Digital Commons Network^™

Common Statistical Concepts In The Supervised Machine Learning Arena, Hooman H Rashidi, Samer Albahra, Scott Robertson, Nam K Tran, Bo Hu

Faculty, Staff and Student Publications

One of the core elements of Machine Learning (ML) is statistics and its embedded foundational rules and without its appropriate integration, ML as we know would not exist. Various aspects of ML platforms are based on statistical rules and most notably the end results of the ML model performance cannot be objectively assessed without appropriate statistical measurements. The scope of statistics within the ML realm is rather broad and cannot be adequately covered in a single review article. Therefore, here we will mainly focus on the common statistical concepts that pertain to supervised ML (i.e. classification and regression) along with …

Conformational Rearrangements In The Sensory Rcsf/Omp Complex Mediate Signal Transduction Across The Bacterial Cell Envelope, Sarah R Lach, Santosh Kumar, Seonghoon Kim, Wonpil Im, Anna Konovalova

Faculty, Staff and Student Publications

Timely detection and repair of envelope damage are paramount for bacterial survival. The Regulator of Capsule Synthesis (Rcs) stress response can transduce the stress signals across the multilayered gram-negative cell envelope to regulate gene expression in the cytoplasm. Previous studies defined the overall pathway, which begins with the sensory lipoprotein RcsF interacting with several outer membrane proteins (OMPs). RcsF can also interact with the periplasmic domain of the negative regulator IgaA, derepressing the downstream RcsCDB phosphorelay. However, how the RcsF/IgaA interaction is regulated at the molecular level to activate the signaling in response to stress remains poorly understood. In this …

Interplay Between Liver Type 1 Innate Lymphoid Cells And Nk Cells Drives The Development Of Alcoholic Steatohepatitis, Chen Cheng, Qian Zhang, Yue Li, Jiali Jiang, Linxi Xie, Haiyuan Shen, Dongqing Wu, Hejiao Zhang, Huiru Zhang, Xuan Wang, Hongyu Wu, Jingjing Xu, Li Gui, Bao Li, Cynthia Ju, Hui Peng, Shi Yin, Long Xu

Faculty, Staff and Student Publications

BACKGROUND & AIMS: Liver contains high frequency of group 1 innate lymphoid cells (ILC), which are composed of comparable number of type 1 ILC (ILC1) and natural killer (NK) cells in steady state. Little is known about whether and how the interaction between ILC1 and NK cells affects the development of alcoholic liver disease.

METHODS: A mouse model of chronic alcohol abuse plus single-binge (Gao-Binge model) was established. The levels of alanine aminotransferase/aspartate aminotransferase, hepatic lipid, and inflammatory cytokines or neutrophils were measured to evaluate the degree of liver injury, steatosis, and inflammation. Flow cytometric analysis, cell depletion, or adoptive …

Risk Factors Associated With Severe Clostridioides Difficile Infection In Patients With Cancer, Denise Marie A Francisco, Liangliang Zhang, Ying Jiang, Adilene Olvera, Javier Adachi, Eduardo Yepez Guevara, Samuel L Aitken, Kevin W Garey, Christine B Peterson, Kim-Anh Do, Ryan Dillon, Engels N Obi, Robert Jenq, Pablo C Okhuysen

Faculty, Staff and Student Publications

INTRODUCTION: Antibiotic use is a risk factor for Clostridioides difficile infection (CDI). Few studies have correlated use of prior antibiotic classes with CDI, microbiome composition, and disease severity in patients with cancer. We hypothesized that previous antibiotic exposure and fecal microbiome composition at time of presentation are risk factors for severe CDI in patients with cancer.

METHODS: This non-interventional, prospective, cohort study examined 200 patients with cancer who had their first episode or first recurrence of CDI. C. difficile was identified using nucleic acid amplification testing. Univariate analysis was used to determine significant risk factors for severe CDI. Fecal microbiome …

Clinical, Dosimetric, And Reporting Considerations For Y-90 Glass Microspheres In Hepatocellular Carcinoma: Updated 2022 Recommendations From An International Multidisciplinary Working Group, Riad Salem, Siddharth A Padia, Marnix Lam, Carlo Chiesa, Paul Haste, Bruno Sangro, Beau Toskich, Kirk Fowers, Joseph M Herman, S Cheenu Kappadath, Thomas Leung, Daniel Y Sze, Edward Kim, Etienne Garin

Faculty, Staff and Student Publications

PURPOSE: In light of recently published clinical reports and trials, the TheraSphere Global Dosimetry Steering Committee (DSC) reconvened to review new data and to update previously published clinical and dosimetric recommendations for the treatment of hepatocellular carcinoma (HCC).

