Digital Commons Network^™

Deep5mc: Predicting 5-Methylcytosine (5mc) Methylation Status Using A Deep Learning Transformer Approach, Evan Kinnear, Houssemeddine Derbel, Zhongming Zhao, Qian Liu

Faculty, Staff and Student Publications

DNA methylations, such as 5-methylcytosine (5mC), are crucial in biological processes, and aberrant methylations are strongly linked to various human diseases. Genomic 5mC is not randomly distributed but exhibits a strong association with genomic sequences. Thus, various computational methods were developed to predict 5mC status based on DNA sequences. These methods generated promising achievements and overcome the limitations of experimental approaches. However, few studies have comprehensively investigated the dependency of 5mC on genomic sequences, and most existing methods focus on specific genomic regions. In this work, we introduce Deep5mC, a deep learning transformer-based method designed to predict 5mC methylations. Deep5mC …

Home Dialysis For Latinx Individuals Living With Kidney Failure: A Qualitative Study Of Interdisciplinary Dialysis Clinicians, Katherine Rizzolo, Rebeca Gonzalez Jauregui, Jade Teakell, Michel Chonchol, Sushrut S Waikar, Lilia Cervantes

Faculty, Staff and Student Publications

Key Points:

1. Individual-level advocacy to overcome structural barriers to home dialysis is key in improving home dialysis access for Latinx individuals.

2. Acknowledging patient influences on dialysis modality choice is critical for Latinx individuals with kidney failure.

3. Early, repeated education from a trusted source is important for Latinx individuals with kidney failure.

Background: Latinx individuals experience two times the incidence of kidney failure compared with non-Latinx individuals and are less likely to use home dialysis therapies. In this qualitative study, interdisciplinary home dialysis clinicians were interviewed to understand the key factors and strategies used by clinicians to improve home dialysis uptake …

Using Content Validity Index Methodology For Cross-Cultural Translation Of A Patient-Reported Outcome Measure For Head And Neck Cancer, Janet H Van Cleave, Alizendie Guerra, Eva Liang, Carolina Gutiérrez, Ron J Karni, Marcely Tsikis, Geanise Pearl C Nguyen, Allison P Squires

Faculty, Staff and Student Publications

Introduction: Translations of patient-reported measures may not account for structural and cultural differences in shared languages spoken in multiple countries, such as English, Spanish, Arabic, or Russian. The objective of this research was to create a cross-cultural Spanish translation of the New York University (NYU) Electronic Patient Visit Assessment (ePVA)© for head and neck cancer (HNC), a patient-reported symptom measure available only in English.

Methods: Using the Content Validity Index (CVI) methodology, an expert panel of nurses (n = 6) proficient in Spanish and English independently reviewed and rated a forward translation of the ePVA, a measure consisting of …

Suicide Phenotyping From Clinical Notes In Safety-Net Psychiatric Hospital Using Multi-Label Classification With Pre-Trained Language Models, Zehan Li, Yan Hu, Scott Lane, Salih Selek, Lokesh Shahani, Rodrigo Machado-Vieira, Jair Soares, Hua Xu, Hongfang Liu, Ming Huang

Faculty, Staff and Student Publications

Accurate identification and categorization of suicidal events can yield better suicide precautions, reducing operational burden, and improving care quality in high-acuity psychiatric settings. Pre-trained language models offer promise for identifying suicidality from unstructured clinical narratives. We evaluated the performance of four BERT-based models using two fine-tuning strategies (multiple single-label and single multi-label) for detecting coexisting suicidal events from 500 annotated psychiatric evaluation notes. The notes were labeled for suicidal ideation (SI), suicide attempts (SA), exposure to suicide (ES), and non-suicidal self-injury (NSSI). RoBERTa outperformed other models using binary relevance (acc=0.86, F1=0.78). MentalBERT (F1=0.74) also exceeded BioClinicalBERT (F1=0.72). RoBERTa fine-tuned with …

The Performance Of Neurologically Intact Sequential Shona-English Bilingual Speakers On The Bilingual Aphasia Test, Mcloddy R. Kadyamusuma, Antony R. Joseph

Faculty Publications – Communication Sciences and Disorders

Background
Currently, no standardized culturally and linguistically appropriate assessment tools may be used to provide speech and language assessment for Shona-English bilingual speakers.

