Life Sciences Commons^™

The Santa Clara, 2024-01-19, Santa Clara University

The Santa Clara

No abstract provided.

Augusta: From Rna-Seq To Gene Regulatory Networks And Boolean Models, Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomáš Helikar, Karel Sedlar

Department of Biochemistry: Faculty Publications

Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of …

Effectiveness Of Mycorrhizae And Vermicompost Seed Inoculation For Germination, Vegetative Growth, Cannabinoid Content, And Cured Flower Weight Of Cbd-Rich Hemp (Cannabis Sativa L.), Hannah Boyer, Nicole Wagner, Merritt Drewery

Journal of Agricultural Hemp Research

Effective germination and vigorous growth of hemp cultivars is paramount to cultivators’ ability to produce high-quality hemp products. Beneficial bacteria and fungi are known symbionts to plants and are used in regenerative agriculture to increase plant health and crop yield. This pilot study investigated the effect of microbial seed inoculation on germination rate, plant height, cured flower weight, and cannabinoid content of cannabidiol (CBD)-rich hemp (Cannabis sativa L). The experiment included a control and the following treatments: 1) seed inoculation of Great White ^â Premium Mycorrhizae (GW), 2) seed inoculation of vermicompost (V), and 3) seed inoculation of Great …

Epstein-Barr Virus-Based Prognostic Model In Nodular Sclerosis Classic Hodgkin Lymphoma, Chen Jiang, Li-Yun Huang, Ji-Hao Zhou, Zhi-Ming Li, Yu Wang, Jian-Chang Fu, Qin Yan, Yu-Yuan Huang, Min Zuo, Shimin Hu, Robert Peter Gale, Yang Liang, Jing-Ping Yun, Yu-Hua Huang

Faculty, Staff and Student Publications

The role of Epstein-Barr virus (EBV) in lymphoma cells of nodular sclerosis classic Hodgkin lymphoma (NScHL) is controversial. Our aim was to explore this and establish a clinically feasible model for risk stratification. We interrogated data from 542 consecutive subjects with NScHL receiving ABVD therapy and demonstrated EBV-infection in their lymphoma cells with EBV-encoded small RNAs (EBERs) in situ hybridization. Subjects were divided into training and validation datasets. As data from the training dataset suggested EBERs-positivity was the only independent prognostic factor for both progression-free survival (PFS) and overall survival (OS), we developed corresponding prognostic models based on it. Our …

Designing Clinical Trials For Patients Who Are Not Average, Thomas E Yankeelov, David A Hormuth, Ernesto A B F Lima, Guillermo Lorenzo, Chengyue Wu, Gaiane M Rauch, Caroline Chung

Faculty, Staff and Student Publications

The heterogeneity inherent in cancer means that even a successful clinical trial merely results in a therapeutic regimen that achieves, on average, a positive result only in a subset of patients. The only way to optimize an intervention for an individual patient is to reframe their treatment as their own, personalized trial. Toward this goal, we formulate a computational framework for performing personalized trials that rely on four mathematical techniques. First, mathematical models that can be calibrated with patient-specific data to make accurate predictions of response. Second, digital twins built on these models capable of simulating the effects of interventions. …

Bispecific Bcma/Cd24 Car-T Cells Control Multiple Myeloma Growth, Fumou Sun, Yan Cheng, Visanu Wanchai, Wancheng Guo, David Mery, Dongzheng Gai, Clyde Bailey, Cody Ashby, Samer Al Hadidi, Carolina Schinke, Sharmilan Thanendrarajan, Yupo Ma, Qing Yi, Robert Z Orlowski, Maurizio Zangari, Frits Van Rhee, Siegfried Janz, Gail Bishop, Guido Tricot, John D Shaughnessy, Fenghuang Zhan

Faculty, Staff and Student Publications

Anti-multiple myeloma B cell maturation antigen (BCMA)-specific chimeric antigen receptor (CAR) T-cell therapies represent a promising treatment strategy with high response rates in myeloma. However, durable cures following anti-BCMA CAR-T cell treatment of myeloma are rare. One potential reason is that a small subset of minimal residual myeloma cells seeds relapse. Residual myeloma cells following BCMA-CAR-T-mediated treatment show less-differentiated features and express stem-like genes, including CD24. CD24-positive myeloma cells represent a large fraction of residual myeloma cells after BCMA-CAR-T therapy. In this work, we develop CD24-CAR-T cells and test their ability to eliminate myeloma cells. We find that CD24-CAR-T cells …

An Incidental Finding Of A High-Grade Glioma With Pleomorphic And Pseudopapillary Features (Hpap) With Pbrm1 Mutation, Maria A Gubbiotti, Jeffrey S Weinberg, Shiao-Pei Weathers, Pushan Dasgupta, Martin C Tom, Martha Quezado, Jason T Huse, Leomar Y Ballester

Faculty, Staff and Student Publications

No abstract provided.

