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2024

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Recent Trends In The Incidence Of Gastric Cancer In The United States, Kyle S Liu, Syed Ahsan Raza, Hashem B El-Serag, Aaron P Thrift Jan 2024

Recent Trends In The Incidence Of Gastric Cancer In The United States, Kyle S Liu, Syed Ahsan Raza, Hashem B El-Serag, Aaron P Thrift

Faculty, Staff and Students Publications

BACKGROUND: Gastric cancer (GC) incidence rates overall in the United States have declined over recent decades and are predicted to continue declining. However, there have been mixed recent findings regarding the potential stabilization of rates and potential divergent trends by age group. We used the most recent cancer data for the United States and examined trends in GC between 1992 and 2019, overall and in important subgroups of the population.

METHODS: Age-adjusted GC incidence rates and trends in adults 20 years or older were calculated using data from the Surveillance, Epidemiology, and End Results (SEER) 12 program. Secular trends were …


Translational Symmetry In Convolutions With Localized Kernels Causes An Implicit Bias Toward High Frequency Adversarial Examples, Josue O Caro, Yilong Ju, Ryan Pyle, Sourav Dey, Wieland Brendel, Fabio Anselmi, Ankit B Patel Jan 2024

Translational Symmetry In Convolutions With Localized Kernels Causes An Implicit Bias Toward High Frequency Adversarial Examples, Josue O Caro, Yilong Ju, Ryan Pyle, Sourav Dey, Wieland Brendel, Fabio Anselmi, Ankit B Patel

Faculty, Staff and Students Publications

Adversarial attacks are still a significant challenge for neural networks. Recent efforts have shown that adversarial perturbations typically contain high-frequency features, but the root cause of this phenomenon remains unknown. Inspired by theoretical work on linear convolutional models, we hypothesize that translational symmetry in convolutional operations together with localized kernels implicitly bias the learning of high-frequency features, and that this is one of the main causes of high frequency adversarial examples. To test this hypothesis, we analyzed the impact of different choices of linear and non-linear architectures on the implicit bias of the learned features and adversarial perturbations, …


Development Of A Multi-Level/Multi-Modal Intervention For Health Care Transition Preparation, Beth H Garland, Mary Majumder, Constance M Wiemann, Blanca Sanchez-Fournier, Jordyn Babla, Albert C Hergenroeder Jan 2024

Development Of A Multi-Level/Multi-Modal Intervention For Health Care Transition Preparation, Beth H Garland, Mary Majumder, Constance M Wiemann, Blanca Sanchez-Fournier, Jordyn Babla, Albert C Hergenroeder

Center for Medical Ethics and Health Policy Staff Publications

Aims: Health care transition (HCT) to adult care and young adult disease self-management is a multi-step process involving three major stakeholders - the adolescent, the caregiver, and the provider. Preparation gaps exist within each of these stakeholder groups. This paper presents the development of the Intervention to Promote Autonomy and Competence in Transition-aged Youth (IPACT), a multi-level (adolescent, caregiver, provider), multi-modal (interactive skill building sessions, educational materials, videos) intervention to address gaps in all three stakeholder groups simultaneously and help support achieving the three core elements of HCT planning.

Methods: Eight processes were utilized to develop the IPACT intervention, including …


Flowering Rush (Butomus Umbellatus) Id Guide For The Columbia River, Gabriel Campbell, Jacob Rose Jan 2024

Flowering Rush (Butomus Umbellatus) Id Guide For The Columbia River, Gabriel Campbell, Jacob Rose

Center for Lakes and Reservoirs Publications and Presentations

This is a picture based field guide for how to identify Flowering Rush (Butomus umbellatus) in the Columbia River throughout Oregon and Washington. It includes how to tell this species from commonly co-occurring look-alike species.


Advances In Nanoprobes For Molecular Mri Of Alzheimer’S Disease, Parag Parekh, Andrew A Badachhape, Eric A Tanifum, Ananth V Annapragada, Ketan B Ghaghada Jan 2024

Advances In Nanoprobes For Molecular Mri Of Alzheimer’S Disease, Parag Parekh, Andrew A Badachhape, Eric A Tanifum, Ananth V Annapragada, Ketan B Ghaghada

