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2024

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Experiences Of Counselors Working With Adolescents, Allison Bradford Chow Jan 2024

Experiences Of Counselors Working With Adolescents, Allison Bradford Chow

Antioch University Dissertations & Theses

This qualitative study aimed to examine the lived experience of clinical mental health counselors working with adolescents. Participants included pre-licensed (associate) or licensed counselors who predominately work with and have a strong preference for working with adolescent clients. Data was collected through individual interviews and analyzed with a descriptive-interpretative approach. Ten domains were identified as part of data analysis: (a) Understanding Adolescent Culture and Building a Therapeutic Alliance, (b) The Intersection of Counselor and Adolescent Emotions, (c) Transference and Countertransference, (d) Clinical Challenges and Barriers, (e) The Multifaceted Role of Parents, (f) Nuances of Confidentiality, (g) Adolescent Development and Strengths, …


Therapeutic Interventions For Adolescents With Non-Epileptic Seizures, Noah Trantel Jan 2024

Therapeutic Interventions For Adolescents With Non-Epileptic Seizures, Noah Trantel

Antioch University Dissertations & Theses

Although there have been some studies that explore the lived experiences of adults with non-epileptic seizures, there have been limited studies that examine the lived experiences of adolescents and emerging adults with non-epileptic seizures. This qualitative study explored the experiences of emerging adults who had been diagnosed with non-epileptic seizures during adolescence. The study focused on specific interventions utilized in therapy that they found helpful, highlighted what their experiences were throughout their daily lives, and what treatment recommendations were provided. The research will also help guide parents, clinicians, and individuals with NES towards treatment recommendations. Eight participants completed an in-depth, …


Feminized Servanthood, Gendered Scapegoating, And The Disappearance Of Gen-X/Millennial Protestant Clergy Women, Lynn Horan Jan 2024

Feminized Servanthood, Gendered Scapegoating, And The Disappearance Of Gen-X/Millennial Protestant Clergy Women, Lynn Horan

Antioch University Dissertations & Theses

In today’s mainline Protestant churches, young women clergy navigate a precarious leadership space. While women’s ordination is well-established in American Protestantism (Burnett, 2017), Gen-X/Millennial clergy women find themselves at the crosshairs of conflicting gender narratives and unsustainable expectations of what it means to be both a woman and an ordained pastoral leader. Through the use of feminist constructivist grounded theory methodology, this study explored the lived experiences of Gen-X/Millennial clergy women who have left active ministry or a specific pastoral position due to concerns over their own interpersonal boundaries and psychological safety. Through dimensional analysis of in-depth interviews with 20 …


Lioness Of Lisabi: A Creative Dissertation Characterizing Funimilayo Ransome-Kuti As A Foremost Yoruba Feminist Leader, Oyewole Sobo Jan 2024

Lioness Of Lisabi: A Creative Dissertation Characterizing Funimilayo Ransome-Kuti As A Foremost Yoruba Feminist Leader, Oyewole Sobo

Antioch University Dissertations & Theses

This creative dissertation highlights the feminist leadership qualities of a social revolutionist, Funmilayo Ransome Kuti, a native of Abeokuta, Nigeria. Her struggle for equity and justice profoundly encouraged the empowerment of Indigenous women during her time. The undeniable truth is that black women have played a pivotal role in the fight for equal rights and justice, particularly in the United States. While the social struggles of American black female revolutionaries such as Rosa Parks, Coretta Scott King, Dorothy Height, Ella Baker, and Dorothy Cotton are documented and celebrated, little or nothing is known about their African counterparts. This creative dissertation …


Examining Social Identity Among Urban School Leaders: A Case Study Of Five Principals In New York City, Victor G. Frias Jr. Jan 2024

Examining Social Identity Among Urban School Leaders: A Case Study Of Five Principals In New York City, Victor G. Frias Jr.