Aims
This study examined the performance of Shona-English sequential bilingual speakers on the full versions of the Shona and English Bilingual Aphasia Test (BAT).

Methods and Procedures
The adapted BAT-Sh and BAT-E were administered to 20 neurologically intact sequential bilingual individuals 30 to 40 years of age. Each participant was administered 32 tasks to facilitate a complete assessment of language skills at all levels of processing and for all modalities.

Results
The Shona-English sequential bilingual speakers performed …

Journey To Well-Being: An Exploration Of Thrivership Post-Domestic Violence, Kader Gumus

Antioch University Dissertations & Theses

Domestic violence profoundly affects multiple facets of a survivor’s life. While most existing literature on survivorship addresses the immediate aftermath of domestic violence, this study delves into the extended process following the trauma of abuse to attain “thrivership,” a new concept in the scholarly and practice literature that emphasizes enduring well-being and flourishing. This dissertation examines the journeys from surviving to thriving for 13 women who transformed themselves and their lives to achieve well-being after traumatic domestic violence. Bronfenbrenner’s ecological systems theory was applied to examine the multiple layers of environmental influences on an individual’s development, including the micro, meso, …

Post-Migration Living Distress And Suicidal Behavior In Refugee Populations Resettled In Vermont, Phoebe K. Lewis

Antioch University Dissertations & Theses

The study of refugee psychology and suicidal distress is a comparatively nascent field when compared with the body of research concerning non-refugee populations. Over the past fifty years, however, the post-migration refugee experience has been the subject of growing clinical interest. In particular, the construct of post-migration living distress (PMLD) has been identified as a salient factor contributing to psychological distress in refugee populations. This dissertation explores the relationship between PMLD and suicidality in a sample of refugees resettled in a New England city. Guided by the Interpersonal Theory of Suicide (IPTS), this dissertation considers how elements of the post-migration …

How Marriage And Family Therapy Graduate Programs Awaken, Develop, And Teach Clinical Intuition: A Hermeneutic Qualitative Phenomenological Study, Jessica Fountas

Antioch University Dissertations & Theses

This research explored how marriage and family therapy graduate programs awaken, develop, and teach clinical intuition. Using criterion-based sampling and snowball sampling, six licensed marriage and family therapists participated in a two-step hermeneutic phenomenological study consisting of individual semistructured interviews and a follow-up focus group. Requirements for participation were licensed marriage and family therapists who were in clinical practice, had experienced the phenomenon of clinical intuition and awakening of clinical intuition, and used clinical intuition in therapy with clients and in systemic supervision with supervisees. The research findings highlighted 14 themes: Reflection of the Experience of Clinical Intuition; Bodily Knowing, …

Frozen: A Grounded Theory Of Transgenerational Trauma Cycles In The Evangelical Slavic Diaspora Of Former Soviet Union Refugees, Yulia Shtareva

Antioch University Dissertations & Theses

This dissertation builds on historical and scientific assertions that Former Soviet Union immigrants survived distinct political traumas, resulting in unique, culturally adaptive behaviors and beliefs. Using constructivist grounded theory, it examined how these behaviors manifest in the evangelical Slavic community (ESC) of former Soviet Union Refugees (FSURs) in the U.S. The researcher asserts that (a) adaptations are generationally preserved in the ESC through a “cycle of authoritarianism,” and (b) survival strategies became maladaptive in new social environments. Narratives from eight young adults raised in the ESC were analyzed alongside a literature review and lived experience. Findings show that coping strategies …

Developing A Gpt-Based Virtual Training System For Medical Undergraduates' History Taking In Stroke Rehabilitation, Chao-Yu Hsu, Ching-Lin Hsieh, Jeng-Cheng Wu, Wen-Hsuan Hou

Rehabilitation Practice and Science

Background: Effective history taking in stroke rehabilitation requires comprehensive assessment skills, yet opportunities for medical undergraduates to practice such skills remain limited. Virtual patients (VPs), especially those powered by large language models (LLMs), offer a promising solution. This study aimed to develop and evaluate a GPT-based virtual training system for functional assessments in stroke rehabilitation history taking.

