Engineering Commons^™

The Santa Clara, 2023-02-17, Santa Clara University

The Santa Clara

No abstract provided.

Deutj: An Imagej Plugin For Improved Automatic Masking And Segmentation Of Images From Confocal Microscopy, Sunny Cui

Independent Student Projects and Publications

Due to advances in microscopic imaging, there are a plethora of biological molecules that can now be tagged and subsequentially imaged from almost any cell, organism, or tissue. However, the ability of software to analyze these images remains to be a challenge. ImageJ is open source software that allows for the processing of these images, but faces challenges when dealing with images that show weak contrast between objects of interest and background. DeutJ is an ImageJ plugin that color corrects and brightness corrects gradients that inhibit segmentation in confocal microscopy images. It can analyze hundreds of images from a given …

Graphene-Conductive Polymer-Based Electrochemical Sensor For Dopamine Detection, Dipannita Ghosh, Md Ashiqur Rahman, Ali Ashraf, Nazmul Islam

Electrical and Computer Engineering Faculty Publications

The central nervous system's (CNS) dopaminergic system dysfunction has been linked to neurological illnesses like schizophrenia and Parkinson's disease. As a result, sensitive and selective detection of dopamine is critical for the early diagnosis of illnesses associated with aberrant dopamine levels. In this research, we have investigated the performance of electrochemical screen-printed sensors for different concentrations of dopamine detection using graphene-based conductive PEDOT: PSS(G-PEDOT: PSS) and Polyaniline(GPANI) inks on the working electrode and compared the sensitivity. SEM characterization technique has been performed to visualize the microstructures of the proposed inks. We have investigated cyclic voltammetry (CV) electrochemical techniques with ferri/ferrocyanide …

Formulation Of Encapsulated Nanoparticles Of Leek Extract As Antimicrobial And Anticancer Agent, Rawan Hassan Mohamed Elghanam

Theses and Dissertations

Leek extract (LEK) has broad therapeutic activity. However, plant extract use has many drawbacks, which could be resolved using nanocarriers. The purpose of this research work was to prepare chitosan nanoparticles (CS NPs) encapsulating LEK and investigate their antioxidant, antimicrobial, and anticancer activity. Gas chromatography-mass spectroscopy was used to determine the LEK components. The CS-LEK NPs were produced by tripolyphosphate (TPP) crosslinking with chitosan (CS) the ionic gelation methodology. The particle size was 331 nm, zeta potential (ZP) was 28.9 mv, polydispersity index (PDI) was 0.4, encapsulation efficiency (EE) was 65.6%, and loading capacity (LC) was 28.8 % of the …

Session 12: Active Learning To Minimize The Possible Risk From Future Epidemics, Kc Santosh

SDSU Data Science Symposium

In medical imaging informatics, for any future epidemics (e.g., Covid-19), deep learning (DL) models are of no use as they require a large dataset as they take months and even years to collect enough data (with annotations). In such a context, active learning (or human/expert-in-the-loop) is the must, where a machine can learn from the first day with minimum possible labeled data. In unsupervised learning, we propose to build pre-trained DL models that iteratively learn independently over time, where human/expert intervenes only when it makes mistakes and for only a limited data. In our work, deep features are used to …

2d Respiratory Sound Analysis To Detect Lung Abnormalities, Rafia Sharmin Alice, Kc Santosh

SDSU Data Science Symposium

Abstract. In this paper, we analyze deep visual features from 2D data representation(s) of the respiratory sound to detect evidence of lung abnormalities. The primary motivation behind this is that visual cues are more important in decision-making than raw data (lung sound). Early detection and prompt treatments are essential for any future possible respiratory disorders, and respiratory sound is proven to be one of the biomarkers. In contrast to state-of-the-art approaches, we aim at understanding/analyzing visual features using our Convolutional Neural Networks (CNN) tailored Deep Learning Models, where we consider all possible 2D data such as Spectrogram, Mel-frequency Cepstral Coefficients …

Therapeutic Options For Covid-19: Drug Repurposing Of Serine Protease Inhibitor Against Tmprss2, Mohammad Wildan Abiyyi, Surya Dwira, Arleni Bustami, Linda Erlina

Indonesian Journal of Medical Chemistry and Bioinformatics

The SARS-Coronavirus 2 (SARS-CoV-2) outbreak is a serious global public health threat. Researchers around the world are conducting mass research to control this epidemic, starting from the discovery of vaccines, to new drugs that have specific activities as antivirals. Drug repurposing is a potential method of using drugs with known activity for reuse as COVID-19 therapy. This method has the advantage that it can reduce costs and also the duration in the development of potential drugs. The initial step in drug repurposing can be done computationally to determine the effectiveness and specificity of the drug on the target protein. Molecular …

