Life Sciences Commons^™

The Impact Framework And Implementation For Accessible In Silico Clinical Phenotyping In The Digital Era, Kurt Miller, Liwei Wang, Kirk E Roberts, Steven D Bedrick, William R Hersh, Hongfang Liu

Faculty, Staff and Student Publications

Clinical phenotyping is often a foundational requirement for obtaining datasets necessary for the development of digital health applications. Traditionally done via manual abstraction, this task is often a bottleneck in development due to time and cost requirements, therefore raising significant interest in accomplishing this task via in-silico means. Nevertheless, current in-silico phenotyping development tends to be focused on a single phenotyping task resulting in a dearth of reusable tools supporting cross-task generalizable in-silico phenotyping. In addition, in-silico phenotyping remains largely inaccessible for a substantial portion of potentially interested users. Here, we highlight the barriers to the usage of in-silico phenotyping …

Non-Invasive Arterial Blood Pressure Measurement And Spo2 Estimation Using Ppg Signal: A Deep Learning Framework, Dulin Wang, Wentao Li, Sean I Savitz, Xiaoqian Jiang, Shayan Shams

Faculty, Staff and Student Publications

BACKGROUND: Monitoring blood pressure and peripheral capillary oxygen saturation plays a crucial role in healthcare management for patients with chronic diseases, especially hypertension and vascular disease. However, current blood pressure measurement methods have intrinsic limitations; for instance, arterial blood pressure is measured by inserting a catheter in the artery causing discomfort and infection.

METHOD: Photoplethysmogram (PPG) signals can be collected via non-invasive devices, and therefore have stimulated researchers' interest in exploring blood pressure estimation using machine learning and PPG signals as a non-invasive alternative. In this paper, we propose a Transformer-based deep learning architecture that utilizes PPG signals to conduct …

Clinical And Functional Correlates Of Parkinsonism In A Population-Based Sample Of Individuals Aged 75 +: The Pietà Study, Thiago Cardoso Vale, Francisco Eduardo Costa Cardoso, Danilo Jorge Da Silva, Elisa De Paula Franca Resende, Débora Palma Maia, Henrique Cerqueira Guimarães, Antônio Lúcio Teixeira, Paulo Caramelli, Maira Tonidandel Barbosa

Faculty, Staff and Student Publications

BACKGROUND: Parkinsonism is strongly associated with ageing, and many studies have suggested that parkinsonian signs may affect up to half of older adults and is associated with a wide range of adverse health outcomes. We compared clinical and functional characteristics of oldest-old community-dwelling individuals with parkinsonism (parkinsonian group [PG]) to individuals without parkinsonism (non-parkinsonian group [NPG].

METHODS: The Pietà study is a population-based study conducted in Caeté, southeast Brazil, involving 607 individuals aged 75 + years submitted to an extensive clinical evaluation. A subset of 65 PG individuals (61.5% women, median age of 82 years) was compared to 542 NPG …

Targeting Polyploid Giant Cancer Cells Potentiates A Therapeutic Response And Overcomes Resistance To Parp Inhibitors In Ovarian Cancer, Xudong Zhang, Jun Yao, Xiaoran Li, Na Niu, Yan Liu, Guang Peng, Anil K Sood, Jinsong Liu

Faculty, Staff and Student Publications

To understand the mechanism of acquired resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) olaparib, we induced the formation of polyploid giant cancer cells (PGCCs) in ovarian and breast cancer cell lines, high-grade serous cancer (HGSC)-derived organoids, and patient-derived xenografts (PDXs). Time-lapse tracking of ovarian cancer cells revealed that PGCCs primarily developed from endoreplication after exposure to sublethal concentrations of olaparib. PGCCs exhibited features of senescent cells but, after olaparib withdrawal, can escape senescence via restitutional multipolar endomitosis and other noncanonical modes of cell division to generate mitotically competent resistant daughter cells. The contraceptive drug mifepristone blocked PGCC formation and daughter cell …

Single-Cell Sequencing Reveals The Landscape Of The Human Brain Metastatic Microenvironment, Qianqian Song, Jimmy Ruiz, Fei Xing, Hui-Wen Lo, Lou Craddock, Lance D Miller, Stacey S O'Neill, Kounosuke Watabe, Michael D Chan, Jing Su

Faculty, Staff and Student Publications

Brain metastases is the most common intracranial tumor and account for approximately 20% of all systematic cancer cases. It is a leading cause of death in advanced-stage cancer, resulting in a five-year overall survival rate below 10%. Therefore, there is a critical need to identify effective biomarkers that can support frequent surveillance and promote efficient drug guidance in brain metastasis. Recently, the remarkable breakthroughs in single-cell RNA-sequencing (scRNA-seq) technology have advanced our insights into the tumor microenvironment (TME) at single-cell resolution, which offers the potential to unravel the metastasis-related cellular crosstalk and provides the potential for improving therapeutic effects mediated …