Methods: A mixed-methods design was employed in which VPs were modeled on a clinical stroke case and 10 core domains of functional assessments in stroke rehabilitation were integrated. A virtual examiner (VE) module provided automated scoring and feedback. Phase 1 evaluated the reliability …

Development Of A Stress Response Framework For Understanding Sogie Refugee Health, Arooran Saravanan Ananthavel Murugan

Theses and Dissertations (Comprehensive)

As an increasing number of individuals flee persecution on the basis of sexual orientation and gender identity expression (SOGIE), Canada has become a prominent destination for SOGIE refugees. The chronic stressors encountered by this marginalized population remain insufficiently studied, particularly in relation to physical health outcomes. This qualitative study investigates the cumulative health impacts of chronic stress among SOGIE refugees through the application of a cell-to-society framework, underpinned by Minority Stress Theory (MST). The study seeks to develop a SOGIE-specific stress response framework that theorizes the processes by which social and environmental stressors become biologically embedded, thereby contributing to elevated …

Changes In Functional Connectivity Are Associated With Functional Independence In The Early Postoperative Period Following Awake Surgical Resection Of Language-Eloquent Glioma, Kyle R Noll, Evan D Bander, Henry S Chen, Mariana Bradshaw, Jeffrey S Wefel, Vinodh A Kumar, Sujit S Prabhu, Ho-Ling Liu

Faculty, Staff and Student Publications

Background: Neurocognitive decline in patients with primary brain tumors is associated with alterations in the functional connectome and reduced independence in daily living. This study explores postoperative connectomic changes associated with functional independence outcomes in patients with eloquent glioma, and how these associations differ from neurocognitive-connetcomic relationships.

Methods: Fifteen patients with left perisylvian glioma underwent resting-state functional magnetic resonance imaging (fMRI) and neuropsychological evaluation within 2 weeks before and on average 1 month after resection. Functional independence was measured with the Physical Self-Maintenance Scale (PSMS) and the Instrumental Activities of Daily Living scale (IADL). Graph theoretical analysis quantified functional brain …

State Of The States: Blueprints For Building Age-Friendly Futures, Megan Stubbs-Richardson, Lauren E. Etheredge, Tockie V. Hemphill, Zaccheus J. Ahonle, Danielle K. Nadorff

Publications

Executive Summary:

Mississippi’s aging population growth mirrors national trends and suggests a need to establish equitable and sustainable age-friendly policies and programs. This report offers an overview of the best practices from age-friendly states, which can be adapted to meet unique challenges and opportunities for Mississippi’s aging population. We highlight five age-friendly policy areas that can improve Mississippi’s livability.

• Aging in Place: Best practices from California, Florida, and Massachusetts can be adapted to promote aging in place through structural changes to homes via universal design and home modifications, or through supportive housing programs and home care.

• Cross-Sector Collaboration: …

Therapeutic Alliance In A Culturally Tailored Transition Program For Latino Young Adults With Autism And Their Families, Antonio F Pagán, Katherine A Loveland, Ron Acierno

Faculty, Staff and Student Publications

Latino young adults with autism spectrum disorder (ASD) often face barriers to accessing culturally appropriate interventions that support adaptive functioning and family dynamics. Therapeutic alliance, the collaborative and trusting relationship between participants and providers, is a critical component of intervention success, yet its role in culturally tailored programs for Latino families remains underexplored. The present study examined therapeutic alliance in ¡Iniciando! la Adultez, a 12-week, culturally adapted intervention for Latino young adults with ASD and their Spanish-speaking parents. The program integrates Latino cultural values and language and consists of parent group therapy, young adult group therapy, and individual therapy sessions. …

Comusichiamo. First Language, Life-Soundtracks And Storytelling To Support The Cultural Wellbeing Of Migrants Living With Dementia, Simone Marino, Loretta Baldassar

Research outputs 2022 to 2026

This study, located at the intersection of anthropology, ageing, music therapy and dementia, explores the value of music, life-storytelling and first language, to support the cultural identity and wellbeing of people from culturally and linguistically diverse backgrounds living with dementia in Australia. It uses participant observation, the collection of oral histories and ‘life soundtracks’ to co-create a song with older Italian migrants and their families. This paper presents the first case study which informed the development of the music engagement program we call Comusichiamo (let’s make music together). The case study shows that the co-creation of a culturally tailored song, …