Antioch University Dissertations & Theses

Exploring how school leaders address underrepresented student voices, meaning those of marginalized experiences along the continuum of social identity including though not limited to race, class, gender, immigration, and LGBTQ issues in schools is more essential than ever following the novel coronavirus of 2019 (COVID-19). Principals’ social identities (i.e., race, class, and gender), and their connected social locations and personal histories reveal how their leadership styles can contribute to the support of marginalized communities. Hence, this qualitative research study employed a case study methodology to investigate whether and how the social identities and lived experiences of principals in the Brooklyn …


Educators Remedying Linguicism Through Critical Language Awareness And Critical Trans/Multilingualism: Towards Planetary Justice, Kate Alice Garnett Jan 2024

Educators Remedying Linguicism Through Critical Language Awareness And Critical Trans/Multilingualism: Towards Planetary Justice, Kate Alice Garnett

Antioch University Dissertations & Theses

The aim of this dissertation is to investigate how a critical understanding of language use, language ideologies, and linguicism can influence educators’ praxis and identities. Specifically, the research explores how Critical Language Awareness (CLA) impacts educators’ praxis, their lingua-cultural identities, and their relationships with language and linguicism towards planetary justice. These inquiries were examined through participants’ involvement in a 6-week teacher educator course designed by this researcher entitled Humane Language Education. The course aimed to enable participants to analyze and address language injustices individually, communally, and globally. Unexamined language biases erode linguistic and cultural diversity, disseminate violence and discrimination, and …


Exploring Integrated Active Learning Practices In An Accelerated Fully Online Graduate-Level Course At A Hispanic Serving Institution, P. Ming-Tsan Lu, Seokmin Kang Jan 2024

Exploring Integrated Active Learning Practices In An Accelerated Fully Online Graduate-Level Course At A Hispanic Serving Institution, P. Ming-Tsan Lu, Seokmin Kang

Teaching and Learning Faculty Publications

The purpose of the study aimed to explore integrated active learning (IAL) practices in a graduate-level fully online, accelerated course at an HSI, with a focus on students’ perceptions, and to evaluate the implementation of integrated active learning based on student feedback and reflections. Course instructors started implementing IAL practices for the same course in 2022. Data from before and after IAL implementation in terms of course syllabi and course designs on Blackboard, the LMS used in the HSI, were collected. To investigate students’ perceptions, survey methods were also conducted. Findings revealed that graduate students overwhelmingly preferred IAL over traditional …


Promoting Understanding Of Three Dimensions Of Science Learning Plus Nature Of Science Using Phenomenon-Based Learning, Maryam Saberi, Noushin Nouri Jan 2024

Promoting Understanding Of Three Dimensions Of Science Learning Plus Nature Of Science Using Phenomenon-Based Learning, Maryam Saberi, Noushin Nouri

Teaching and Learning Faculty Publications

The utilization of phenomenon-based learning (PhBL) for science instruction remains limited despite its alignment with the goals outlined in the Next Generation Science Standards (NGSS; NGSS Lead States, 2013) due to the lack of exemplary materials and inadequate training opportunities for teachers. The aim of this article is to illustrate the steps of the PhBL method by providing an exploratory learning experience as it was implemented in a preservice setting. In this study, we provide an innovative perspective by illuminating how this kind of instruction can be used as a context to explicitly discuss the three dimensions of learning (i.e., …


Gvsu Undergraduate And Graduate Catalog, 2024-2025, Grand Valley State University Jan 2024

Gvsu Undergraduate And Graduate Catalog, 2024-2025, Grand Valley State University

Course Catalogs, 1963 - Current

Grand Valley State University 2024-2025 undergraduate and graduate course catalog. Course catalogs are published annually to provide students with information and guidance for enrollment.