METHODS: The TheraSphere Global DSC is comprised of health care providers across multiple disciplines involved in the treatment of HCC with yttrium-90 (Y-90) glass microsphere-based transarterial radioembolization (TARE). Literature published between January 2019 and September 2021 was reviewed, discussed, and adjudicated by the Delphi method. Recommendations included in this updated document incorporate both the results of the literature review and the expert …

The Interplay Between Neoantigens And Immune Cells In Sarcomas Treated With Checkpoint Inhibition, Irantzu Anzar, Brandon Malone, Pubudu Samarakoon, Ioannis Vardaxis, Boris Simovski, Hugues Fontenelle, Leonardo A Meza-Zepeda, Richard Stratford, Emily Z Keung, Melissa Burgess, Hussein A Tawbi, Ola Myklebost, Trevor Clancy

Faculty, Staff and Student Publications

INTRODUCTION: Sarcomas are comprised of diverse bone and connective tissue tumors with few effective therapeutic options for locally advanced unresectable and/or metastatic disease. Recent advances in immunotherapy, in particular immune checkpoint inhibition (ICI), have shown promising outcomes in several cancer indications. Unfortunately, ICI therapy has provided only modest clinical responses and seems moderately effective in a subset of the diverse subtypes.

METHODS: To explore the immune parameters governing ICI therapy resistance or immune escape, we performed whole exome sequencing (WES) on tumors and their matched normal blood, in addition to RNA-seq from tumors of 31 sarcoma patients treated with pembrolizumab. …

A Novel Case Of Eus-Guided Targeted Radiofrequency Ablation Of Metastatic Duodenal Renal Cell Carcinoma, Muhammad Vohra, Hemant Goyal, Putao Cen, Mairin Joseph-Talreja, Nirav Thosani

Faculty, Staff and Student Publications

No abstract provided.

Lysosomal Tmem9-Lamtor4-Controlled Mtor Signaling Integrity Is Required For Mammary Tumorigenesis, Shengzhe Zhang, Sung Ho Lee, Litong Nie, Yuanjian Huang, Gengyi Zou, Youn-Sang Jung, Sohee Jun, Jie Zhang, Esther M Lien, Junjie Chen, Jae-Il Park

Faculty, Staff and Student Publications

No abstract provided.

Severe Radiation-Induced Lymphopenia During Concurrent Chemoradiotherapy For Stage Iii Non-Small Cell Lung Cancer: External Validation Of Two Prediction Models, Peter S N Van Rossum, Celia Juan-Cruz, Barbara Stam, Maddalena M G Rossi, Steven H Lin, Azadeh Abravan, José S A Belderbos, Jan-Jakob Sonke

Faculty, Staff and Student Publications

BACKGROUND: Severe radiation-induced lymphopenia (RIL) in patients undergoing chemoradiotherapy (CRT) for non-small cell lung cancer (NSCLC) is associated with decreased immunotherapy efficacy and survival. At The Christie and MD Anderson Cancer Center (MDACC), prediction models for lymphopenia were developed in lung and esophageal cancer patients, respectively. The aim of this study was to externally validate both models in patients with stage III NSCLC.

METHODS: Patients who underwent concurrent CRT for stage III NSCLC in 2019-2021 were studied. Outcomes were grade ≥3 and grade 4 lymphopenia during CRT. The Christie model predictors for grade ≥3 lymphopenia included age, baseline lymphocyte count, …

Potential Chemoprotective Effects Of Active Ingredients In Salvia Miltiorrhiza On Doxorubicin-Induced Cardiotoxicity: A Systematic Review Of In Vitro And In Vivo Studies, Qingqing Wang, Jiaxian Li, Xuelei Chu, Xiaochen Jiang, Chuanlong Zhang, Fudong Liu, Xiyuan Zhang, Yi Li, Qian Shen, Bo Pang