Faculty, Staff and Students Publications

Alzheimer's disease is the most common cause of dementia and a leading cause of mortality in the elderly population. Diagnosis of Alzheimer's disease has traditionally relied on evaluation of clinical symptoms for cognitive impairment with a definitive diagnosis requiring post-mortem demonstration of neuropathology. However, advances in disease pathogenesis have revealed that patients exhibit Alzheimer's disease pathology several decades before the manifestation of clinical symptoms. Magnetic resonance imaging (MRI) plays an important role in the management of patients with Alzheimer's disease. The clinical availability of molecular MRI (mMRI) contrast agents can revolutionize the diagnosis of Alzheimer's disease. In this article, we …


Developing A Framework For Musical Ekphrasis In Jazz Composition, Jessica Carlton Jan 2024

Developing A Framework For Musical Ekphrasis In Jazz Composition, Jessica Carlton

Theses: Doctorates and Masters

Musical ekphrasis, as defined by musicologist Siglind Bruhn (2001), refers to musical compositions that transform, re-create, or ‘re-present’ a work of visual art or poetry. Though there exists a significant body of musical works that are based on visual art and poetry, there is a distinct lack of research and documentation on musical ekphrasis, particularly in the field of jazz and improvised music. Further, a formalised process framework for practitioners approaching ekphrastic composition has yet to be developed. This research project investigated musical ekphrasis through qualitative interviews with key practitioners, and a combination of practice-led research and research-led practice methodologies, …


Attitudes And Perceptions Towards Privacy And Surveillance In Australia, Aleatha J. Shanley Jan 2024

Attitudes And Perceptions Towards Privacy And Surveillance In Australia, Aleatha J. Shanley

Theses: Doctorates and Masters

Understanding attitudes towards privacy and surveillance technologies used to enhance security objectives is a complex, but crucial aspect for policy makers to consider. Historically, terrorism-related incidents justified the uptake of surveillance practices. More recently however, biosecurity concerns have motivated nation-states to adopt more intrusive surveillance measures. There is a growing body of literature that supports the public’s desire to maintain privacy despite fears of biological or physical threats.

This research set out to explore attitudes towards privacy and surveillance in an Australian context. Throughout the course of this endeavour, the COVID-19 pandemic emerged bringing with it a variety of track …


Enhancing Resilience In The Australian Security Vetting Process: Application Of The Psycho-Social Resources For Resilience Scale – Vetting (Prrs-V), Alan James Jnr Davies Jan 2024

Enhancing Resilience In The Australian Security Vetting Process: Application Of The Psycho-Social Resources For Resilience Scale – Vetting (Prrs-V), Alan James Jnr Davies

Theses: Doctorates and Masters

The disclosure or leaking of classified information by a trusted insider is an ongoing challenge for the national security apparatus in Australia and globally (Auditor General, 2018; Scott, 2020). In an effort to ensure that those with access to sensitive information will not disclose it, the Australian Government has a security vetting process. The Australian security vetting process measures a person's integrity by conducting a 'whole of person' assessment against several suitability indicators. In 2015, the Australian Government added resilience as a suitability indicator to its prescribed guidance on personnel security vetting, the Personnel Security Eligibility and Suitability of Personnel …


Searching For Equity In Positivity: A Two-Year Case Study Of The Effectiveness Of The Implementation Of Positive Education In A West Australian Public Secondary School Following A Year 7 Cohort To Year 8, Veronica J. Sutton Jan 2024

Searching For Equity In Positivity: A Two-Year Case Study Of The Effectiveness Of The Implementation Of Positive Education In A West Australian Public Secondary School Following A Year 7 Cohort To Year 8, Veronica J. Sutton

Theses: Doctorates and Masters

This research evaluated the effectiveness of explicitly teaching Positive Education to early adolescent learners transitioning into a metropolitan, secondary public school in Western Australia and to understand the source of their stress and where they felt supported. Based on teacher feedback, a model for embedding the development of social and emotional competencies (Equity in Positivity) in the Western Australian secondary metropolitan public-school context, in a sustainable and cost-effective way, was developed over a six year period and linked to the Australian Wellbeing Hub (2020).

The researcher adopted a mixed method, instrumental bounded case study methodology, longitudinally applied through the lens …


Data Justice In Education: Toward A Research Agenda, Luci Pangrazio, Glenn Auld, Julianne Lynch, Carly Sawatzki, Gavin Duffy, Shelley Hannigan, Jo O'Mara Jan 2024

Data Justice In Education: Toward A Research Agenda, Luci Pangrazio, Glenn Auld, Julianne Lynch, Carly Sawatzki, Gavin Duffy, Shelley Hannigan, Jo O'Mara