Genome-Wide Crispr-Cas9 Screen Analyzed By Slider Identifies Network Of Repressor Complexes That Regulate Trim24, Lalit R Patel, Sabrina A Stratton, Megan Mclaughlin, Patrick Krause, Kendra Allton, Daniela Barbosa, Michelle C Barton

Faculty, Staff and Student Publications

TRIM24 is an oncogenic chromatin reader that is frequently overexpressed in human tumors and associated with poor prognosis. However, TRIM24 is rarely mutated, duplicated, or rearranged in cancer. This raises questions about how TRIM24 is regulated and what changes in its regulation are responsible for its overexpression. Here, we perform a genome-wide CRISPR-Cas9 screen by fluorescence-activated cell sorting (FACS) that nominated 220 negative regulators and elucidated a regulatory network that includes the KAP1 corepressor, CNOT deadenylase, and GID/CTLH E3 ligase. Knocking out required components of these three complexes caused TRIM24 overexpression, confirming their negative regulation of TRIM24. Our findings …

Gold Nanoparticles For Monitoring Of Mesenchymal Stem-Cell-Loaded Bioresorbable Polymeric Wraps For Arteriovenous Fistula Maturation, Allan John R Barcena, Joy Vanessa D Perez, Jossana A Damasco, Marvin R Bernardino, Erin Marie D San Valentin, Benjamin Martin, Gino Martin Canlas, Huckie C Del Mundo, Francisco M Heralde, Rony Avritscher, Natalie Fowlkes, Richard R Bouchard, Jizhong Cheng, Steven Y Huang, Marites P Melancon

Faculty, Staff and Student Publications

Mesenchymal stem cell (MSC)-seeded polymeric perivascular wraps have been shown to enhance arteriovenous fistula (AVF) maturation. However, the wraps' radiolucency makes their placement and integrity difficult to monitor. Through electrospinning, we infused gold nanoparticles (AuNPs) into polycaprolactone (PCL) wraps to improve their radiopacity and tested whether infusion affects the previously reported beneficial effects of the wraps on the AVF's outflow vein. Sprague Dawley rat MSCs were seeded on the surface of the wraps. We then compared the effects of five AVF treatments-no perivascular wrap (i.e., control), PCL wrap, PCL + MSC wrap, PCL-Au wrap, and PCL-Au + MSC wrap-on AVF …

Differential Effects Of Bariatric Surgery And Caloric Restriction On Hepatic One-Carbon And Fatty Acid Metabolism, Arnon Haran, Michael Bergel, Doron Kleiman, Liron Hefetz, Hadar Israeli, Bella Agranovich, Rachel Ben-Haroush Schyr, Eyal Gottlieb, Danny Ben-Zvi

Faculty, Staff and Student Publications

Weight loss interventions, including dietary changes, pharmacotherapy, or bariatric surgery, prevent many of the adverse consequences of obesity, and may also confer intervention-specific benefits beyond those seen with decreased weight alone. We compared the molecular effects of different interventions on liver metabolism to understand the mechanisms underlying these benefits. Male rats on a high-fat, high-sucrose diet underwent sleeve gastrectomy (SG) or intermittent fasting with caloric restriction (IF-CR), achieving equivalent weight loss. The interventions were compared to

Blood Flow Restriction As A Potential Therapy To Restore Physical Function Following Covid-19 Infection, Isaac J. Wedig, John J. Durocher, John Mcdaniel, Steve Elmer

Michigan Tech Publications

Accumulating evidence indicates that some COVID-19 survivors display reduced muscle mass, muscle strength, and aerobic capacity, which contribute to impairments in physical function that can persist for months after the acute phase of illness. Accordingly, strategies to restore muscle mass, muscle strength, and aerobic capacity following infection are critical to mitigate the long-term consequences of COVID-19. Blood flow restriction (BFR), which involves the application of mechanical compression to the limbs, presents a promising therapy that could be utilized throughout different phases of COVID-19 illness. Specifically, we hypothesize that: 1) use of passive BFR modalities can mitigate losses of muscle mass …

A Cost-Effective And Smart Sensing Tissue-Like Testbed For Surgical Training, Lysette Zaragoza