Faculty, Staff and Student Publications

BACKGROUND: Recently, attention has been paid to the protective properties of active ingredients in

METHODS: According to the PRISMA guideline, the current systematic review was conducted in the Web of Science, PubMed, Embase, and the Cochrane Library to collect all relevant

RESULTS: Twenty-two eligible articles were included in this systematic review. Eleven types of active ingredients in

CONCLUSION: This systematic review demonstrated that AISM have chemoprotective effects on DIC

Lysosomes, Curcumin, And Anti-Tumor Effects: How Are They Linked?, Qian Shen, Xue Pan, Yi Li, Junchen Li, Chuanlong Zhang, Xiaochen Jiang, Fudong Liu, Bo Pang

Faculty, Staff and Student Publications

Curcumin is a natural active ingredient from traditional Chinese medicine (TCM) that has multi-target characteristics to exert extensive pharmacological activities and thus has been applied in the treatment of various diseases such as cancer, cardiovascular diseases, nervous system, and autoimmune disorders. As an important class of membranous organelles in the intracellular membrane system, lysosomes are involved in biological processes such as programmed cell death, cell metabolism, and immune regulation, thus affecting tumor initiation and progression. It has been shown that curcumin can modulate lysosomal function through the aforementioned pathways, thereby affecting tumor proliferation, invasion, metastasis, drug resistance, and immune function. …

Pepsim: T-Cell Cross-Reactivity Prediction Via Comparison Of Peptide Sequence And Peptide-Hla Structure, Sarah Hall-Swan, Jared Slone, Mauricio M Rigo, Dinler A Antunes, Gregory Lizée, Lydia E Kavraki

Faculty, Staff and Student Publications

INTRODUCTION: Peptide-HLA class I (pHLA) complexes on the surface of tumor cells can be targeted by cytotoxic T-cells to eliminate tumors, and this is one of the bases for T-cell-based immunotherapies. However, there exist cases where therapeutic T-cells directed towards tumor pHLA complexes may also recognize pHLAs from healthy normal cells. The process where the same T-cell clone recognizes more than one pHLA is referred to as T-cell cross-reactivity and this process is driven mainly by features that make pHLAs similar to each other. T-cell cross-reactivity prediction is critical for designing T-cell-based cancer immunotherapies that are both effective and safe. …

The Cx3cl1-Cx3cr1 Chemokine Axis Can Contribute To Tumor Immune Evasion And Blockade With A Novel Cx3cr1 Monoclonal Antibody Enhances Response To Anti-Pd-1 Immunotherapy, Apoorvi Chaudhri, Xia Bu, Yunfei Wang, Michael Gomez, James A Torchia, Ping Hua, Shao-Hsi Hung, Michael A Davies, Gregory A Lizee, Ulrich Von Andrian, Patrick Hwu, Gordon J Freeman

Faculty, Staff and Student Publications

CX3CL1 secreted in the tumor microenvironment serves as a chemoattractant playing a critical role in metastasis of CX3CR1 expressing cancer cells. CX3CR1 can be expressed in both cancer and immune-inhibitory myeloid cells to facilitate their migration. We generated a novel monoclonal antibody against mouse CX3CR1 that binds to CX3CR1 and blocks the CX3CL1-CX3CR1 interaction. We next explored the immune evasion strategies implemented by the CX3CL1-CX3CR1 axis and find that it initiates a resistance program in cancer cells that results in 1) facilitation of tumor cell migration, 2) secretion of soluble mediators to generate a pro-metastatic niche, 3) secretion of soluble …

Nano-Embedded Medical Devices And Delivery Systems In Interventional Radiology, Erin Marie D San Valentin, Allan John R Barcena, Carleigh Klusman, Benjamin Martin, Marites P Melancon

Faculty, Staff and Student Publications

Nanomaterials research has significantly accelerated the development of the field of vascular and interventional radiology. The incorporation of nanoparticles with unique and functional properties in medical devices and delivery systems has paved the way for the creation of novel diagnostic and therapeutic procedures for various clinical disorders. In this review, we discuss the advancements in the field of interventional radiology and the role of nanotechnology in maximizing the benefits and mitigating the disadvantages of interventional radiology theranostic procedures. Several nanomaterials have been studied to improve the efficacy of interventional radiology interventions, reduce the complications associated with medical devices, improve the …