Articles

Educational institutions increasingly rely on digital platforms to deliver content and learning, monitor attendance, communicate with stakeholders, and evaluate institutional performance. Despite the efficiency and accessibility gains they offer, digital platforms are powered by personal data which, through a process of datafication, can be used to track, monitor, and profile staff and students. The insights drawn from this data can be used to shape educational and professional futures. This article examines how datafication has become a social justice issue in education, discussing the implications for well-being, decision-making, governance, and power in education. Using Hintz and colleagues framework for data justice, …


An Image Processing Approach For Real-Time Safety Assessment Of Autonomous Drone Delivery, Assem A. Abdelhak, Dan Moss, Alan Hicks, Susan Mckeever Jan 2024

An Image Processing Approach For Real-Time Safety Assessment Of Autonomous Drone Delivery, Assem A. Abdelhak, Dan Moss, Alan Hicks, Susan Mckeever

Articles

The aim of producing self-driving drones has driven many researchers to automate various drone driving functions, such as take-off, navigation, and landing. However, despite the emergence of delivery as one of the most important uses of autonomous drones, there is still no automatic way to verify the safety of the delivery stage. One of the primary steps in the delivery operation is to ensure that the dropping zone is a safe area on arrival and during the dropping process. This paper proposes an image-processing-based classification approach for the delivery drone dropping process at a predefined destination. It employs live streaming …


A Novel Integration Of Data-Driven Rule Generation And Computational Argumentation For Enhanced Explainable Ai, Lucas Rizzo, Damiano Verda, Serena Berretta, Luca Longo Jan 2024

A Novel Integration Of Data-Driven Rule Generation And Computational Argumentation For Enhanced Explainable Ai, Lucas Rizzo, Damiano Verda, Serena Berretta, Luca Longo

Articles

Explainable Artificial Intelligence (XAI) is a research area that clarifies AI decision-making processes to build user trust and promote responsible AI. Hence, a key scientific challenge in XAI is the development of methods that generate transparent and interpretable explanations while maintaining scalability and effectiveness in complex scenarios. Rule-based methods in XAI generate rules that can potentially explain AI inferences, yet they can also become convoluted in large scenarios, hindering their readability and scalability. Moreover, they often lack contrastive explanations, leaving users uncertain why specific predictions are preferred. To address this scientific problem, we explore the integration of computational argumentation—a sub-field …


Early-Phase Insulin Secretion During Mixed-Meal Tolerance Testing Predicts Β-Cell Function And Secretory Capacity In Cystic Fibrosis, Saba Sheikh, Darko Stefanovski, Marissa J Kilberg, Denis Hadjiliadis, Ronald C Rubenstein, Michael R Rickels, Andrea Kelly Jan 2024

Early-Phase Insulin Secretion During Mixed-Meal Tolerance Testing Predicts Β-Cell Function And Secretory Capacity In Cystic Fibrosis, Saba Sheikh, Darko Stefanovski, Marissa J Kilberg, Denis Hadjiliadis, Ronald C Rubenstein, Michael R Rickels, Andrea Kelly

2020-Current year OA Pubs

UNLABELLED: Insulin secretion within 30 minutes of nutrient ingestion is reduced in people with cystic fibrosis (PwCF) and pancreatic insufficiency and declines with worsening glucose tolerance. The glucose potentiated arginine (GPA) test is validated for quantifying β-cell secretory capacity as an estimate of functional β-cell mass but requires technical expertise and is burdensome. This study sought to compare insulin secretion during mixed-meal tolerance testing (MMTT) to GPA-derived parameters in PwCF.

METHODS: Secondary data analysis of CF-focused prospective studies was performed in PwCF categorized as 1) pancreatic insufficient [PI-CF] or 2) pancreatic sufficient [PS-CF] and in 3) non-CF controls. MMTT: insulin …


Referent Data For Investigations Of Upper Limb Accelerometry: Harmonized Data From Three Cohorts Of Typically-Developing Children, Catherine E Lang, Catherine R Hoyt, Jeffrey D Konrad, Kayla R Bell, Natasha Marrus, Marghuretta D Bland, Keith R Lohse, Allison E Miller Jan 2024

Referent Data For Investigations Of Upper Limb Accelerometry: Harmonized Data From Three Cohorts Of Typically-Developing Children, Catherine E Lang, Catherine R Hoyt, Jeffrey D Konrad, Kayla R Bell, Natasha Marrus, Marghuretta D Bland, Keith R Lohse, Allison E Miller

2020-Current year OA Pubs

AIM: The rise of wearable sensing technology shows promise for addressing the challenges of measuring motor behavior in pediatric populations. The current pediatric wearable sensing literature is highly variable with respect to the number of sensors used, sensor placement, wearing time, and how data extracted from the sensors are analyzed. Many studies derive conceptually similar variables via different calculation methods, making it hard to compare across studies and clinical populations. In hopes of moving the field forward, this report provides referent upper limb wearable sensor data from accelerometers on 25 variables in typically-developing children, ages 3-17 years.