Cultural Influences, Experiences And Interventions Targeting Self-Management Behaviours For Prediabetes Or Type 2 Diabetes In First-Generation Immigrants: A Scoping Review, Min Zhang, Kirsten Coppell, Johnny Lo, Lisa Whitehead

Research outputs 2022 to 2026

Aim: To map the existing evidence and identify research gaps regarding the self-management of prediabetes or type 2 diabetes among first-generation immigrants ≥ 18 years. Design: A scoping review followed the JBI guidelines and was in accordance with the PRISMA extension for Scoping Reviews. Methods: A systematic search of CINAHL, Cochrane, EMBASE, MEDLINE, PsycINFO, ProQuest, SCOPUS and the Web of Science was conducted. Grey literature and reference lists of included studies were searched for additional citations. Articles published in English from the database inception to February 2023 were included. Results: We included 96 studies, of which 28.1% were published within …

Association Of Item-Level Responses To Cognitive Function Index With Tau Pathology And Hippocampal Volume In The A4 Study, Idris Demirsoy, Elham Ghanbarian, Babak Khorsand, Bhargav T Nallapu, Kellen K Petersen, Richard B Lipton, S Ahmad Sajjadi, Laura A Rabin, Ali Ezzati

2020-Current year OA Pubs

INTRODUCTION: Alzheimer's disease (AD) has a long preclinical phase in which individuals may accumulate amyloid beta (Aβ) and tau pathology without noticeable cognitive impairment. Subjective cognitive impairment reports can provide early insights into cognitive decline.

METHODS: In the A4 Study, 339 cognitively unimpaired, Aβ-positive individuals underwent tau positron emission tomography imaging. Tau status was classified based on medial temporal lobe tau standardized uptake value ratios (tau

RESULTS: Higher tau

DISCUSSION: These findings support the utility of participant- and study partner-reported concerns as early indicators of preclinical AD pathology, with potential value for early detection and trial enrichment strategies.

HIGHLIGHTS: Higher …

Protocol For The Asian Cohort For Alzheimer's Disease (Acad) Study, Pei-Chuan Ho, Walter A Kukull, Et Al.

2020-Current year OA Pubs

INTRODUCTION: To address knowledge gaps in Alzheimer's disease (AD) research, the Asian Cohort for Alzheimer's Disease (ACAD) Study will recruit over 5000 participants of Asian descent aged 60 or older in the United States and Canada. The current focus is on participants with Chinese, Korean, or Vietnamese ancestry, with the goal of characterizing both genetic and non-genetic risk factors. ACAD has assembled a culturally and linguistically appropriate data collection protocol, as well as a biosample collection protocol. Recruitment strategies follow community-based participatory research (CBPR) approaches to encourage research participation and engage Asian communities in brain health education.

METHODS: The ACAD …

Application Of Machine Learning And Large Language Models In Healthcare For Data Prediction And Summarization, Chiazam Chisom Izuchukwu

College of Graduate Studies: Theses & Dissertations

This study aims to examine the use of machine learning (ML) and large language models (LLMs) in healthcare to enhance disease prediction, clinical decision-making, and information management. Five supervised ML models—Logistic Regression (LR), Support Vector Machine (SVM), Random Forest (RF), Decision Trees (DT), and Naïve Bayes (NB)—on three different computing platforms—Google Colab, Databricks, and Snowflake—were employed for disease classification. Data preprocessing included treating missing values, encoding categorical variables utilizing one-hot-encoding, feature scaling when needed, and tackling class imbalance with Synthetic Minority Over-sampling Technique (SMOTE) before an 80-20 train-test separation. Models were created with Scikit-learn (Google Collab), Spark MLlib (Databricks), and …

Tracking The Evolving Role Of Artificial Intelligence In Implementation Science: Protocol For A Living Scoping Review Of Applications, Evaluation Approaches And Outcomes [Version 2; Peer Review: 2 Approved], Guillaume Fontaine, Byron J Powell, Et Al.

2020-Current year OA Pubs

BACKGROUND: Artificial intelligence (AI) offers significant opportunities to improve the field of implementation science by supporting key activities such as evidence synthesis, contextual analysis, and decision-making to promote the adoption and sustainability of evidence-based practices. This living scoping review aims to: (1) map applications of AI in implementation research and practice; (2) identify evaluation approaches, reported outcomes, and potential risks; and (3) synthesize reported research gaps and opportunities for advancing the use of AI in implementation science.

