Digital Commons Network^™

Identify Rna-Associated Subcellular Localizations Based On Multi-Label Learning Using Chou’S 5-Steps Rule, Hao Wang, Yijie Ding, Jijun Tang Ph.D., Quan Zou, Fei Guo

Faculty Publications

Background: Biological functions of biomolecules rely on the cellular compartments where they are located in cells. Importantly, RNAs are assigned in specific locations of a cell, enabling the cell to implement diverse biochemical processes in the way of concurrency. However, lots of existing RNA subcellular localization classifiers only solve the problem of single-label classification. It is of great practical significance to expand RNA subcellular localization into multi-label classification problem.

Results: In this study, we extract multi-label classification datasets about RNA-associated subcellular localizations on various types of RNAs, and then construct subcellular localization datasets on four RNA categories. In order to …

Transdisciplinary Ai Observatory—Retrospective Analyses And Future-Oriented Contradistinctions, Nadisha Marie Aliman, Leon Kester, Roman Yampolskiy

Faculty and Staff Scholarship

In the last years, artificial intelligence (AI) safety gained international recognition in the light of heterogeneous safety-critical and ethical issues that risk overshadowing the broad beneficial impacts of AI. In this context, the implementation of AI observatory endeavors represents one key research direction. This paper motivates the need for an inherently transdisciplinary AI observatory approach integrating diverse retrospective and counterfactual views. We delineate aims and limitations while providing hands-on-advice utilizing concrete practical examples. Distinguishing between unintentionally and intentionally triggered AI risks with diverse socio-psycho-technological impacts, we exemplify a retrospective descriptive analysis followed by a retrospective counterfactual risk analysis. Building on …

Isolation And Purification Of Glycoglycerolipids To Induce Apoptosis In Breast Cancer Cells, Muhammad Raisul Abedin, Sutapa Barua

Chemical and Biochemical Engineering Faculty Research & Creative Works

Monogalactosyldiacylglycerol (MGDG) is the most abundant type of glycoglycerolipid found in the plant cell membrane and mostly in the chloroplast thylakoid membrane. The amphiphilic nature of MGDG is attractive in pharmaceutical fields for interaction with other biological molecules and hence exerting therapeutic anti-cancer, anti-viral, and anti-inflammatory activities. In this study, we investigated the therapeutic efficacy of cyanobacteria derived MGDG to inhibit breast cancer cell growth. MGDG was extracted from a cyanobacteria Synechocystis sp. PCC 6803 followed by a subsequent fractionation by column chromatographic technique. The purity and molecular structure of MGDG were analyzed by nuclear magnetic resonance (NMR) spectroscopy analysis. …

Methods For Object Tracking With Machine Vision, Zachary Simon Stamler

Dissertations and Theses

As machine learning and deep learning systems continue to find applications in science and engineering, the problem of providing these systems with high-quality data continues to increase in importance. Many of these systems utilize machine vision as their primary source of information, and in order to maximally leverage their abilities it is important to be able to provide them with high quality, accurate data. Unfortunately, many sets of tracking data extracted from video suffer from the problem of missing frames, which can arise from a multitude of causes depending on the system. These missing frames can result in confusion between …

The 3-O-Sulfation Of Heparan Sulfate Modulates Protein Binding And Lyase Degradation, Pradeep Chopra, Apoorva Joshi, Jiandong Wu, Weigang Lu, Tejabhiram Yadavalli, Margreet A. Wolfert, Deepak Shukla, Joseph Zaia, Geert Jan Boons

Chemical and Biochemical Engineering Faculty Research & Creative Works

Humans Express Seven Heparan Sulfate (HS) 3-O-Sulfotransferases that Differ in Substrate Specificity and Tissue Expression. Although Genetic Studies Have Indicated that 3-O-Sulfated HS Modulates Many Biological Processes, Ligand Requirements for Proteins Engaging with HS Modified by 3-O-Sulfate (3-OS) Have Been Difficult to Determine. in Particular, the Context in Which the 3-OS Group Needs to Be Presented for Binding is Largely Unknown. We Describe Herein a Modular Synthetic Approach that Can Provide Structurally Diverse HS Oligosaccharides with and Without 3-OS. the Methodology Was Employed to Prepare 27 Hexasaccharides that Were Printed as a Glycan Microarray to Examine Ligand Requirements of a …