METHODS: This is …


Sillyputty: Improved Clustering By Optimizing The Silhouette Width, Polina Bombina, Dwayne Tally, Zachary B. Abrams, Kevin R. Coombes Jan 2024

Sillyputty: Improved Clustering By Optimizing The Silhouette Width, Polina Bombina, Dwayne Tally, Zachary B. Abrams, Kevin R. Coombes

2020-Current year OA Pubs

Clustering is an important task in biomedical science, and it is widely believed that different data sets are best clustered using different algorithms. When choosing between clustering algorithms on the same data set, reseachers typically rely on global measures of quality, such as the mean silhouette width, and overlook the fine details of clustering. However, the silhouette width actually computes scores that describe how well each individual element is clustered. Inspired by this observation, we developed a novel clustering method, called SillyPutty. Unlike existing methods, SillyPutty uses the silhouette width for individual elements as a tool to optimize the mean …


A Neural Mechanism For Conserved Value Computations Integrating Information And Rewards, Ethan S Bromberg-Martin, Yang-Yang Feng, Takaya Ogasawara, J Kael White, Kaining Zhang, Ilya E Monosov Jan 2024

A Neural Mechanism For Conserved Value Computations Integrating Information And Rewards, Ethan S Bromberg-Martin, Yang-Yang Feng, Takaya Ogasawara, J Kael White, Kaining Zhang, Ilya E Monosov

2020-Current year OA Pubs

Behavioral and economic theory dictate that we decide between options based on their values. However, humans and animals eagerly seek information about uncertain future rewards, even when this does not provide any objective value. This implies that decisions are made by endowing information with subjective value and integrating it with the value of extrinsic rewards, but the mechanism is unknown. Here, we show that human and monkey value judgements obey strikingly conserved computational principles during multi-attribute decisions trading off information and extrinsic reward. We then identify a neural substrate in a highly conserved ancient structure, the lateral habenula (LHb). LHb …


Using Information Technology For Comprehensive Analysis And Prediction In Forensic Evidence, Faris Kamil Hasan Mihna, Mustafa Abdulfattah Habeeb, Yahya Layth Khaleel, Yasir Hussein Ali, Yasir Hussein Ali Jan 2024

Using Information Technology For Comprehensive Analysis And Prediction In Forensic Evidence, Faris Kamil Hasan Mihna, Mustafa Abdulfattah Habeeb, Yahya Layth Khaleel, Yasir Hussein Ali, Yasir Hussein Ali

Mesopotamian Journal of CyberSecurity

With the escalation of cybercriminal activities, the demand for forensic investigations into these crimes has grown significantly. However, the concept of systematic pre-preparation for potential forensic examinations during the software design phase, known as forensic readiness, has only recently gained attention. Against the backdrop of surging urban crime rates, this study aims to conduct a rigorous and precise analysis and forecast of crime rates in Los Angeles, employing advanced Artificial Intelligence (AI) technologies. This research amalgamates diverse datasets encompassing crime history, various socio-economic indicators, and geographical locations to attain a comprehensive understanding of how crimes manifest within the city. Leveraging …


Exploring Teachers’ Perspectives On Integrating Gaming Into Agriculture Education Through Nasef Farmcraft, Carrie Settles Livers Jan 2024

Exploring Teachers’ Perspectives On Integrating Gaming Into Agriculture Education Through Nasef Farmcraft, Carrie Settles Livers

Murray State Theses and Dissertations

With a growing population and a decrease in arable land, it is vital to prepare the next generation of agriculturalists. However, enrollment in agricultural education programs has been on the decline. Incorporating digital games into the classroom could serve to engage future students and encourage careers in agriculture. This study explored how Georgia agriculture teachers' technological and pedagogical knowledge influences their willingness to adopt digital games, specifically Georgia Farmcraft and Minecraft for Education, in their teaching. Additionally, it sought to identify demographic factors that might impact adoption and to determine effective professional development strategies to support teachers in using these …


Physician Decision Making Under Uncertainty In A Post-Dobbs America, Molly J. Walker Wilson, Michael S. Sinha Jan 2024