Virtual Screening On Indonesian Herbal Compounds As Sars-Cov-2 Spike (S2) Glycoprotein Inhibitors: Pharmacophore Modelling & Molecular Docking Approaches, Syailendra Karuna Sugito, Artha Uli Cristina, Putri Saskia Harimurti, Gabriella Regita Cendani, Fauzi Azhar Insani, Linda Erlina, Rafika Indah Paramita, Fadilah Fadilah

Indonesian Journal of Medical Chemistry and Bioinformatics

Background: There are still no specific treatments for coronavirus disease (COVID-19) until present days. Several studies have been conducted to determine whether herbal medicine can be an option to be used as a definitive medicine for COVID-19. S2 subunit of spike protein which is responsible for SARS-CoV-2 entry to the host cell, is a potential drug target to inhibit the viral infection. In this study, we aimed to find some compounds from the HerbalDB database that have potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor.

Methods: The 6LXT protein was used as the target protein. The procedure in this study consisted …

Supporting Compliance Of Occupational Safety And Health Requirements - European Labour Inspection Systems Of Sanctions And Standardised Measures, Victor Hrymak

Articles

European legislation for occupational safety and health (OSH) is based on the prevention of accidents and ill health. Apart from European directives, all Member States have national laws and strategies and expect enterprises to implement this preventative ethos, and thereby ensure adequate performance in OSH. Labour Inspectorates monitor and if necessary enforce these laws by deploying individual Labour Inspectors to chosen enterprises. If workplace safety and health conditions are found to be substandard, Labour Inspectors are expected to improve the situation using persuasion and, if necessary, their authority to compel enterprises through specific sanction powers. Bruhn (2009) describes this interaction …

Process Intensification Strategies For Green Solvent Mediated Biomass Pretreatment, Ahamed Ullah, Yuxuan Zhang, Can Liu, Qi Qiao, Qing Shao, Jian Shi

Markey Cancer Center Faculty Publications

Demonstrated to be highly effective for lignocellulosic biomass pretreatment, deep eutectic solvent (DES) has attracted increasing attention owing to its advantages of simple synthesis, relatively low chemical cost, and better biocompatibility as compared to certain ionic liquids. Here we provide a critical review of the status of the design/selection of DES for the pretreatment of biomass feedstocks with an emphasis on the process intensification strategies: 1) integration of microwave, ultrasound, and high solid extrusion for pretreating biomass, 2) one-pot DES pretreatment, enzymatic hydrolysis, and fermentation, 3) strategies for DES recycling and product recovery; and 4) recent progress on molecular simulations …

Mathematical Modeling Of Microscale Biology: Ion Pairing, Spatially Varying Permittivity, And Born Energy In Glycosaminoglycan Brushes, William J. Ceely, Marina Chugunova, Ali Nadim, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

Biological macromolecules including nucleic acids, proteins, and glycosaminoglycans are typically anionic and can span domains of up to hundreds of nanometers and even micron length scales. The structures exist in crowded environments that are dominated by multivalent electrostatic interactions that can be modeled using mean-field continuum approaches that represent underlying molecular nanoscale biophysics. We develop such models for glycosaminoglycan brushes using steady state modified Poisson-Boltzmann models that incorporate important ion-specific (Hofmeister) effects. The results quantify how electroneutrality is attained through ion electrophoresis, spatially varying permittivity hydration forces, and ion-specific pairing. Brush-salt interfacial profiles of the electrostatic potential as well as …

Gasdermin D Deficiency In Vascular Smooth Muscle Cells Ameliorates Abdominal Aortic Aneurysm Through Reducing Putrescine Synthesis, Jianing Gao, Yanghui Chen, Huiqing Wang, Xin Li, Ke Li, Yangkai Xu, Xianwei Xie, Yansong Guo, Nana Yang, Xinhua Zhang, Dong Ma, Hong S. Lu, Ying H. Shen, Yong Liu, Jifeng Zhang, Y. Eugene Chen, Alan Daugherty, Dao Wen Wang, Lemin Zheng