Evaluation Of Potential Biomarkers For Lenvatinib Plus Pembrolizumab Among Patients With Advanced Endometrial Cancer: Results From Study 111/Keynote-146, Vicky Makker, Matthew H Taylor, Carol Aghajanian, Allen L Cohn, Marcia S Brose, Zhu Alexander Cao, Andrey Loboda, Razvan Cristescu, Petar Jelinic, Robert Orlowski, Lea Dutta, Junji Matsui, Corina E Dutcus, Yukinori Minoshima, Mark J Messing

Faculty, Staff and Student Publications

BACKGROUND: Lenvatinib plus pembrolizumab demonstrated clinically meaningful benefit in patients with previously treated advanced endometrial carcinoma in Study 111/KEYNOTE-146 (NCT02501096). In these exploratory analyses from this study, we evaluated the associations between clinical outcomes and gene expression signature scores and descriptively summarized response in biomarker subpopulations defined by tumor mutational burden (TMB) and DNA variants for individual genes of interest.

METHODS: Patients with histologically confirmed metastatic endometrial carcinoma received oral lenvatinib 20 mg once daily plus intravenous pembrolizumab 200 mg every 3 weeks for 35 cycles. Archived formalin-fixed paraffin-embedded tissue was obtained from all patients. T-cell-inflamed gene expression profile (Tcell …

Induced Degradation Of Lineage-Specific Oncoproteins Drives The Therapeutic Vulnerability Of Small Cell Lung Cancer To Parp Inhibitors, Chiho Kim, Xu-Dong Wang, Zhengshuai Liu, Jianwei Hao, Shuai Wang, Zhenzhen Zi, Seoyeon Jang, Jiwoong Kim, Yikai Luo, Kenneth E Huffman, Shreoshi Pal Choudhuri, Sofia Del Rio, Ling Cai, Han Liang, Benjamin J Drapkin, John D Minna, Yonghao Yu

Faculty, Staff and Student Publications

Although BRCA1/2 mutations are not commonly found in small cell lung cancer (SCLC), a substantial fraction of SCLC shows clinically relevant response to PARP inhibitors (PARPis). However, the underlying mechanism(s) of PARPi sensitivity in SCLC is poorly understood. We performed quantitative proteomic analyses and identified proteomic changes that signify PARPi responses in SCLC cells. We found that the vulnerability of SCLC to PARPi could be explained by the degradation of lineage-specific oncoproteins (e.g., ASCL1). PARPi-induced activation of the E3 ligase HUWE1 mediated the ubiquitin-proteasome system (UPS)-dependent ASCL1 degradation. Although PARPi induced a general DNA damage response in SCLC cells, this …

Non-Invasive Methods For Monitoring Weasels: Emerging Technologies And Priorities For Future Research, David S. Jachowski, Scott M. Bergeson, Stacy Cotey, Elizabeth Croose, Tim R. Hofmeester, Jenny Macpherson, Et Al.

Michigan Tech Publications

Weasels (genus Mustela and Neogale) are of management concern as declining native species in some regions and invasive species in others. Regardless of the need to conserve or remove weasels, there is increasingly a need to use non-invasive monitoring methods to assess population trends. We conducted a literature review and held the first ever International Weasel Monitoring Symposium to synthesise information on historical and current non-invasive monitoring techniques for weasels. We also explored current limitations, opportunities, and areas of development to guide future research and long-term monitoring. Our literature search revealed that in the past 20 years, camera traps were …

Computer Models Can Help Us Learn More About How Eye Diseases Progress, Cassandra Corry

Research on Capitol Hill

Eye diseases are difficult to study because taking samples from living eyes can be challenging and uncomfortable. We need a model that mimics the human eye; running computer simulations seems like a promising way to conduct this research.

Colloidal Calcium Phosphate (Ccp) Causes Problematic Acid Variation In Cheddar Cheese, Sakshi Singh

Research on Capitol Hill

pH variation in cheese during the early ripening stages causes changes in the texture, body, and flavor of cheese. The dairy industry, encompassing over 50,000 dairy farms nationwide and several regional dairy farmers and companies in Utah, suffers substantial financial loss as cheese with varying pH is rendered mostly useless.