A Microscale Approach To Investigate Breast Cancer Cellular Communication And Migration, Sharif Mohammad Mizanur Rahman

LSU Doctoral Dissertations

Metastatic breast cancer significantly decreases patient survival, with the majority of deaths caused by secondary metastasis. Cancer metastasis is a multi-step process that starts with the detachment of a cancer cell from the primary tumor and ends with establishing a secondary tumor at a distal location. This work's focus was to use an interdisciplinary microscale approach to study how cancer cells respond to neighboring cells and how they migrate in response to chemical gradients. Two distinct devices, a microfluidic device, and a 3D-printed plate insert, were developed to perform co-culture studies to elucidate the impact of ASCs on cancer cell …

Management Of The Phosphorus-Cladophora Dynamic At A Site On Lake Ontario Using A Multi-Module Bioavailable P Model, Martin Auer, Cory P. Mcdonald, Anika Kuczynski, Chenfu Huang

Michigan Tech Publications, Part 1

The filamentous green alga Cladophora grows to nuisance proportions in Lake Ontario. Stimulated by high phosphorus concentrations, nuisance growth results in the degradation of beaches and clogging of industrial water intakes with attendant loss of beneficial uses. We develop a multi-module bioavailable phosphorus model to examine the efficacy of phosphorus management strategies in mitigating nuisance algal growth. The model platform includes modules simulating hydrodynamics (FVCOM), phosphorus-phytoplankton dynamics (GEM) and Cladophora growth (GLCMv3). The model is applied along a 25 km stretch of the Lake Ontario nearshore, extending east from Toronto, ON and receiving effluent from three wastewater treatment plants. Simulation …

Research Trend Of Metal Matrix Composites Reinforced With Silica Extracted By Green Route: A Bibliometric Analysis, Rinku Datkhile, Meena Laad, Babaji Ghule

Library Philosophy and Practice (e-journal)

Metal Matrix Composites have acquired an important place in the engineering applications due to their distinctive characteristics such as high specific strength, lower specific gravity, improved material stiffness, better durability, enhanced creep and fatigue strength etc. Worldwide scientists are working on the improvement of mechanical properties of composite materials. The present work attempts to summarise all the research carried out on metal matrix composites reinforced with silica extracted by green route and provides up-to-date research material for researchers who are interested in the field of composites with metal matrices. Scopus databases and software such as Gephi Vos Viewer and Table2Net …

Gas Measurement Device, Megan C. Frost, Weilue He

Michigan Tech Patents

A device including a first chamber, a second chamber, and a membrane permeable to neutral gases but impermeable to water that is positioned between the first chamber and the second chamber. The membrane includes a first layer including PVDF and PDMS, and the PVDF has a plurality of pores at least partially filled with at least some of the PDMS.

Clinical Evaluation Of Respiratory Rate Measurements On Copd (Male) Patients Using Wearable Inkjet-Printed Sensor, Ala'aldeen Al-Halhouli, Loiy Al-Ghussain, Osama Khallouf, Alexander Rabadi, Jafar Alawadi, Haipeng Liu, Khaled Al Oweidat, Fei Chen, Dingchang Zheng

Mechanical Engineering Graduate Research

Introduction: Chronic Obstructive Pulmonary Disease (COPD) is a progressive disease that causes long-term breathing problems. The reliable monitoring of respiratory rate (RR) is very important for the treatment and management of COPD. Based on inkjet printing technology, we have developed a stretchable and wearable sensor that can accurately measure RR on normal subjects. Currently, there is a lack of comprehensive evaluation of stretchable sensors in the monitoring of RR on COPD patients. We aimed to investigate the measurement accuracy of our sensor on COPD patients. Methodology: Thirty-five patients (Mean ± SD of age: 55.25 ± 13.76 years) in different stages …

Liposomal Delivery Of Remdesivir For Localized And Targeted Treatment Of Covid-19, Anupama Melam

McKelvey School of Engineering Graduate Student Theses & Dissertations

Liposomal delivery of Remdesivir for localized and targeted treatment of COVID-19