A Novel Humanized Chi3l1 Blocking Antibody Attenuates Acetaminophen-Induced Liver Injury In Mice, Leike Li, Yankai Wen, Daniel Wrapp, Jongmin Jeong, Peng Zhao, Wei Xiong, Constance Lynn Atkins, Zhao Shan, Deng Hui, Jason S Mclellan, Ningyan Zhang, Cynthia Ju, Zhiqiang An

Faculty, Staff and Student Publications

Acetaminophen (APAP) overdose is a leading cause of acute liver injury in the USA. The chitinase 3-like-1 (Chi3l1) protein contributes to APAP-induced liver injury (AILI) by promoting hepatic platelet recruitment. Here, we report the development of a Chi3l1-targeting antibody as a potential therapy for AILI. By immunizing a rabbit successively with the human and mouse Chi3l1 proteins, we isolated cross-reactive monoclonal antibodies (mAbs) from single memory B cells. One of the human and mouse Chi3l1 cross-reactive mAbs was humanized and characterized in both

Spatial And Temporal Organization Of The Genome: Current State And Future Aims Of The 4d Nucleome Project, Clara Agudo-Rios, Amber Rogers, Isaiah King, Virali Bhagat, Le My Tu Nguyen, Carlos Córdova-Fletes, Diego Krapf, Jerome F Strauss, Lena Arévalo, Gina Esther Merges, Hubert Schorle, Eduardo R S Roldan, Maria Eugenia Teves

Faculty, Staff and Student Publications

Protamines (PRM1 and PRM2) are small, arginine-rich, nuclear proteins that replace histones in the final stages of spermiogenesis, ensuring chromatin compaction and nuclear remodeling. Defects in protamination lead to increased DNA fragmentation and reduced male fertility. Since efficient sperm production requires the translocation of protamines from the cytoplasm to the nucleus, we investigated whether SPAG17, a protein crucial for intracellular protein trafficking during spermiogenesis, participates in protamine transport. Initially, we assessed the protein-protein interaction between SPAG17 and protamines using proximity ligation assays, revealing a significant interaction originating in the cytoplasm and persisting within the nucleus. Subsequently, immunoprecipitation and mass spectrometry …

Can Coral Reef Restoration Programmes Facilitate Changes In Environmental Attitudes? A Case Study On A Rural Fisher Community In North Bali, Indonesia, Zach Boakes, Luh Putu Mahyuni, Alice E. Hall, Marin Cvitanovic, Richard Stafford

School of Biological and Marine Sciences

There is currently limited research assessing the ecological potential of coral restoration programmes of habitat enhancement and restoration of benthic and mobile populations for influencing the attitudes (and subsequent behaviours) of the communities where they are based. Our qualitative study investigated the impact of a coral reef restoration programmes on local environmental attitudes in a rural fishing community in north Bali, Indonesia. We conducted semi-structured interviews with individuals and multi-stakeholder focus groups (n = 31) in Tianyar Village, where the NGO ‘North Bali Reef Conservation’ (‘Yowana Bhakti Segara’) was based. Our results highlight several factors that influenced environmental behaviours, including …

A Mixed Methods Study Investigating Sources Of Fertility And Reproductive Health Information In The Uk, B. Grace, J. Shawe, J. Stephenson

School of Nursing and Midwifery

No abstract provided.

Parental Effects Of Social Density On Mating Behaviour, Reproductive Success, And Longevity, Shaun Rowlands

School of Biological and Marine Sciences Theses

Organisms can adapt to changing environments, changing their investment strategies to increase their lifetime reproductive success. Contemporary evolutionary theory would suggest that organisms have evolved mechanisms which allow them to assess competition and acquire phenotypic responses that accurately responds to the environment, allowing for rapid changes in response to the social context. Selection would favour organisms which can make nongenetic parental effects, with parents evolving an ability pass on plasticity responses that optimize offspring fitness related traits to suit ecological challenges. In this thesis , I investigate how the social density affects the mating behaviour and offspring production of the …

Ecological And Oceanographic Interactions Of An Offshore Longline Mussel Farm, Llucia Mascorda-Cabre