Physician Decision Making Under Uncertainty In A Post-Dobbs America, Molly J. Walker Wilson, Michael S. Sinha

All Faculty Scholarship

Following the Supreme Court's decision in Dobbs v. Jackson Women's Health Organization and a series of restrictive state laws post-Dobbs, physicians in many states now face difficult choices between evidence-based practice and criminal penalties. Previously, when deciding whether to provide abortion care, concern for the health of the patient was paramount. Now, fear of criminal penalties drives decision-making for physicians practicing in many areas of the country, including our home state: Missouri. For certain life-threatening complications, termination of pregnancy is warranted, but since Dobbs, physicians have been delaying these potentially lifesaving procedures for fear of criminal repercussions. Behavioral research on …


Relationship Analysis Of Storyline Curriculum Engagement And Academic Performance, Cassandra Shockley Jan 2024

Relationship Analysis Of Storyline Curriculum Engagement And Academic Performance, Cassandra Shockley

Murray State Theses and Dissertations

Secondary educators are responsible for moving students from dependent learners to independent individuals who can solve problems and be productive members of society. Science education has changed since 2012 when the PISA and TIMSS results were analyzed and showed that American students perform significantly lower than other countries. In 2013, Kentucky adopted new science standards that replaced the extensive lists of facts to be memorized with a set of performance expectations. Students are now tested on their ability to apply content knowledge to solve a phenomenon. Seventh-grade science teachers in classrooms with wide ranges of academic readiness have resisted switching …


The Effect Of Asynchronous Pre-Service Training On Aac Strategy Use, Cheri Dodge Chin Jan 2024

The Effect Of Asynchronous Pre-Service Training On Aac Strategy Use, Cheri Dodge Chin

Murray State Theses and Dissertations

This dissertation investigates the impact of a one-time online, asynchronous training program on graduate students' use of communication partner strategies for Augmentative and Alternative Communication (AAC) users. The study examines the training effect on the overall correct usage of naturalistic communication partner strategies, the implementation immediacy, the influence of feedback, and the training's benefits and drawbacks. Using an A-B single case research design with qualitative feedback, the study included pre-service university students studying speech pathology or education. Participants engaged in storybook reading activities with communication devices at a university clinic to establish baseline measures. Following this, they completed a one-hour …


Changing Demographics In Career & Technical Student Organizations, Elizabeth Hunt Galloway Jan 2024

Changing Demographics In Career & Technical Student Organizations, Elizabeth Hunt Galloway

Murray State Theses and Dissertations

The state of Georgia’s demographics has consistently changed in the last twenty years. Since 2010, the population of Georgia has steadily increased by 1% (Georgia Population by Year, County, Race, & More, 2023). A mirror of the state population increases occurred in the school system with 1% growth each year between 2010 and 2022 (Georgia Population by Year, County, Race, & More, 2023). The demographics of the state of Georgia has changed along with the population with an increase in Hispanic and Black population while the White population has decreased (Hauer, n.d.). The need to increase membership in Career Technical …


Examining Stigma In Rural Mental Health Care Settings: A Mixed Methods Approach, Lainie Krumenacker Jan 2024

Examining Stigma In Rural Mental Health Care Settings: A Mixed Methods Approach, Lainie Krumenacker

Murray State Theses and Dissertations

More than half of Americans will be diagnosed with a mental illness in their lifetime (CDC, 2021), yet stigma towards mental health affects both patients and providers. Although programs exist to address stigma, improve cultural competency among providers, and educate families on the importance of support, facilities are often limited on programs they provide due to allocation of resources and funds. Without a shift in treatment and programing, stigma will continue to impact patient care and outcome.

This study explored stigma among mental health providers in rural communities, while exploring potential differences in treatment among patients due to race. Mental …


Georgia Elementary Agriculture Education Pilot Program: An Extensive Look Into The History, Development, And Success, Christa Steinkamp Jan 2024

Georgia Elementary Agriculture Education Pilot Program: An Extensive Look Into The History, Development, And Success, Christa Steinkamp

Murray State Theses and Dissertations

Georgia Elementary Agricultural Education (EAE) was formally introduced through the 2018 Senate Bill 330 (SB33); a two-part bill passed with unanimous support in both the House & the Senate. The first part of the bill included the three-component model of school-based agricultural education for high schools and middle schools which includes classroom/laboratory instruction, supervised agricultural experience, and leadership development through the National FFA Organization. The second part of SB330 introduced an elementary agricultural education (EAE) pilot program. The three-year pilot program started in the 2019-2020 school year with twenty-five schools; and concluded with thirty-one schools at the end of the …