Microbes From Native Plants Show Drought Tolerance Potential, Ty Wilson

Research on Capitol Hill

Climate-induced environmental stresses, and the increased use of fertilizers, significantly threaten food production and soil health. In natural soils, microbes perform a vital function of restoring the soil and assisting native plants’ growth.

Queering The Herbarium: Plants, Poetry, And Multimodal Expression, Basil Payne

Research on Capitol Hill

Herbarium specimens are pressed, preserved plants that are used for scientific study. The plants are dried and adhered to the page using glue or thread. If kept in the right conditions, they can last hundreds of years.

The Key To Breeding Drought Adapted Spring Wheat In Utah May Be Below The Soil, Kylie Hansen

Research on Capitol Hill

Drought conditions reduce yield and quality and are unavoidable in rainfed farms across the globe; we need to breed drought tolerant wheat lines to meet this challenge. The key may lie in how these plants grow prior to emerging from the ground.

Deficit Irrigation Of Pastures, Matt Yost, Clara Anderson, Niel Allen, Burdette Barker, Melanie Heaton, Justin Wyatt Clawson, Earl Creech

All Current Publications

Deficit irrigation is any irrigation level that does not meet the crop’s full evapotranspiration (ET) demand, meaning evaporation from plant and soil surface and transpiration through plant growth. This strategy is often a last resort for optimizing water use as opposed to those that will not limit production. However, deficit irrigation is often necessary in parts of Utah due to drought or inadequate water supplies. This was especially true in 2021–2022 due to record droughts. Deficit irrigation strategies for pastures have been developed, but they have yet to be compared and evaluated in Utah. This fact sheet summarizes 6 years …

Making The Connection: How Membrane Contact Sites Have Changed Our View Of Organelle Biology, G. Voeltz, E. Sawyer, G. Hajnóczky, W. Prinz

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

The view of organelles and how they operate together has changed dramatically over the last two decades. The textbook view of organelles was that they operated largely independently and were connected by vesicular trafficking and the diffusion of signals through the cytoplasm. We now know that all organelles make functional close contacts with one another, often called membrane contact sites. The study of these sites has moved to center stage in cell biology as it has become clear that they play critical roles in healthy and developing cells and during cell stress and disease states. Contact sites have important roles …

Australian Cool-Season Pulse Seed-Borne Virus Research: 1. Alfalfa And Cucumber Mosaic Viruses And Less Important Viruses, Roger A C Jones, Benjamin S. Congdon

Biosecurity Research Articles

Here, we review the research undertaken since the 1950s in Australia’s grain cropping regions on seed-borne virus diseases of cool-season pulses caused by alfalfa mosaic virus (AMV) and cucumber mosaic virus (CMV). We present brief background information about the continent’s pulse industry, virus epidemiology, management principles and future threats to virus disease management. We then take a historical approach towards all past investigations with these two seed-borne pulse viruses in the principal cool-season pulse crops grown: chickpea, faba bean, field pea, lentil, narrow-leafed lupin and white lupin. With each pathosystem, the main focus is on its biology, epidemiology and management, …

Pilot Implementation Of A Nutrition-Focused Community-Health-Worker Intervention Among Formerly Chronically Homeless Adults In Permanent Supportive Housing, Farrah Hmaidan, Clara Smith, Eva Thibaudeau-Graczyk, Shreela V Sharma

Faculty, Staff and Student Publications

Food insecurity is a known health equity threat for formerly chronically homeless populations even after they transition into permanent housing. This project utilized a human-centered design methodology to plan and implement a nutrition-focused community-health-worker (CHW) intervention in permanent supportive housing (PSH). The project aimed to increase access to healthy foods, improve nutritional literacy, healthy cooking/eating practices, and build community/social connectedness among 140 PSH residents. Validated food-security screening conducted by CHWs identified low or very low food security among 64% of 83 residents who completed the baseline survey, which is similar to rates found in a previous study among formerly homeless …

Revealing Chronic Disease Progression Patterns Using Gaussian Process For Stage Inference, Hongyu Wang, Xiaobo Zhou

Faculty, Staff and Student Publications

OBJECTIVE: The early stages of chronic disease typically progress slowly, so symptoms are usually only noticed until the disease is advanced. Slow progression and heterogeneous manifestations make it challenging to model the transition from normal to disease status. As patient conditions are only observed at discrete timestamps with varying intervals, an incomplete understanding of disease progression and heterogeneity affects clinical practice and drug development.