School of Biological and Marine Sciences Theses

A growing human population coupled with the need to protect marine ecosystems, requires sources of sustainable protein. Finfish aquaculture can produce a wide range of environmental impacts while shellfish aquaculture reports fewer negative effects, being classed a sustainable protein source. Mussels are ecosystem engineers and farms can mitigate the consequences of eutrophication while providing ecosystem services. The development of mussel farming has been limited by competition for coastal space, intensification of the industry causing environmental impacts due to bioaccumulation around farms, negative public perception and lack of research. Offshore aquaculture has the potential to overcome such issues but knowledge on …

The Criticality Of Teacher Educator Wellbeing: Reflecting Through Arts-Based Methods, Kristina Turner, Georgina M. Barton Dr, Susanne Garvis, Ellen Larsen

Australian Journal of Teacher Education

Teacher educators face many challenges related to workload and government-mandated reforms in Initial Teacher Education programs. Evidence suggests that COVID-19 has exacerbated these challenges as universities must become more cost-effective and improve research outcomes and impact, often resulting in heavier workloads. While these challenges may be faced in other disciplines, teacher educator wellbeing, stress and burnout is an under-researched field, and little is known about if and how teacher educators maintain their wellbeing during times of uncertainty. This collaborative autoethnographic study applied an arts-based research method to explore the wellbeing challenges faced by four Australian teacher educators through the lens …

"Sky-High Motivation": Intradisciplinary Integrative- Courses For Excelling Teachers' Training, Yael Kimhi

Australian Journal of Teacher Education

In many teacher education programs, curricula are comprised of fragmented courses within an academic discipline. This longitudinal study followed one cohort of teacher trainees in a fast-track B.Ed. program in Israel and explored an integrative approach to intradisciplinary courses. These courses were organized around significant themes and issues. A mixed-method methodology was implemented. The data included 81 teacher trainee responses, 16 mentor responses, and 11 college staff responses. Data were gathered during three years at four different time points: 1) online questionnaire for trainees and mentors (end of 1^st and 3^rd year); 2) trainee focus groups and steering …

Transformative Learning Experiences Of The Vocationally Interested And Vocationally Disinterested Pre-Service Teachers In Teacher Training Colleges In Zimbabwe, Esnati Macharaga, Tabitha Grace Mukeredzi

Australian Journal of Teacher Education

This article reports on some of the findings from a doctoral research project that explored how the vocationally interested and vocationally disinterested pre-service teachers in selected teacher training colleges in Zimbabwe experienced transformative learning. Through multiple-site case study and qualitative approach within an interpretive paradigm, guided by Mezirow’s ten-phase Transformative Learning Theory, the study sought to understand the pre-service teacher transformative learning experiences. The study employed a multi-modal approach which involved focus group discussions, individual face to face interviews and continuum drawing and discussions to generate data from a purposive sample of 40 participants. Findings suggest that, both vocationally interested …

Teachers' Views On The Nature Of Science: An Epistemological Analysis, Rafael Amador Rodríguez, Natalia Ospina Quintero, Agustín Adúriz Bravo

Australian Journal of Teacher Education

This article presents results of research analysing the views on the nature of science (NOS) among primary and secondary teachers working in state schools in two different cities in Colombia. Previous studies have reported that science teachers maintain ‘eclectic’ epistemological perspectives on science; in this article, we test if such hypothesis holds when teachers’ ideas are ‘anchored’ in specific periods and topics of the philosophy of science. Thirty-five teachers attending a postgraduate teaching course with emphasis on the natural sciences at the Universidad del Norte (Barranquilla, Colombia) were assessed with the use of quantitative, descriptive and parametric research methods. The …

Ecologies Of Learning For Inclusive Pedagogy In Spanish Secondary Education, Inmaculada Orozco, Anabel Moriña

Australian Journal of Teacher Education

From the theoretical basis of the ecology of learning and inclusive pedagogy, this article explores the activities, resources and interactions practised by 25 Spanish teachers in compulsory secondary education. This qualitative study involved semi-structured and individual interviews. A progressive analysis of the data was carried out using an inductive system of categories and codes. The results show that the activities were varied and all of them put students at the centre of the teaching-learning process. The resources that stood out were technologies and peer support. Interactions were characterised by the need to nurture affection and get to know and motivate …