Distribution: Understanding Customer-Facing Logistics In Africa, Emmanuel T. Kodzi Jan 2024

Distribution: Understanding Customer-Facing Logistics In Africa, Emmanuel T. Kodzi

Faculty Publications

Companies seeking to do business in Africa often focus more on challenges they need to address, rather than opportunities presented to them. The need to manage their investments across diverse countries, population profiles, infrastructure development levels, and local capabilities is viewed in terms of complexity. However, improved situational understanding will better inform investment decisions regarding product movements among points of origin, production, and consumption. Several aspects of logistics may be considered in this regard, but we focus on customer-facing logistics. We assume that few companies have the capability and resources to both produce and deliver products to end-buyers in a …


Coalescence: A Carnivore Coexistence Curriculum That Braids Indigenous & Western Ecological Knowledge Into A Relevant And Experiential Learning Opportunity For Youth, Stephanie Anne Barron Jan 2024

Coalescence: A Carnivore Coexistence Curriculum That Braids Indigenous & Western Ecological Knowledge Into A Relevant And Experiential Learning Opportunity For Youth, Stephanie Anne Barron

Graduate Student Theses, Dissertations, & Professional Papers

As grizzly bears (Ursus arctos horriblis) begin to reoccupy more of their historic range, and as humans and large carnivore populations continue to increase, incidences of human carnivore conflict are on the rise. A decolonial curriculum designed in collaboration with the Confederated Salish and Kootenai Tribe’s wildlife biologists stands to increase awareness of Indigenous ecological knowledge and teach youth about the importance of coexistence with carnivores. Additionally, this project could greatly influence youth perceptions of grizzly bears and other large carnivores. This research project examines the development and implementation of a carnivore coexistence curriculum for youth that is guided by …


American Indian Census Rolls: An Underutilized Source Of Historical Demographic Information On Tribal Populations, David Swanson, Jeff Tayman Jan 2024

American Indian Census Rolls: An Underutilized Source Of Historical Demographic Information On Tribal Populations, David Swanson, Jeff Tayman

Publications, Reports and Presentations

Historical information on tribal populations in the United States is incomplete. American Indians and Alaska Natives were not enumerated with the general population until the 1940 decennial census. However, Indian Census Rolls were produced for the period 1885 – 1940 under the auspices of the Bureau of Indian Affairs in the U.S. The information given in the Indian Census Rolls varies but usually includes the roll number, age, gender, tribal identity, and relationship to the head of the family. In this paper, we present background information on Indian Census Rolls and demonstrate how the digitized microfiche census roll schedules can …


Evidence That Ericoid Mycorrhizal Shrubs Can Outcompete Ectomycorrhizal Trees For Nitrogen In Tannin-Rich Litter, Kai C. Rains, Caroline Bledsoe, Tamara E. Kraus, Nina Wurzburger Jan 2024

Evidence That Ericoid Mycorrhizal Shrubs Can Outcompete Ectomycorrhizal Trees For Nitrogen In Tannin-Rich Litter, Kai C. Rains, Caroline Bledsoe, Tamara E. Kraus, Nina Wurzburger

School of Geosciences Faculty and Staff Publications

Mycorrhizal associations of trees play a key role in ecosystem biogeochemistry, yet we know relatively little about the nutrient acquisition strategies of ericoid mycorrhizal (ErM) shrubs, despite their prevalence in forest understories. ErM shrubs tend to produce litter with high concentrations of polyphenols, which form decay-resistant complexes with organic nitrogen (N). Some ErM fungi appear capable of producing a diverse suite of extracellular enzymes, but it is unclear whether this enables ErM shrubs to acquire the N from their own litter, and whether this ability is greater than that of ectomycorrhizal (EcM) trees, with which they commonly co-occur. Here, we …


Aquatic Invasive Species Survey And Treatment On Lake Umatilla And Lake Celilo 2024-2025 Report, Jacob Rose, Gabriel E. Campbell Jan 2024

Aquatic Invasive Species Survey And Treatment On Lake Umatilla And Lake Celilo 2024-2025 Report, Jacob Rose, Gabriel E. Campbell

Center for Lakes and Reservoirs Publications and Presentations

Flowering Rush (Butomus umbellatus) is an invasive aquatic plant in the Pacific Northwest that threatens salmon habitat. The Center for Lakes and Reservoirs staff surveyed for this and other aquatic species from 2024 and 2025 in the Columbia River in Lake Umatilla and Lake Celilo. This document summarizes their survey efforts including their protocols, data, and small-scale removal efforts.