McNair Research Journal SJSU

A low-cost tissue-like testbed with six nodes of varying stiffness was developed for surgical training to provide pressure and force feedback data through image reception to human operators. Using SolidWorks, a 3D model of the box trainer housing was created. A pad for the distribution of smartsensing nodes and microcontroller connections was designed with open spaces for the respective components. The pad was 3D-printed with PLA filament. Flat piezoelectric pressure sensors were fabricated with conductive materials and velostat sensor material. Using static and dynamic analyses, three top sensors were chosen to be used in three pressure sensing nodes. A calibration …

Understanding Our Airways: How Lung Structure And Function Is Impacted By Respiratory Infections And Immune Responses, Katherine Coll

McNair Research Journal SJSU

Understanding the underlying functions and interplaying systems that make up the respiratory system is a crucial step in the research and development of treatments for respiratory illnesses. In this literature review, I explore the complex biochemical processes that occur in the pulmonary epithelium and endothelium. As epithelial and endothelial cells serve a multitude of functions such as host protection and nutrient regulation, discussing the interplay between these cells and intercellular junctions and their immediate impact on the respiratory system is essential to understanding the impact of respiratory dysfunctions and diseases. This review further examines the different types of intercellular junctions …

The Effects Of Pain Levels On Static And Dynamic Postural Control And Visual Reliance In Chronic Ankle Instability Individuals, Minsub Oh

Theses and Dissertations

Context: Chronic ankle instability (CAI) individuals experience residual symptoms including pain, swelling, ankle instability, etc. A small majority of CAI individuals report ankle pain during daily or physical activity. Despite the known negative effects of chronic pain on neuromuscular control, there is a paucity of research exploring the specific impact of chronic pain mechanisms on altered neuromuscular control in CAI individuals. Purpose: The purpose of this study was to identify the effects of pain levels on static and dynamic postural control and visual reliance in CAI individuals. Methods: A total of 60 participants were recruited, consisting of 20 CAI individuals …

The Structural Characterization And Bioactivity Assessment Of Nonspecific Lipid Transfer Protein 1 (Nsltp1) From Caraway (Carum Carvi) Seeds, Taibah Aldakhil, Saud O. Alshammari, Bushra Siraj, Bishoy El-Aarag, Shamshad Zarina, David Salehi, Aftab Ahmed

Pharmacy Faculty Articles and Research

Background

Carum carvi (caraway) of the Apiaceae family has been used in many cultures as a cooking spice and part of the folk medicine. Previous reports primarily focus on the medicinal properties of caraway seed essential oil and the whole seeds extract. However, no effort has been made to study caraway proteins and their potential pharmacological properties, including nonspecific lipid transfer protein (nsLTP), necessitating further research. The current study aimed to characterize nonspecific lipid transfer protein 1 (nsLTP1) from caraway seed, determine its three-dimensional structure, and analyze protein–ligand complex interactions through docking studies. We also evaluated nsLTP1 in vitro cytotoxic …

Method Developments To Identify Loci And Selection Patterns Associated With Genotype By Environment Interactions In Soybean, Mary M. Happ

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

For many complex traits such as grain yield, genotype by environment (GxE) interactions are a prevalent source of phenotypic variation. Exploring the capacity of different methodologies to help describe and quantify the GxE interaction landscape for grain yield is an important step in informing plant breeders what the most viable strategies for management and exploitation of GxE may be. In this endeavor, we compared the results from multiple genome wide association studies (GWAS) that used either stability estimators as a phenotype to capture GxE variance, or directly mapped GxE in a mixed model for yield. Leading into this study, a …

Studies Of Intracellular Trafficking Of Phospholipids Triggered By Osh6, Ilham Hassoon Kadhim

Theses and Dissertations

Yeast vacuoles (mammalian lysosomes) and their closely related organelle late endosomes (LE) play a central role in anti-aging processes since they host the target of rapamycin complex 1 (TORC1). A recent study showed that the vacuolar TORC1 stimulates protein synthesis and cell growth while the late endosomal TORC1 inhibits autophagy, an anti-aging process. This raises a question as to which membrane trafficking pathways toward LE/vacuoles are critical in controlling endosomal TORC1 and anti-aging processes. Members of the family of oxysterol-binding proteins mediate non-vesicular lipid transport between membranes and contribute to longevity in different manners. We previously found that a 2-fold …

Ranchsatdb: A Genome-Wide Simple Sequence Repeat (Ssr) Markers Database Of Livestock Species For Mutant Germplasm Characterization And Improving Farm Animal Health, Naveen Duhan, Simardeep Kaur, Rakesh Kaundal