COVID-19 is a serious, and in many cases lethal, disease that is caused by infection of the upper respiratory tract by the novel betacoronavirus, SARS-Cov-2 virus. This disease has a very high mortality rate and has affected the world in a global pandemic. SARS-Cov-2 binds to the ACE2 receptor via the receptor-binding domain (RBD) in the S protein. After this, the virus fuses with the cell membrane by the formation of a six-helix bundle. Thus, the S protein plays a major role in ensuring that the virus attaches to …

Development Of Artificial Neural Network Models For Predicting Lipid Profile Using Smartmf Electrical Parameters, Ahmad Zulkhairi Zulkefl

Student Works (2020-2029)

This research project aims in the development of artificial neural network (ANN) to classify lipid profile parameters; total cholesterol (TC), triglycerides (TG), high density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) by utilizing a non-invasive bioelectrical impedance analysis (BIA) device (SmartMF). Data were obtained from volunteer patients requiring lipid profile testing at the primary care department of University Malaya Medical Centre (UMMC). The data were divided into two categories for each lipid profile parameters, normal and abnormal. Statistical analysis including T-Test and logistic regression analysis for the bioelectrical parameters were employed to understand the data and determine suitable predictors …

Special Issue On Professor John M. Tarbell’S Contribution To Cardiovascular Engineering, Hanjoong Jo, Keefe Manning, John M. Tarbell

Publications and Research

No abstract provided.

Electrical Double Layer In Nanopores For Detection And Identification Of Molecules And Submolecular Units, Guigen Zhang, Samuel Bearden

Biomedical Engineering Faculty Patents

Systems for detecting analytes in electrical double layer nanopore devices and methods of use are provided.

In Vivo Optical Metabolic Imaging Of Long-Chain Fatty Acid Uptake In Orthotopic Models Of Triple-Negative Breast Cancer, Megan C. Madonna, Joy E. Duer, Joyce V. Lee, Jeremy Williams, Baris Avsaroglu, Caigang Zhu, Riley Deutsch, Roujia Wang, Brian T. Crouch, Matthew D. Hirschey, Andrei Goga, Nirmala Ramanujam

Biomedical Engineering Faculty Publications

Targeting a tumor’s metabolic dependencies is a clinically actionable therapeutic approach; however, identifying subtypes of tumors likely to respond remains difficult. The use of lipids as a nutrient source is of particular importance, especially in breast cancer. Imaging techniques offer the opportunity to quantify nutrient use in preclinical tumor models to guide development of new drugs that restrict uptake or utilization of these nutrients. We describe a fast and dynamic approach to image fatty acid uptake in vivo and demonstrate its relevance to study both tumor metabolic reprogramming directly, as well as the effectiveness of drugs targeting lipid metabolism. Specifically, …

Viability And Application Of Mounting Personal Pid Voc Sensors To Small Unmanned Aircraft Systems, Cheryl Lynn Marcham, Scott Burgess, Joseph Cerreta, Patti J. Clark, James P. Solti, Brandon Breault, Joshua G. Marcham

Publications

Using a UAS-mounted sensor to allow for a rapid response to areas that may be difficult to reach or potentially dangerous to human health can increase the situational awareness of first responders of an aircraft crash site through the remote detection, identification, and quantification of airborne hazardous materials. The primary purpose of this research was to evaluate the remote sensing viability and application of integrating existing commercial-off-the-shelf (COTS) sensors with small unmanned aircraft system (UAS) technology to detect potentially hazardous airborne contaminants in emergency leak or spill response situations. By mounting the personal photoionization detector (PID) with volatile organic compound …

Removal Of Selected Organic Pollutants In Landfill Leachate Using Natural Coagulant From Dillenia Indica Seed Extract, Aziz Ahmed

Student Works (2020-2029)

This study is aimed to identify and characterise novel green coagulant from Dillenia indica seed extracts for the removal of selected persistent organic pollutants (POPs) in landfill leachate using coagulation-flocculation process. The removal efficacy of D. indica seed extracts was compared with commercially available coagulants namely Locust Bean Gum (LBG) and alum. Additionally, it focused on the optimisation of the variables of the coagulation-flocculation process such as coagulants dosage, pH and mixing speed for POPs removal. The functional groups, morphological behaviour and surface area of the dried flocs and samples were analysed using Fourier transform infrared (FTIR), Scanning Electron Microscopy …

