis And Crohn’S Disease Using Smote (Synthetic Minority Oversampling Technique) Methods, Kris Ghimire, Walter Lai, Yasser Omar, Thad Schwebke, Jamie Vo

SMU Data Science Review

Irritable Bowel Disease (IBD) affects a sizable portion of the US population, causing symptoms such as vomiting, abdominal pain, and diarrhea. Despite the disease’s prevalence, the precise cause is not fully understood. This study consists of endoscopic and histological data from patients diagnosed with IBD and a control population for reference. The machine learning models' focus is to classify patients into IBD types. Several models were analyzed, including decision trees, logistic regression, and k-nearest neighbors. In addition, various methods of SMOTE were applied to determine the most effective transformation and ensuring that the dataset is balanced. The best model with …

The Concurrence Of Dna Methylation And Demethylation Is Associated With Transcription Regulation, Jiejun Shi, Jianfeng Xu, Yiling Elaine Chen, Jason Sheng Li, Ya Cui, Lanlan Shen, Jingyi Jessica Li, Wei Li

Children’s Nutrition Research Center Staff Publications

The mammalian DNA methylome is formed by two antagonizing processes, methylation by DNA methyltransferases (DNMT) and demethylation by ten-eleven translocation (TET) dioxygenases. Although the dynamics of either methylation or demethylation have been intensively studied in the past decade, the direct effects of their interaction on gene expression remain elusive. Here, we quantify the concurrence of DNA methylation and demethylation by the percentage of unmethylated CpGs within a partially methylated read from bisulfite sequencing. After verifying 'methylation concurrence' by its strong association with the co-localization of DNMT and TET enzymes, we observe that methylation concurrence is strongly correlated with gene expression. …

A Comparison Of Exhaustive And Non-Lattice-Based Methods For Auditing Hierarchical Relations In Gene Ontology, Rashmie Abeysinghe, Fengbo Zheng, Licong Cui

Faculty, Staff and Student Publications

Uncovering and fixing errors in biomedical terminologies is essential so that they provide accurate knowledge to downstream applications that rely on them. Non-lattice-based methods have been applied to identify various kinds of inconsistencies in different biomedical terminologies. In previous work, we have introduced two inference-based approaches that were applied in an exhaustive manner to audit hierarchical relations in the Gene Ontology: (1) Lexical-based inference framework, and (2) Subsumption-based sub-term inference framework. However, it is unclear how effective these exhaustive approaches perform compared with their corresponding non-lattice-based approaches. Therefore, in this paper, we implement the non-lattice versions of these two exhaustive …

Automatic Recognition, Segmentation, And Sex Assignment Of Nocturnal Asthmatic Coughs And Cough Epochs In Smartphone Audio Recordings: Observational Field Study, Filipe Barata, Peter Tinschert, Frank Rassouli, Claudia Steurer-Stey, Elgar Fleisch, Milo Puhan, Martin Brutsche, David Kotz, Tobias Kowatsch

Dartmouth Scholarship

Background: Asthma is one of the most prevalent chronic respiratory diseases. Despite increased investment in treatment, little progress has been made in the early recognition and treatment of asthma exacerbations over the last decade. Nocturnal cough monitoring may provide an opportunity to identify patients at risk for imminent exacerbations. Recently developed approaches enable smartphone-based cough monitoring. These approaches, however, have not undergone longitudinal overnight testing nor have they been specifically evaluated in the context of asthma. Also, the problem of distinguishing partner coughs from patient coughs when two or more people are sleeping in the same room using contact-free audio …

Development Of Fully Balanced Ssfp And Computer Vision Applications For Mri-Assisted Radiosurgery (Mars), Jeremiah Sanders

Dissertations and Theses (Open Access)

Prostate cancer is the second most common cancer in men and the second-leading cause of cancer death in men. Brachytherapy is a highly effective treatment option for prostate cancer, and is the most cost-effective initial treatment among all other therapeutic options for low to intermediate risk patients of prostate cancer. In low-dose-rate (LDR) brachytherapy, verifying the location of the radioactive seeds within the prostate and in relation to critical normal structures after seed implantation is essential to ensuring positive treatment outcomes.

One current gap in knowledge is how to simultaneously image the prostate, surrounding anatomy, and radioactive seeds within the …

Searching For The Majority: Algorithms Of Voluntary Control, Jin Fan, Kevin G. Guise, Xun Liu, Hongbin Wang

Faculty, Staff and Student Publications

Voluntary control of information processing is crucial to allocate resources and prioritize the processes that are most important under a given situation; the algorithms underlying such control, however, are often not clear. We investigated possible algorithms of control for the performance of the majority function, in which participants searched for and identified one of two alternative categories (left or right pointing arrows) as composing the majority in each stimulus set. We manipulated the amount (set size of 1, 3, and 5) and content (ratio of left and right pointing arrows within a set) of the inputs to test competing hypotheses …

Exploration Of Computational Methods For Classification Of Movement Intention During Human Voluntary Movement From Single Trial Eeg, Ou Bai, Peter Lin, Sherry Vorbach, Jiang Li, Steve Furlani, Mark Hallett

Electrical & Computer Engineering Faculty Publications

Objective: To explore effective combinations of computational methods for the prediction of movement intention preceding the production of self-paced right and left hand movements from single trial scalp electroencephalogram (EEG).

Methods: Twelve naïve subjects performed self-paced movements consisting of three key strokes with either hand. EEG was recorded from 128 channels. The exploration was performed offline on single trial EEG data. We proposed that a successful computational procedure for classification would consist of spatial filtering, temporal filtering, feature selection, and pattern classification. A systematic investigation was performed with combinations of spatial filtering using principal component analysis (PCA), independent component analysis …