Saha Cardiovascular Research Center Faculty Publications

Abdominal aortic aneurysm (AAA) is a common vascular disease associated with significant phenotypic alterations in vascular smooth muscle cells (VSMCs). Gasdermin D (GSDMD) is a pore-forming effector of pyroptosis. In this study, the role of VSMC-specific GSDMD in the phenotypic alteration of VSMCs and AAA formation is determined. Single-cell transcriptome analyses reveal Gsdmd upregulation in aortic VSMCs in angiotensin (Ang) II-induced AAA. VSMC-specific Gsdmd deletion ameliorates Ang II-induced AAA in apolipoprotein E (ApoE)−/− mice. Using untargeted metabolomic analysis, it is found that putrescine is significantly reduced in the plasma and aortic tissues of VSMC-specific GSDMD deficient mice. High putrescine levels …

Salt Doping Of Hyaluronic Acid Glycopolymer Biocondensates, James D. Sterling, Lu Fu, Kenisha Pudun, Shenda Baker, Megan Lord, Henry E. Riggs

Business and Information Technology Faculty Research & Creative Works

Biocondensates are largely studied with regard to intracellular components, while recognition of the formation of extracellular biocondensates are emerging, such as for cell surface heparan sulfate binding with basic fibroblast growth factor. This study analyzed the formation of biocondensates in vitro between the ubiquitous extracellular component, hyaluronan an anionic glycosaminoglycan, and cationic derivitized polyglucosamines known to bind to mucosal interfaces. The effect of molecular weight and net charge ratio was studied using a combination of microscopy, turbidity, laser diffraction particle sizing and zeta potential measurements. These analyses revealed that molecular weight affected the ability to form biocondensates while the surface …

Lignin Derived Hydrophobic Deep Eutectic Solvents As Sustainable Extractants, Yuxuan Zhang, Qi Qiao, Usman Lame Abbas, Jun Liu, Yi Zheng, Christopher Jones, Qing Shao, Jian Shi

Markey Cancer Center Faculty Publications

Solvent innovation has become a central task for improving the sustainability of chemical processes1. Deep eutectic solvents (DESs) emerge as environmentally friendly alternatives to toxic and volatile organic solvents. One appealing aspect for DESs is that they can be synthesized using naturally occurring compounds from biomass. Herein, we prepared novel hydrophobic DESs based on lignin derivatives and characterized their physicochemical properties including density, viscosity, and thermal behavior. The results showed that five lignin-derived hydrophobic DESs made from menthol, thymol, and 2,6-dimethoxyphenol were promising as green solvents due to their low viscosities and environmentally friendly constituents. To evaluate the potential application …

Electrochemical Sensors And Biosensors Of Biomarkers And Therapeutic Agents Detection, Mahmoud Abdelhakem

Theses and Dissertations

Electrochemical sensing is a pioneering tool amongst all other sensing techniques even though it had been started in the early 20th century. Due to their cost efficacy, accuracy, and real-time measurement, electrochemical sensing has been utilized in a vast of biomedical applications in therapeutic drug monitoring and biomarker detection. This thesis work concerned the monitoring of three therapeutic agents in spiked plasma, urine, dosage form, and interstitial skin fluid with high specificity and accuracy. Two of our sensing platforms utilized nanomaterials for sensing (sensors) of Cilostazol and Velpatasvir utilizing α-MnO2-V2O5 (metal oxide nanorods) and NH2- MIL-53 (Aluminum-based metal organic frameworks), …

A Cohort Retrospective Study Of Framingham Score And Ecg Abnormality Among Coal Mining Workers, Faizal Ablansah Anandita, Isman Firdaus, Rino Alvani Gani, Retno Asti Werdhani, Muchtaruddin Mansyur

Occupational and Environmental Medicine Journal of Indonesia

Introduction. ECG is widely used for detecting cardiovascular disease in coal mine worker’s medical check-up. As the study has proven, coal mine workers have a double cardiovascular risk from their workplace hazard and their own medical risks as individuals. An early detection and risk assessment method is needed to predict ECG abnormalities in the future. This study will analyze the relationship between ECG abnormality and Framingham Risk Score on coal mine workers’. Methods. We examine ECG result from medical check-up of male coal worker during 2018 and 2021. Using Minnesota Code, we determine ECG abnormality categories in the 2021 result, …

Potential Of Biduri Fiber (Calotropis Gigantea) As Material For Oil Spill Absorbent, Anne Sukmawati, Wulan Septiani

Journal of Materials Exploration and Findings

Biduri fiber (Calotropis gigantea) is a natural hollow fiber with hydrophobic and oleophilic properties potentially used as oil spilled sorbent from seawater. This study aims to determine the absorption capacity and efficiency of the Biduri fiber and membrane to fuel oil. Measurement of oil absorption to seawater was carried out at various fiber weights (0.5-1.5 g), fiber composition (50-95%), contact time (10-90 minutes), temperature (30 and 50°C), and compared with commercial products. The results showed that the fiber weight variation of 0.5-1.5 g has an average absorption efficiency of 96.67%, and the highest absorption was obtained in a weight of …

Intro To Primary Sources, Katie Strand, Jen Kirk, Dan Davis, Lara Petersen

All E-Learning Resources

Attention: As of 2026 updated versions of this item will no longer be available on Digital Commons. Please contact [email protected] for more information.