Alpha Band Prefrontal Asymmetry Does Not Underlie Pain Approach-Avoidance: Results From Two Eeg Studies, Tracy W. Brown, Kayli N. Colpitts, Cristian M. Botello, Abby K. Hartman, Kathryn P. Seymour

Psychological Science Faculty Publications

Pain research is often focused on escape from pain or approach of relief, yet individuals with chronic pain make complex choices to face their pain to satiate other drives (approach-avoidance conflicts). An abundance of research has indicated that prefrontal alpha band asymmetry (PFA) underlies approach-avoidance in general, but there is limited information about whether PFA underlies pain approach-avoidance conflicts. Electroencephalogram activity was recorded while 70 participants with chronic pain (n=33) and without chronic pain (n=37) approached/avoided stimuli containing simultaneous pain (low-high) and monetary reward (low-high). Findings from both studies revealed that approach-avoidance for pain stimuli is not accompanied by prefrontal …

The Influence Of Intrinsic And Extrinsic Factors In A Trap-Neuter-Release (Tnr) Program And Its Effects On Urban And Rural Demographics As A Long-Term Solution For Community Cat Management, Hannah E. Litke

Graduate Research Papers

Trap-neuter-release is a humane alternative solution to aid in decreasing community cat populations. This research paper evaluates the intrinsic and extrinsic factors contributing to successful community cat populations, including reproductive success, transmission of feline and zoonotic diseases, population size, cat immigration between colonies, food availability, and wildlife extinction. Additionally, this research paper evaluates and analyzes TNR's impacts on urban and rural demographics. Furthermore, the paper will evaluate TNR as a long-term solution and its effectiveness in decreasing community cat populations. Lastly, this paper provides suggestions for future research regarding community cat populations.

Effect Of Soil And Climatic Conditions On Brown Spot Occurrence In Rice Lowland Across Four Agro-Climatic Zones Of Côte D’Ivoire, Jean-Fabrice Akouemaho Dominique Adanve, Brahima Koné, Rachidatou Sikirou, Elliott Dossou-Yovo, Geoffrey Onaga, Fatogoma Sorho

All Rsif Scholars' Publications

Methodology: BS characterization were done in different farmer fields where soil samples were also collected during dry and rainy seasons. Soil silicon and acidity were determined in those samples and rice grain yield at harvest time were recorded in different sites. Weather data related to sites and seasons were used to find out correlations. Results: Occurrence of BS was found in forest zones with scores of 4 and 3 compared to 1 and 2 in savanna and transitional zones, respectively, with seasonal variation. Both rice production and the occurrence of BS were explained by soil parameters in conjunction with climatic …

Editorial: Perspective Challenges For Applied Research In Potato Pathogens: From Molecular Biology To Bioinformatics, Grace Wanjiku Gachara, Rachid Lahlali, Göksel Özer, Hussain Touseef

All Rsif Scholars' Publications

The potato crop is prone to infection by an estimated 50 different categories of pests and diseases whose causal agents are either viruses, bacteria, nematodes, insects, or fungi (Hussain and Singh, 2016; Jansson and Raman, 2019; Mangal et al., 2022; Munyaneza and Bizimungu, 2022). These pathogenic organisms are either soil or air-borne and usually inflict harm on all plant parts. The most commonly encountered diseases that affect potato growth and development include common scab, dry rot, black scurf, late blight, stem canker, premature deaths, and a wide array of nematodes. Soil-based infections that affect the quality of tubers include pink …

Economic And Input-Use Efficiency Of Nitrogen Management Techniques In Non-Irrigated Maize Production, Katie J. Bathke

Honors Program: Senior Projects (Public)

The efficiency of nitrogen (N) management has become a main concern in agricultural cropping systems for understanding the optimal N rate to help producers improve economically and reduce the exhaustion of natural resources environmentally. Nitrogen rates vary both temporally and spatially by the interactions of the soil environment and rainfall through a growing season. Thus, a site-specific approach can further optimize this variability with the understanding of the role soil variability plays in the N rate applied to a non-irrigated field. The objective of this study was to evaluate the various nitrogen treatments for their nutrient use efficiency and economic …