Plants, Soils and Climate Student Research

Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface …

Devoting Continuous Efforts To Innovations And Development Of Ruminant Livestock Life-Cycle Nutrition Program, Zhixiong He, Zhaomin Hu, Hongsheng Wang, Jinzhen Jiao, Xuefeng Han, Yong Liu, Shaoxun Tang, Chuanshe Zhou, Min Wang, Zhiliang Tan

Bulletin of Chinese Academy of Sciences (Chinese Version)

Ruminant livestock such as cattle and sheep can provide high-quality beef, mutton and milk, which are high-quality protein sources meeting the increasingly diverse food consumption needs for human being. Developing high-quality herbivorous animal husbandry is a concrete practice of practicing the “Greater Food” approach. The precise supply of forages and concentrates meeting the requirements of all nutrients in the whole life cycle is vital for cost saving and efficiency increasing of ruminant livestock industry, which is an important way to high-quality development. The whole life cycle nutrition is developed on the basis of traditional ruminant nutrition and new technologies made …

Mechanisms Of Fibrillar Aggregation Of The Lens Small Heat Shock Proteins, Αa- And Αb-Crystallin, Russell James Mcfarland

Dissertations and Theses

The protein αB-crystallin represents the archetypical small heat-shock protein (sHSP), and together with αA-crystallin makes up the primary chaperone system in the eye lens, where they play a critical role in maintaining proteostasis. To achieve transparency, the lens undergoes a loss of organelles and both protein turnover halts, requiring that proteins remain functional for long periods of time as they accumulate chemical damage. The α-crystallins are highly abundant in the lens to stabilize proteostasis for multiple decades. Over time though, the small heat-shock proteins become overwhelmed by a high burden of destabilized clients and their own accumulated chemical damage. Mechanistic …

Structures Of Channelrhodopsin Paralogs In Peptidiscs Explain Their Contrasting K+ And Na+ Selectivities, Takefumi Morizumi, Kyumhyuk Kim, Hai Li, Elena G Govorunova, Oleg A Sineshchekov, Lei Zheng, Ana-Nicoleta Bondar, Azam Askari, Leonid S Brown, John L Spudich, Oliver P Ernst

Faculty, Staff and Student Publications

Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K+ over Na+ in the absence of the canonical tetrameric K+ selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na+ channel with >100-fold larger Na+ to K+ permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show …

Measuring And Enhancing The Ionic Conductivity Of Chloroaluminate Electrolytes For Al-Ion Batteries, Anthony J Lucio, Iwan Sumarlan, Elena Bulmer, Igor Efimov, Stephen Viles, Christopher J Zaleski

Faculty, Staff and Student Publications

At the core of the aluminum (Al) ion battery is the liquid electrolyte, which governs the underlying chemistry. Optimizing the rheological properties of the electrolyte is critical to advance the state of the art. In the present work, the chloroaluminate electrolyte is made by reacting AlCl3 with a recently reported acetamidinium chloride (Acet-Cl) salt in an effort to make a more performant liquid electrolyte. Using AlCl3:Acet-Cl as a model electrolyte, we build on our previous work, which established a new method for extracting the ionic conductivity from fitting voltammetric data, and in this contribution, we validate the method across a …

Study Of Polytopic Membrane Protein Topological Organization As A Function Of Membrane Lipid Composition, Oleg A Sineshchekov, Ana-Nicoleta Bondar, Azam Askari, Leonid S Brown, John L Spudich, Oliver P Ernst

Faculty, Staff and Student Publications

Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K+ over Na+ in the absence of the canonical tetrameric K+ selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na+ channel with >100-fold larger Na+ to K+ permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show that K+ versus Na+ …

Asian Americans In Stem Are Not A Monolith, Zer Vue, Chia Vang, Neng Vue, Vijayvardhan Kamalumpundi, Taylor Barongan, Sunny Huang, Mein Vue, Nancy Vang, Jianqiang Shao, Coohleenann Coombes, Prasanna Katti, Kaihua Liu, Kailee Yoshimura, Michelle Biete, Dao-Fu Dai, Mark A Phillips, Richard R Behringer

Faculty, Staff and Student Publications

Despite tremendous diversity, Asian Americans in STEM are grouped and viewed as a homogeneous monolith, facing stereotypes and disparities. We propose solutions that include disaggregating the Asian American grouping and recognizing the diverse individual ethnic subgroups that comprise Americans of Asian ancestry to implement change within the STEM field.