METHODS: This scoping review will follow the Joanna Briggs Institute (JBI) methodology and the Cochrane guidance for living systematic reviews. A living scoping …

When Nurses Worry: A Concept Analysis Of Intuition In Clinical Deterioration, Amy Louise Byrne, Deb Massey, Tracy Flenady, Justine Connor, Wei Ling Chua, Danielle Le Lagadec

Research outputs 2022 to 2026

Background: Nurse worry is a criterion often included in early warning systems tools and used to escalate care when other clinical markers do not indicate deterioration. What it means to worry, however, is not always clear. Aims: To generate a concept analysis of nurse worry in relation to clinical deterioration. Design: Rodgers's evolutionary method was used. Method: A review was first conducted in April 2024, searching the Cumulative Index for Nursing and Allied Health Literature, Pubmed, EmCare, and Embase databases. A total of 22 articles were subjected to analysis of the antecedents, attributes, and consequences of nurse worry in the …

Assessment Of Multilingual Children By Western Australian Speech-Language Pathologists: A Survey Of Practices, Barriers And Facilitators, Emily Frances Hunt, Charn Nang, Suzanne Jacqueline Meldrum, Elizabeth Armstrong

Research outputs 2022 to 2026

Purpose: In the past decade, diagnostic criteria for developmental language disorder, guidelines for assessment of multilingual children, and reviews of the diagnostic utility of dynamic assessment have been published. It is unknown how Australian speech-language pathologists currently assess multilingual children or how local factors influence assessment. Method: A mixed-method anonymous online survey of Western Australian speech-language pathologists explored the frequency and perceived usefulness of assessment practices recommended for multilingual children, elements of dynamic assessment used, and the utility of specific client factors for diagnosis. Confidence ratings and descriptions of barriers and facilitators that affect assessment of multilingual children were also …

Advancing Person-Centred Care Through Palliative Care Wa’S Acp Workshops: The Longer-Term Impact, Gertrude G. Phiri, Emma Gunner, Philip Bafile, Davina Porock

Research outputs 2022 to 2026

Planning for end-of-life and associated decision-making is one of global significance as it impacts the quality of care in palliative care settings, including ensuring that personal preferences are honoured. It is a priority for the Australian health system to use Advance Care Planning (ACP) as it is an effective tool for individuals and their families to make their personal preferences known and implemented. The aim of this project was to evaluate the longer-term impact of the Palliative Care Western Australia (PCWA) ACP workshops. Semi-structured, open-ended questions were used to collect data from 21 participants. Reflexive thematic analysis was used to …

Mental Health Support Workers Perspectives On Barriers To And Facilitators Of The Effective Delivery Of Their Roles: A Systematic Review And Meta-Aggregation, Martha Njuguna, Irene Ngune, Yvonne Middlewick

Research outputs 2022 to 2026

Mental health support workers (MHSWs) are an important workforce within the mental health care system. Research shows that support services delivered by MHSWs are effective at improving the outcomes of individuals with mental illness. However, there is also literature suggesting that this group of workers are facing many challenges in their roles. This qualitative systematic review sought to explore, analyze and synthesize available primary research literature on the experiences of MHSWs with the aim of identifying the barriers to and facilitators of effective delivery of their roles. An electronic search of Medline, CINAHL, PsycINFO, and Web of Science was conducted …

Facilitators, Barriers, And Strategies For Supporting Shared Decision-Making With People With Intellectual Disability: A West Australian Primary Healthcare Professional Perspective, Kathryn Teale, Abigail Lewis, Rachel Skoss

Research outputs 2022 to 2026

Background: Shared decision-making between patients and primary healthcare professionals positively impacts health outcomes. However, people with intellectual disability face additional barriers and require supported shared decision-making (SSDM) to participate. Little is known about how healthcare professionals use SSDM with this population. This paper explores the facilitators and barriers experienced, and strategies/resources employed by healthcare professionals working with people with intellectual disability. Method: Ten purposively sampled primary healthcare professionals participated in semi-structured interviews. This descriptive qualitative study used content analysis. Findings were compared with a proposed model of factors influencing triadic (the person with intellectual disability, their caregiver and the healthcare …