Exposing Nuclear Power Plants, Sophia Austin

Copley Library Undergraduate Research Awards

This paper will begin by outlining the eco-justice topic of nuclear power and its resulting nuclear waste, and then move on to examining and making claims about the justice (distributive, procedural, and recognition-based), evidence, and process behind the development and decommissioning of these plants. Through this, we will discover historical and present ties to racism - especially as we explore the relationship between nuclear power and the white racial frame, resulting in the objectification, oppression, and suppression of the voices of Indigenous communities and people of color throughout history and into the present moment. After addressing and reflecting on many …

2021 Civil And Environmental Engineering Department News, Department Of Civil And Environmental Engineering, Michigan Technological University

Department of Civil, Environmental, and Geospatial Engineering Newsletters

Table of Contents

• CEEPAC
• Great Lakes Models
• Wastewater Treatment
• Enterprise
• Outreach
• Rail Program
• Alumni Feature
• Lifetime Giving

Pulse Decay Thermal Conductivity Device, Matthew Schrenk

All Undergraduate Projects

Currently, there are several ways in which thermal conductivity can be calculated or assessed on a given material. However, with each method of testing comes potential limitations such as size, material state, complexity, and time. The goal of this study was to develop a pulse heated thermistor that would reduce all four limitations, thus provide precise and timely results regardless of the material state and size. A thermistor is resistor which changes resistance in accordance to temperature. To achieve the design, heat transfer and electrical methods were applied. As with all resistors, heat is dissipated across the element and released …

Applying Model Approaches In Non-Model Systems: A Review And Case Study On Coral Cell Culture, Liza M. Roger, Hannah Reich, Evan Lawrence, Shuaifeng Li, Whitney Vizgaudis, Nathan Brenner, Lokender Kumar, Judith Klein-Seetharaman, Jinkyu Yang, Hollie M. Putnam, Nastassja Lewinski

Chemical and Life Science Engineering Publications

Model systems approaches search for commonality in patterns underlying biological diversity and complexity led by common evolutionary paths. The success of the approach does not rest on the species chosen but on the scalability of the model and methods used to develop the model and engage research. Fine-tuning approaches to improve coral cell cultures will provide a robust platform for studying symbiosis breakdown, the calcification mechanism and its disruption, protein interactions, micronutrient transport/exchange, and the toxicity of nanoparticles, among other key biological aspects, with the added advantage of minimizing the ethical conundrum of repeated testing on ecologically threatened organisms. The …

Machine Assisted Experimentation Of Extrusion-Based Bioprinting Systems, Shuyu Tian, Rory Stevens, Bridget T. Mcinnes, Nastassja Lewinski

Chemical and Life Science Engineering Publications

Optimization of extrusion-based bioprinting (EBB) parameters have been systematically conducted through experimentation. However, the process is time- and resource-intensive and not easily translatable to other laboratories. This study approaches EBB parameter optimization through machine learning (ML) models trained using data collected from the published literature. We investigated regression-based and classification-based ML models and their abilities to predict printing outcomes of cell viability and filament diameter for cell-containing alginate and gelatin composite bioinks. In addition, we interrogated if regression-based models can predict suitable extrusion pressure given the desired cell viability when keeping other experimental parameters constant. We also compared models trained …

Hybrid Modelling For Stroke Care: Review And Suggestions Of New Approaches For Risk Assessment And Simulation Of Scenarios, Tilda Herrgårdh, Vince I. Madai, John Kelleher, Rasmus Magnusson, Mika Gustafsson, Lili Milani, Peter Gennemark, Gunnar Cedersund

Articles

Stroke is an example of a complex and multi-factorial disease involving multiple organs, timescales, and disease mechanisms. To deal with this complexity, and to realize Precision Medicine of stroke, mathematical models are needed. Such approaches include: 1) machine learning, 2) bioinformatic network models, and 3) mechanistic models. Since these three approaches have complementary strengths and weaknesses, a hybrid modelling approach combining them would be the most beneficial. However, no concrete approach ready to be implemented for a specific disease has been presented to date. In this paper, we both review the strengths and weaknesses of the three approaches, and propose …