MATERIALS AND METHODS: We developed the Gaussian Process for Stage Inference (GPSI) approach to uncover chronic disease progression patterns and assess the dynamic contribution of clinical features. We tested the ability of the GPSI to reliably …

Predicting Radiotherapy Patient Outcomes With Real-Time Clinical Data Using Mathematical Modelling, Alexander P Browning, Thomas D Lewin, Ruth E Baker, Philip K Maini, Eduardo G Moros, Helen M Byrne

Faculty, Staff and Student Publications

Longitudinal tumour volume data from head-and-neck cancer patients show that tumours of comparable pre-treatment size and stage may respond very differently to the same radiotherapy fractionation protocol. Mathematical models are often proposed to predict treatment outcome in this context, and have the potential to guide clinical decision-making and inform personalised fractionation protocols. Hindering effective use of models in this context is the sparsity of clinical measurements juxtaposed with the model complexity required to produce the full range of possible patient responses. In this work, we present a compartment model of tumour volume and tumour composition, which, despite relative simplicity, is …

Complementary And Integrative Health Information In The Literature: Its Lexicon And Named Entity Recognition, Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg Marc Silverman, Yuqi Zhou, Hua Xu

Faculty, Staff and Student Publications

Objective: To construct an exhaustive Complementary and Integrative Health (CIH) Lexicon (CIHLex) to help better represent the often underrepresented physical and psychological CIH approaches in standard terminologies, and to also apply state-of-the-art natural language processing (NLP) techniques to help recognize them in the biomedical literature.

Materials and methods: We constructed the CIHLex by integrating various resources, compiling and integrating data from biomedical literature and relevant sources of knowledge. The Lexicon encompasses 724 unique concepts with 885 corresponding unique terms. We matched these concepts to the Unified Medical Language System (UMLS), and we developed and utilized BERT models comparing their efficiency …

Polygenic Scores For Tobacco Use Provide Insights Into Systemic Health Risks In A Diverse Ehr-Linked Biobank In Los Angeles, Vidhya Venkateswaran, Kristin Boulier, Yi Ding, Ruth Johnson, Arjun Bhattacharya

Faculty, Staff and Student Publications

Tobacco use is a major risk factor for many diseases and is heavily influenced by environmental factors with significant underlying genetic contributions. Here, we evaluated the predictive performance, risk stratification, and potential systemic health effects of tobacco use disorder (TUD) predisposing germline variants using a European- ancestry-derived polygenic score (PGS) in 24,202 participants from the multi-ancestry, hospital-based UCLA ATLAS biobank. Among genetically inferred ancestry groups (GIAs), TUD-PGS was significantly associated with TUD in European American (EA) (OR: 1.20, CI: [1.16, 1.24]), Hispanic/Latin American (HL) (OR:1.19, CI: [1.11, 1.28]), and East Asian American (EAA) (OR: 1.18, CI: [1.06, 1.31]) GIAs but …

Alternative Dosing Regimen Of Exemestane In A Randomized Presurgical Trial: The Role Of Obesity In Biomarker Modulation, Harriet Johansson, Aliana Guerrieri-Gonzaga, Sara Gandini, Bjørn-Erik Bertelsen, Debora Macis, Gunnar Mellgren, Parijatham S Thomas, Katherine D Crew, Nagi B Kumar, Irene Maria Briata, Viviana Galimberti, Giuseppe Viale, Lana A Vornik, Valentina Aristarco, Tania Buttiron Webber, Stefano Spinaci, Powel H Brown, Brandy M Heckman-Stoddard, Eva Szabo, Bernardo Bonanni, Andrea Decensi

Faculty, Staff and Student Publications

In a 3-arm presurgical trial, four-six weeks exemestane 25 mg three times/week (TIW) was non-inferior to 25 mg/day (QD) in suppressing circulating estradiol in postmenopausal women with ER-positive breast cancer. Since obesity may decrease exemestane efficacy, we analyzed changes in sex steroids, adipokines, Ki-67, and drug levels in relation to obesity. Postmenopausal women with early-stage ER-positive breast cancer were randomized to either exemestane 25 mg QD (n = 57), 25 mg TIW (n = 57), or 25 mg/week (QW, n = 62) for 4-6 weeks before breast surgery. Serum and tissue pre- and post-treatment biomarkers were stratified by body mass …

Enabling The Clinical Application Of Artificial Intelligence In Genomics: A Perspective Of The Amia Genomics And Translational Bioinformatics Workgroup, Robert R Freimuth, David B Everman, Derek C Walton, Scott P Mcgrath, Dominick J Lemas, Panayiotis V Benos, Alexander V Alekseyenko, Qianqian Song, Ece Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas Nate Person, Nadav Rappoport, Zhongming Zhao, Marc S Williams

Faculty, Staff and Student Publications

OBJECTIVE: Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space.