The Identifying Primary Sources tutorial teaches students how they find, evaluate, and use primary sources in their own research. Along the way, they'll learn about some great places to start researching when looking for primary sources.

Current Topics In Technology-Enabled Stroke Rehabilitation And Reintegration: A Scoping Review And Content Analysis, Katryna Cisek

Articles

Background. There is a worldwide health crisis stemming from the rising incidence of various debilitating chronic diseases, with stroke as a leading contributor. Chronic stroke management encompasses rehabilitation and reintegration, and can require decades of personalized medicine and care. Information technology (IT) tools have the potential to support individuals managing chronic stroke symptoms. Objectives. This scoping review identifies prevalent topics and concepts in research literature on IT technology for stroke rehabilitation and reintegration, utilizing content analysis, based on topic modelling techniques from natural language processing to identify gaps in this literature. Eligibility Criteria. Our methodological search initially identified over 14,000 …

The Future Of Clinical Trials Of Myopia Control, Mark A. Bullimore, Noel A. Brennan, Daniel I. Flintcroft

Articles

In the field of myopia control, effective optical or pharmaceutical therapies are now available to patients in many markets. This creates challenges for the conduct of placebo-controlled, randomised clinical trials, including ethics, recruitment, retention, selective loss of faster progressors and non-protocol treatments: 1. Ethics: It is valid to question whether withholding treatment in control subjects is ethical. 2. Recruitment: Availability of treatments is making recruitment into clinical trials more difficult. 3. Retention: If masking is not possible, parents may immediately withdraw their child if randomised to no treatment. 4. Selective loss: Withdrawal of fast progressors in the control group leading …

Monitoring And Modelling The Glutamine Metabolic Pathway: A Review And Future Perspectives, Zohreh Mirveis, Paul Cahill, Nitin Patel, Hugh Byrne

Articles

In this review, the contribution of NMR to the metabolomics field will be discussed—particularly as it relates to cancer and drug metabolism research. An overview of the typical NMR metabolomic experiment will be presented while emphasizing important caveats ranging from experimental design to data interpretation.

Machine-Learning-Based Head Impact Subtyping Based On The Spectral Densities Of The Measurable Head Kinematics, Xianghao Zhan, Yiheng Li, Yuzhe Liu, Nicholas J. Cecchi, Samuel J. Raymond, Zhou Zhou, Hossein Vahid Alizadeh, Jesse Ruan, Saeed Barbat, Stephen Tiernan, Olivier Gevaert, Michael M. Zeineh, Gerald A. Grant, David B. Camarillo

Articles

Traumatic brain injury can be caused by head impacts, but many brain injury risk estimation models are not equally accurate across the variety of impacts that patients may undergo and the characteristics of different types of impacts are not well studied. We investigated the spectral characteristics of different head impact types with kinematics classification. Methods: Data was analyzed from 3,262 head impacts from lab reconstruction, American football, mixed martial arts, and publicly available car crash data. A random forest classifier with spectral densities of linear acceleration and angular velocity was built to classify head impact types (e.g., football, car crash, …

Management Of Patients Treated With Antithrombotic Drugs In Dentistry: Comparison Of Sfco And Baos Recommendations, Meryem Lahlou, Yousef Naji, Ossama Nabih, Ihsane Ben Yahya

Health Sciences

Background Patients on antithrombotic drugs are at risk of thrombosis; when prescribed these medications they develop a risk of haemorrhage. To our knowledge, there is no published global consensus on the management of these patients and only expert panels guidelines exist. Objectives The aims of this study were to (1) compare the clinical guidelines issued by the French Society of Oral Surgery (SFCO) and the clinical guidelines issued by the British Association of Oral Surgery (BAOS), and (2) to summarize the guidelines recommendations. Methods This article is a descriptive comparative review based on published clinical guidelines issued by the French …

Advanced Microstructural Characterization Of Functionally Graded Dental Ceramic Material For Materials-Informed Finishing, Angani Vigneswaran