The Next Generation, Jeremiah Chin Jan 2024

The Next Generation, Jeremiah Chin

Articles

What would the law look like if we let children remake it? Laws govern, classify, and circumscribe children who inherit the law and its consequences. Discourses of power invoke children as rhetorical strategies to gain political favor or obviate a position—yet children are uncritically excluded from participating in the systems that control them. Children are subjected to the laws and objects of legislation, but denied the rights, autonomy, or authority to participate in the making of law and policy. Even the conceptualization of the constitutional rights of children is treated as an assumption, ill-defined and under theorized by traditional legal …


Artificial Intelligence- Driven Fvm-Ann Model For Entropy Analysis Of Mhd Natural Bioconvection In Nanofluid-Filled Porous Cavities, N. Elsedais, M. A. Mansour, A. M. Aly, Sara Abdelsalam Jan 2024

Artificial Intelligence- Driven Fvm-Ann Model For Entropy Analysis Of Mhd Natural Bioconvection In Nanofluid-Filled Porous Cavities, N. Elsedais, M. A. Mansour, A. M. Aly, Sara Abdelsalam

Basic Science Engineering

No abstract provided.


Statistical Analysis Of Single-Cell Protein Data., Brooke L. Fridley, Simon Vandekar, Inna Chervoneva, Julia Wrobel, Siyuan Ma Jan 2024

Statistical Analysis Of Single-Cell Protein Data., Brooke L. Fridley, Simon Vandekar, Inna Chervoneva, Julia Wrobel, Siyuan Ma

Manuscripts, Articles, Book Chapters and Other Papers

Immune modulation is considered a hallmark of cancer initiation and progression, with immune cell density being consistently associated with clinical outcomes of individuals with cancer. Multiplex immunofluorescence (mIF) microscopy combined with automated image analysis is a novel and increasingly used technique that allows for the assessment and visualization of the tumor microenvironment (TME). Recently, application of this new technology to tissue microarrays (TMAs) or whole tissue sections from large cancer studies has been used to characterize different cell populations in the TME with enhanced reproducibility and accuracy. Generally, mIF data has been used to examine the presence and abundance of …


Exploring Angiotensin Ii And Oxidative Stress In Radiation-Induced Cataract Formation: Potential For Therapeutic Intervention, Vidya P. Kumar, Yali Kong, Riana Dolland, Sandra R. Brown, Kan Wang, Damian Dolland, David Mu, Milton L. Brown Jan 2024

Exploring Angiotensin Ii And Oxidative Stress In Radiation-Induced Cataract Formation: Potential For Therapeutic Intervention, Vidya P. Kumar, Yali Kong, Riana Dolland, Sandra R. Brown, Kan Wang, Damian Dolland, David Mu, Milton L. Brown

Department of Biomedical and Translational Sciences Faculty Publications

Radiation-induced cataracts (RICs) represent a significant public health challenge, particularly impacting individuals exposed to ionizing radiation (IR) through medical treatments, occupational settings, and environmental factors. Effective therapeutic strategies require a deep understanding of the mechanisms underlying RIC formation (RICF). This study investigates the roles of angiotensin II (Ang II) and oxidative stress in RIC development, with a focus on their combined effects on lens transparency and cellular function. Key mechanisms include the generation of reactive oxygen species (ROS) and oxidative damage to lens proteins and lipids, as well as the impact of Ang II on inflammatory responses and cellular apoptosis. …


Student Interaction With Generative Ai: An Exploration Of An Emergent Information-Search Process, Ryan M. Schuetzler, Justin Scott Giboney, Taylor M. Wells, Benjamin Richardson, Tom Meservy, Cole Sutton, Clay Posey, Jacob Steffen, Amanda Lee Hughes Jan 2024

Student Interaction With Generative Ai: An Exploration Of An Emergent Information-Search Process, Ryan M. Schuetzler, Justin Scott Giboney, Taylor M. Wells, Benjamin Richardson, Tom Meservy, Cole Sutton, Clay Posey, Jacob Steffen, Amanda Lee Hughes

Faculty Publications

ChatGPT, a generative artificial intelligence, is one of the fastest-adopted tools in history and has quickly become a valued tool in education. This study seeks to understand how generative artificial intelligence has changed the information search process. We collected prompts submitted to ChatGPT and thoughts about ChatGPT responses through a survey of 455 students at a US university. Using thematic analysis, we identified ways that ChatGPT changes the information search process of students by supporting diverse information needs, allowing cycling of prompt adjustments, and promoting easy adoption of results.