PROCESS: A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members.

CONCLUSIONS: Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of …

Studying Adherence To Reporting Standards In Kinesiology: A Post-Publication Peer Review Brief Report, Nikki M. Watson, Jafra D. Thomas

International Journal of Exercise Science

International Journal of Exercise Science 17(7): 25-37, 2024. To demonstrate how post-publication peer reviews—using journal article reporting standards—could improve the design and write-up of kinesiology research, the authors performed a post-publication peer review on one systematic literature review published in 2020. Two raters (1^st & 2^nd authors) critically appraised the case article between April and May 2021. The latest Journal Article Reporting Standards by the American Psychological Association relevant to the review were used: i.e., Table 1 (quantitative research standards) and Table 9 (research synthesis standards). A standard fully met was deemed satisfactory. Per Krippendorff’s alpha-coefficient, inter-rater agreement …

Effects Of Supramaximal Anderson Quarter-Squats As A Potentiating Stimulus On Discus Performance In Division I Throwers: A Pilot Study, Ogochukwu I. Nwachukwu, Mark Debeliso Phd, Marcus M. Lawrence Phd

International Journal of Exercise Science

International Journal of Exercise Science 17(6): 99-114, 2024. No study has assessed supramaximal (over 100% 1RM) back squat variations as a potentiating stimulus in collegiate throwers. The purpose of this study was to test the hypothesis that a supramaximal Anderson (bottom-up) quarter squat potentiating stimulus would improve discus throw performance in Division I throwers compared to a dynamic warm-up alone. Nine NCAA division I thrower athletes (age: 20.1±1.4 years; 1RM back squat/body weight: 2.5±0.4 kg) randomly completed two sessions separated by at least 72 hours. One session involved a standardized dynamic warm-up alone (DyWU) followed by three trials of maximal …

The Relationship Between Athlete Perceptions Of Coaching Leadership Behaviors And Athlete Grit, Landon Braun, Lindsay Ross-Stewart, Barbara B. Meyer

International Journal of Exercise Science

International Journal of Exercise Science 17(5): 12-23, 2023. Coach leadership style has long been positively correlated with athlete experiences such as motivation, health (i.e., burnout), and performance outcomes (i.e., enhanced execution time to complete tasks) (24). More recently, grit (18) has been positively correlated with athlete experiences such as engagement (39) and decreased burnout (32). Given the impact coaches have on their athletes and the positive psychological benefits of grit, it is reasonable to explore the intersections of coaching behaviors and grit. As such, the purpose of the current study was to examine the relationship between athlete perceptions of coach …

Fat-Free Mass Index In A Large Sample Of Collegiate American Football Athletes, Jennifer B. Fields, Margaret T. Jones, Adam Feit, Meghan K. Magee, Nicholas M. Kuhlman, Andrew R. Jagim

International Journal of Exercise Science

International Journal of Exercise Science 17(4): 129-139, 2024. High levels of fat-free mass (FFM) are favorable for athletes and are related to sport performance. However, fat-free mass index (FFMI), which includes adjustments for height, may offer a better way to characterize FFM beyond raw values. As FFMI is understudied relative to sport, the purpose of the current study was to assess position and age group differences in FFMI among collegiate American football players. National Collegiate Athletic Association DIII (n=111) football players underwent body composition assessment via bioelectrical impedance analysis. FFMI was calculated by dividing FFM by height squared. One-way analyses …

Stance Time And Impact Loading Rates Are Significant Predictors Of Critical Speed During A 3-Minute All-Out Running Test, Trevor Short, Cris Stickley, Bret Freemyer, Andrew Takata, Paulette Yamada

International Journal of Exercise Science

International Journal of Exercise Science 17(4): 115-128, 2024. The addition of wearable technology during a 3-minute all-out overground running test (3MAOT) could provide additional insights to guide training and coaching strategies. The purpose of this study was to explore the relationships between critical speed (CS) and biomechanical parameters (cadence, stride length, vertical oscillation, stance time, form power, leg spring stiffness, and impact loading rate), and changes in biomechanical parameters throughout the 3MAOT. Sixty-three (male, n=37, female, n=26) recreationally active college-aged (23.4±3.9 years) subjects completed a 3MAOT while wearing a Stryd foot-pod. The correlations between CS and biomechanical parameters were evaluated …