Theses and Dissertations--Manufacturing Systems Engineering

Yttria-stabilized tetragonal zirconia polycrystal (Y-TZP) has gained popularity as the choice of material for dental prosthetics. Ivoclar Vivadent’s IPS e.max ZirCAD Prime dental ceramic incorporates a unique gradient technology that varies the yttria content over the thickness of the material. The top layer is composed of 5Y-TZP which is desired for its optical properties while the bottom layer is composed of a much stronger 3Y-TZP. In between the two layers, 5Y-TZP and 3Y-TZP are mixed to form a transition layer. Varying the amount of yttria allows for more esthetically pleasing translucency in the visible areas of the restoration without compromising …

Gamelan Gong Directivity Dataset, Samuel D. Bellows, Dallin T. Harwood, Kent L. Gee, Micah R. Shepherd

Directivity

No abstract provided.

Forecasting Covid-19 Cases Using Dynamic Time Warping And Incremental Machine Learning Methods, Luis Miralles-Pechuán, Ankit Kumar, Andres L. Suarez-Cetrulo

Articles

The investment of time and resources for developing better strategies is key to dealing with future pandemics. In this work, we recreated the situation of COVID-19 across the year 2020, when the pandemic started spreading worldwide. We conducted experiments to predict the coronavirus cases for the 50 countries with the most cases during 2020. We compared the performance of state-of-the-art machine learning algorithms, such as long-short-term memory networks, against that of online incremental machine learning algorithms. To find the best strategy, we performed experiments to test three different approaches. In the first approach (single-country), we trained each model using data …

Artificial Intelligence In Dentistry : Knowledge And Perceptions Of Moroccan Students, Manal Elhijazi, Ihsane Benyahya

Health Sciences

Introduction: Artificial intelligence (AI) is a revolution in education, research and health. The aim of this study is to assess the views and perceptions of dental students regarding artificial intelligence and its impact on their future professional practice. Methods: A voluntary anonymous e-questionnaire was sent to all 4th and 5th year dental students of the Faculty of Dentistry after receiving a course on artificial intelligence. The questionnaire consisted of sections to assess students' knowledge of artificial intelligence and its possible applications in dentistry as well as ethical considerations. Statistical analysis of the data was carried out using SPSS version 23 …

Prepubertal Periodontitis In Children: For An Adequate Diagnosis And Optimal Care, F.Z. El Mouatarif, S. Chemlali, M. Hamza, J. Kissa, S. El Arabi

Health Sciences

Prepubertal periodontitis (PP) is a rare and rapid progressive condition found a young cohort of patients that results in destruction of the periodontal support of the primary dentition. Its generalized form, prepubertal periodontitis is often associated with a significant gingival tissue inflammation and fast bone loss with attachment loss leading to the tooth loss. The localized form of PP is characterized by a much more discreet inflammation and slow evolution. It can be associated with a known underlying systemic disease or may occur as part of a recognized syndrome or as an isolated finding. Different treatment modalities can be used …

Biological Parameters And The Histological Response In Rectal Cancer Treated By Neoadjuvant Chemoradiotherapy: A Moroccan Cohort, A. Naim, N. Bouanani, F. Safini, S. Mounaime, Soumaya Rafii, L. Lachker, F. Guessous, M. Khaliss, N. Tawfiq, A. Badou

Health Sciences

Introduction: Multimodal management of rectal cancer, combining neoadjuvant Radio chemotherapy followed by total Mesorectal therapy (TME), has been shown to improve locoregional control. However, the histological response is variable independently of the initial tumor stage. Some recent data suggest the usefulness of the lymphocyte-monocyte ratio (LMR), neutrophil-lymphocyte ratio (NLR), and platelet-lymphocyte ratio (PLR) in predicting the histological response to neoadjuvant therapy. This study aimed to investigate the correlation between the complete histological response (pCR) after neoadjuvant radio chemotherapy and biological parameters (LMR, NLR and PLR) in rectal cancer patients.

PATIENTS AND METHODS: This retrospective study was conducted in three Moroccan …

Third Arkansas Record Of Mountain Bluebird (Sialia Currucoides), With Notes On Habitat And Behavior, G. R. Graves

Journal of the Arkansas Academy of Science

Mountain Bluebird (Sialia currucoides) breeds in western North America and winters east to the Great Plains from Nebraska to Texas (Johnson and Dawson 2020). Vagrants are occasionally reported in eastern North America, mostly from November through March, but relatively few wintering records have been documented in the lower Mississippi Valley east of 96° W longitude and south of 37° N latitude.