A Novel Statistical Method For Decontaminating T-Cell Receptor Sequencing Data, Ruoxing Li, Mehmet Altan, Alexandre Reuben, Ruitao Lin, John V Heymach, Runzhe Chen, Shawna Hubert, Jianjun Zhang, Ziyi Li

Faculty, Staff and Student Publications

The T-cell receptor (TCR) repertoire is highly diverse among the population and plays an essential role in initiating multiple immune processes. TCR sequencing (TCR-seq) has been developed to profile the T cell repertoire. Similar to other high-throughput experiments, contamination can happen during several steps of TCR-seq, including sample collection, preparation and sequencing. Such contamination creates artifacts in the data, leading to inaccurate or even biased results. Most existing methods assume 'clean' TCR-seq data as the starting point with no ability to handle data contamination. Here, we develop a novel statistical model to systematically detect and remove contamination in TCR-seq data. …

Learning That Matters Is Messy: Experiments Revealing Hidden Potential In Higher Education, Ryan Derby-Talbot

Turning Toward Being: The Journal of Ontological Inquiry in Education

Why are some learning experiences so profound that they alter our worlds, whereas others don’t end up sticking at all? The author investigates this question in the context of undergraduate education, recounting several educational experiments that highlight subtle but powerful aspects of the student learning experience. By exploring a different approach to teaching a math course, an alternative framework for academic specialization instead of traditional majors, and a radical approach to designing new institutions, an encounter with the hidden, ontological dimension of learning becomes possible. Accessing the ontological experience of the learner opens up new possibilities for meaningful, deep, and …

The Effects Of Ankle Taping On Measures Of Ground Reaction Forces And Jump Height During A Sport-Specific Vertical Jump In Youth Basketball Players, Michelle Pratola, Paolo Sanzo

International Journal of Exercise Science

International Journal of Exercise Science 16(6): 898-911, 2023. The purpose of this study was to investigate the effects of ankle taping using zinc oxide tape versus no tape to measure ground reaction forces (GRF) and vertical jump height during a sport-specific vertical jump test in youth basketball players. Participants were recruited through purposive sampling and completed a basketball specific vertical jump test with and without zinc oxide tape. Mean sway velocity, 95% ellipse area, and path length were measured using the AMTI© force platform and vertical jump height using a Vertec© device. A paired t-test with a significance level of …

Crop-Livestock Diversification And Efficiency In Agriculture, Jay Parsons, Maroua Afi

Cornhusker Economics

Diversification is a familiar strategy for managing risk in agriculture. It can take several forms including growing more than one crop or operating a farm with both crop and livestock enterprises. As with other strategies for managing risk, diversification comes with a unique set of costs. Managing a farm with multiple enterprises creates additional overhead as well as additional demands on management, labor, land, capital, and other resources. Diversification adds complexity to an operation and too much complexity can lead to inefficiencies.

A Qualitative Study Of The Experiences Of Obesity, Body Image, And Mental Health Of British-Born Afro-Caribbean Male Students At A West Yorkshire University In England, Johnson Mbabazi, Dorothy Irene Nalweyiso, Fiona Macgregor, Jeff Breckon, Edward Kunonga, Barry Tolchard, Rosemary Dawson, Jennifer Teke, Josette Bettany Saltikov, George William Kagugube, Lawrence Achilles Nnyanzi

International Journal of Physical Activity and Health

Obesity, body image, and depression are all biopsychosocial phenomena that are frequently misunderstood across cultures. Body dissatisfaction is a psychological aspect of obesity that has been associated with disordered eating, low self-esteem, and depression. Nevertheless, body image dissatisfaction may affect non-obese individuals too. Those with a positive body image are more likely to participate in physical activity than those with a negative body image. Individuals who are satisfied with their body image are more likely to possess high self-esteem, confidence, and healthy eating habits. Obesity prevention among the black population is increasingly important. This study sought to examine the perceptions …

Understanding Students’ Cognitive And Affective Attitude And Attitudinal Structures Toward Physical Activity: A Person-Centered Approach, Yubing Wang, Pan Li, Yaogang Han, Binn Zhang

International Journal of Physical Activity and Health

Objectives: The purpose of this study was to determine the proportions of students who were holding positive, negative, and neutral cognitive/affective attitude and different cognitive-affective attitudinal structures toward moderate-to-vigorous physical activity (MVPA) using a person-centered approach. Methods: A total of 3949 students participated in this study (1065 middle-school students, 784 high-school students, and 2100 college students). Results: A majority of students were holding positive cognitive (about 94%) and affective attitude (about 85%) toward MVPA. Most students (about 84%) held the Positive cognitive—Positive affective attitudinal structure toward MVPA. School level influenced the proportions of students who were holding different cognitive …

Smokejumper Obituary: Deinema, John William "Jack" (Mccall 1950), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Smokejumper Obituary: Lince, Jack L. (North Cascades 1950), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.