The U-Net-Based Active Learning Framework For Enhancing Cancer Immunotherapy, Vishwanshi Joshi

Theses, Dissertations and Capstones

Breast cancer is the most common cancer in the world. According to the U.S. Breast Cancer Statistics, about 281,000 new cases of invasive breast cancer are expected to be diagnosed in 2021 (Smith et al., 2019). The death rate of breast cancer is higher than any other cancer type. Early detection and treatment of breast cancer have been challenging over the last few decades. Meanwhile, deep learning algorithms using Convolutional Neural Networks to segment images have achieved considerable success in recent years. These algorithms have continued to assist in exploring the quantitative measurement of cancer cells in the tumor microenvironment. …

A Water Quality And Contaminant Source Assessment Of Arbuckle Creek In Fayette County, West Virginia, Sarah Ashby Simonton

Theses, Dissertations and Capstones

Arbuckle Creek, located in Minden, West Virginia, is a stream that runs through Oak Hill, WV and is characterized by the presence of the Oak Hill Wastewater Treatment Plant and the history of the contamination of polychlorinated biphenyl (PCBs) from the copious amount of contamination from the Shaffer Equipment Site and the pollution from mining completed in the area throughout the 1900’s. In order to assess the reaches of the current water quality, samples were collected and assessed for benthic macroinvertebrates, water parameters, benthic algae, and habitat. This was accomplished using the West Virginia Department of Environmental Protection (WVDEP) agency’s …

Nmr Metabolomics For Optimizing Cell-Free Protein Synthesis, Angela M. Campo

Browse all Theses and Dissertations

Cell-Free Protein Synthesis (CFPS) has been utilized by biochemists to produce a variety of chemicals and therapeutics. While CFPS has spawned research in the biochemistry and medical communities, there are still unknown issues with interlaboratory variability with the technique. This work explored the black box nature of CFPS reactions by analyzing the CFPS reactions in situ with Nuclear Magnetic Resonance (NMR) spectroscopy. Aim 1 developed the protocol for conducting NMR experiments on E. coli cell-free reactions as well as a data analysis pipeline. This was accomplished with 1H NMR, capturing metabolite changes over time. The 1D NOESY experiment proved to …

Multifactorial Media Analysis Via Design Of Experiment For Type Ii Collagen In Primary Rabbit Chondrocytes, Javier A. Velez Toro

Honors Undergraduate Theses

Osteoarthritis is a prevalent disease that affects the articular cartilage of the joints. Millions of people suffer worldwide and it is a major cause of disability in the United States. Current research for treatments of osteoarthritis are studying tissue-engineered cartilage in vitro generated by articular chondrocytes. A challenge faced in vitro for cartilage tissue engineering is the failure of chondrocytes to produce adequate expression of type II collagen. Surprisingly, the media commonly used in vitro lacks 14 vitamins and minerals present in the physiological environment of chondrocytes. Therefore, studying the interactions between micronutrients and chondrocytes may help in potentially increasing …

Nebraska Summary: S1150a Fendt 1050, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Aps March Meeting 2021 (Online) Updates On Scientific Research During Pandemic Times, Vianney Gimenez-Pinto

Title III Professional Development Reports

While the ongoing global pandemic continues to affect our everyday lives, researchers in Science, Technology, Engineering and Math found a way to come together at the American Physical Society (APS) March Meeting 2021. The conference was online-only and had more than 11,000 registered attendants who actively participated in the program during March 14- 19, 2021.

Application Of Analogical Reasoning For Use In Visual Knowledge Extraction, Kara Lian Combs

Browse all Theses and Dissertations

There is a continual push to make Artificial Intelligence (AI) as human-like as possible; however, this is a difficult task because of its inability to learn beyond its current comprehension. Analogical reasoning (AR) has been proposed as one method to achieve this goal. Current literature lacks a technical comparison on psychologically-inspired and natural-language-processing-produced AR algorithms with consistent metrics on multiple-choice word-based analogy problems. Assessment is based on “correctness” and “goodness” metrics. There is not a one-size-fits-all algorithm for all textual problems. As contribution in visual AR, a convolutional neural network (CNN) is integrated with the AR vector space model, Global …