Child And Family Centred Care: A Three-Phased Principle-Based Concept Analysis, Maggie Zgambo, Julie Blamires, Mandie Foster, Mohammad Al-Motlaq, Therese A. O'Sullivan, Davina Houghton, Evalotte Mörelius

Research outputs 2022 to 2026

Introduction: Despite a growing multidisciplinary interest in the Child and Family Centred Care approach, its meaning remains unclear in extant literature. It is, therefore, crucial to explore, analyse, describe, and clarify the concept of the Child and Family Centred Care approach and its associated terms. Method: A three-phased principle-based concept analysis approach was used to analyse the concept of Child and Family Centred Care. A systematic search of literature was completed using the CINAHL, PsycINFO, Medline, Scopus, and Web of Science databases. Peer-reviewed articles on Child and Family Centred Care, published from inception to 2023 were included if they were …

Improving Mental Health Referral Systems In Rural Australia: Co-Design Study With Health Professionals And Consumers, Kate Bartel, Asini Malinka Siriwardene, Paul Worley, Kim Pearce, Niranjan Bidargaddi, Bronwin Patrickson, Simon Moody, Sharon Wingard, Martin Jones, Brian Mckenny, Darryl Cameron, Sharon Lawn, Amy E. Mendham

Research outputs 2022 to 2026

Background: In rural Australia, geographical isolation, limited resources, and complex health care navigation create significant barriers to mental health care access. Mental health care professionals and organizations often work in segregation, exacerbating existing barriers. Digital technology provides an opportunity to improve communication between providers and streamline workflows while supporting a diverse range of consumers. Objective: This co-design study aimed to identify rural community needs and explore digital solutions to enhance mental health service delivery pathways. Methods: Using a design-thinking methodology, we conducted focus groups and workshops with 17 participants (7 consumers and caregivers and 10 health care professionals) from a …

Elizabeth Usher Memorial Lecture 2024: Speech-Language Pathology Practice In Aboriginal Spaces: A Journey Of Learning And Unlearning, Elizabeth Armstrong

Research outputs 2022 to 2026

In this paper I describe learnings gained from 15 years collaboration with Aboriginal colleagues in Australia, in endeavours to improve rehabilitation services for Aboriginal people with brain injury and their families. Colleagues include Aboriginal researchers, clinicians, and people with communication and other disorders associated with brain injury and their families. My research journey in this field has been made possible through the work, mentoring, and support of these colleagues who introduced me to Aboriginal ways of knowing, being, and doing. My journey has involved challenging and un-learning some widely accepted Western tenets of speech-language pathology practice in order to explore …

Synthesising Cross-Speaker Data For Low-Resource Pathological Speech Recognition With Peft, Kesego Mokgosi, Milad Dadgar, Cathy Ennis, Robert Ross

Conference papers

Dysarthric speech recognition is essential for enhancing communication and accessibility for individuals with speech impairments, yet its development is hindered by a scarcity of robust, speaker-specific datasets. This study explores low-resource dysarthric speech recognition through cross-speaker transfer using synthetic data and parameter-efficient fine-tuning (PEFT). We integrate SpeechT5 text-to-speech (TTS) synthesis with x-vector speaker embeddings to generate speaker-specific dysarthric speech, enabling model adaptation while preserving pathological speech characteristics such as prosodic irregularities. Experiments on the TORGO dataset show that mixed cross-synthetic data with LoRA fine-tuning achieves a WER of 0.17, representing a 71.7% improvement over the standard model (0.60 WER) without …

A Systematic Review On Mental Health Chatbots: Trends, Design Principles, Evaluation Methods, And Future Research Agenda, Mohammad Amin Kuhail, Ons Al-Shamaileh, Shahbano Farooq, Hana Shahin, Fatema Abdelzaher, Justin Thomas

All Works

Recent decades have witnessed a rise in the prevalence of common mental health problems coupled with an increasing demand for talk‐based psychological therapies. This has coincided with the rise of mental health chatbots (MHCs), a corollary of which is the use of MHCs, AI‐driven, conversational agents, to provide interactive support, guidance, and therapeutic engagement for persons experiencing mental health challenges. There has been a growing research interest in MHCs, and this study provides a much‐needed systematic review that examines this expanding research literature, identifying themes, trends, and areas worthy of further exploration. This review identified and systematically explored 97 published …