Perceptions Of Benefits From Middle School Agricultural Education Programs, Michael Hunter Jan 2024

Perceptions Of Benefits From Middle School Agricultural Education Programs, Michael Hunter

Murray State Theses and Dissertations

As agriculture education continues to evolve across the state of Georgia and the country, leaders need to understand the dynamic vision and the importance of this industry. Utilizing P-20 education initiatives and new concepts, leaders can implement agriculture education in more schools to increase diversity and provide students with opportunities to participate in the three-component model of agriculture education. This research aimed to explore the perceived benefits that high school principals, CTAE directors, and agriculture teachers have on middle school agriculture education programs. This research was confined to the Georgia FFA North Region. Findings indicated no significant evidence that middle …


A Comparison Of Student Achievement On Agriculture Mechanics End Of Pathway Assessments Among Agriculture Programs In Georgia, William Burt Jan 2024

A Comparison Of Student Achievement On Agriculture Mechanics End Of Pathway Assessments Among Agriculture Programs In Georgia, William Burt

Murray State Theses and Dissertations

Agriculture education programs in Georgia are held to the same standards and evaluations regardless of their location, resource availability, and student clientele. For schools with agriculture mechanics programs specifically, students are expected to obtain proficient skills in welding, electrical wiring, woodworking, small engines, concrete, and machinery. Students' are expected to obtain skill sets in these various content areas, yet the equipment and resources available to the educator differs among schools. The experience that a student encounters also differs among schools. For instance, some schools have multiple agriculture pathways for a student to enroll in, while other schools have minimal. The …


Factors Associated With Never Treatment And Acceptability Of Mass Drug Administration For The Elimination Of Lymphatic Filariasis In Guyana, 2021, Claudia Duguay, Reza A. Niles-Robin, Charles R. Thickstun, Horace Cox, Annastacia Sampson, Jean Seme-Fils Alexandre, Nathely Caleb-Mars, Charles W. Goss, Ana Morice, Ronaldo G. Carvalho Scholte, Alison Krentel Jan 2024

Factors Associated With Never Treatment And Acceptability Of Mass Drug Administration For The Elimination Of Lymphatic Filariasis In Guyana, 2021, Claudia Duguay, Reza A. Niles-Robin, Charles R. Thickstun, Horace Cox, Annastacia Sampson, Jean Seme-Fils Alexandre, Nathely Caleb-Mars, Charles W. Goss, Ana Morice, Ronaldo G. Carvalho Scholte, Alison Krentel

2020-Current year OA Pubs

Guyana remains one of four countries in the Americas endemic for lymphatic filariasis (LF). Elimination of LF requires repeated annual mass drug administration (MDA) with sufficient levels of coverage for success. This study assesses the acceptability and never treatment of LF MDA using data from a routine assessment survey in 2021. A subset of individuals, over 20 years of age (n = 2498), were selected to receive an expanded questionnaire to examine factors associated with acceptability and never treatment. Assessed factors include respondent demographics, knowledge, risk perceptions of LF, and opinions on the MDA programme. The majority (73%) of those …


Simplified Methods For Variance Estimation In Microbiome Abundance Count Data Analysis, Yiming Shi, Lili Liu, Jun Chen, Kristine M Wylie, Todd N Wylie, Molly J Stout, Chan Wang, Haixiang Zhang, Ya-Chen T Shih, Xiaoyi Xu, Ai Zhang, Sung Hee Park, Hongmei Jiang, Lei Liu Jan 2024

Simplified Methods For Variance Estimation In Microbiome Abundance Count Data Analysis, Yiming Shi, Lili Liu, Jun Chen, Kristine M Wylie, Todd N Wylie, Molly J Stout, Chan Wang, Haixiang Zhang, Ya-Chen T Shih, Xiaoyi Xu, Ai Zhang, Sung Hee Park, Hongmei Jiang, Lei Liu

2020-Current year OA Pubs

The complex nature of microbiome data has made the differential abundance analysis challenging. Microbiome abundance counts are often skewed to the right and heteroscedastic (also known as overdispersion), potentially leading to incorrect inferences if not properly addressed. In this paper, we propose a simple yet effective framework to tackle the challenges by integrating Poisson (log-linear) regression with standard error estimation through the Bootstrap method and Sandwich robust estimation. Such standard error estimates are accurate and yield satisfactory inference even if the distributional assumption or the variance structure is incorrect. Our approach is validated through extensive simulation studies, demonstrating its effectiveness …