A Codified Liability Regime To Stimulate Greater Investment In Subpatentable Innovation, Jerome H. Reichman, Ana Santos Rutschman Jan 2024

A Codified Liability Regime To Stimulate Greater Investment In Subpatentable Innovation, Jerome H. Reichman, Ana Santos Rutschman

Faculty Scholarship

The global intellectual property system rests on a distinction between exclusive property rights and free competition. Exclusive rights vary in strength and intensity, but the opposite of protection is almost always free competition. Distinctions of intensity are drawn in terms of the length of protection given to different subject matters plus variable lists of exceptions and limitations to exclusive rights. But the bottom line is that, when protection is not available under the existing system, free competition prevails, and vice-versa (i.e., where there is exclusivity, free competition is deferred for a specified period of time).

This Article departs from a …


Use Of Hydroxychloroquine In Multidrug Protocols For Sars-Cov-2, Eleftherios Gkioulekas, Peter A. Mccullough Jan 2024

Use Of Hydroxychloroquine In Multidrug Protocols For Sars-Cov-2, Eleftherios Gkioulekas, Peter A. Mccullough

School of Mathematical & Statistical Sciences Faculty Publications

We review the available evidence supporting the use of hydroxychloroquine-based multidrug protocols in the treatment of COVID-19, in response to a recently published editorial in the Tasman Medical Journal.


Tigra Scientifica, Full Issue Jan 2024

Tigra Scientifica, Full Issue

Tigra scientifica

Tigra scientifica, showcasing the outstanding work by Clemson University students in the Creative Inquiry course Popular Science Journalism. Science and technology shape our world in profound ways — from the rise of space tourism to the rapid development of new medical treatments. In a democracy, communicating science is essential for informed debate and decision-making, a responsibility these students have embraced with energy and skill. The magazine began in Spring 2011 under Holly Tuten, Ph.D., who founded the CI course to pass along her passion for science writing. Since then, more than 200 students from 14 majors across five colleges have …


Synthesis Ago Nanoparticles By Nd:Yag Laser With Different Pulse Energies, Munaf S. Majeed, Shaymaa M. Mahmoud Mahmoud, Raghad Majeed Rasheed, Alaa Adnan Rashad Jan 2024

Synthesis Ago Nanoparticles By Nd:Yag Laser With Different Pulse Energies, Munaf S. Majeed, Shaymaa M. Mahmoud Mahmoud, Raghad Majeed Rasheed, Alaa Adnan Rashad

Baghdad Science Journal

One technique used to prepare nanoparticles material is Pulsed Laser Ablation in Liquid (PLAL), Silver Oxide nanoparticles (AgO) were prepared by using this technique, where silver target was submerged in ultra-pure water (UPW) at room temperature after that Nd:Yag laser which characteristics by 1064 nm wavelength, Q-switched, and 6ns pulse duration was used to irradiated silver target. This preparation method was used to study the effects of laser irradiation on Nanoparticles synthesized by used varying laser pulse energy 1000 mJ, 500 mJ, and 100 mJ, with 500 pulses each time on the particle size. Nanoparticles are characterized using XRD, SEM, …


Water Treatment Using Zinc Nanoparticles And Apricot Plant Extracts From Organic And Inorganic Pollution, Suzan Muslim Abdullah, Abbas Ali Salih Al-Hamdani, Labeeb Ahmed Al-Zubaidi Jan 2024

Water Treatment Using Zinc Nanoparticles And Apricot Plant Extracts From Organic And Inorganic Pollution, Suzan Muslim Abdullah, Abbas Ali Salih Al-Hamdani, Labeeb Ahmed Al-Zubaidi

Baghdad Science Journal

The apricot plant was washed, dried, and powdered after harvesting to produce a fine powder that was used in water treatment. created an alcoholic extract from the apricot plant using ethanol, which was then analysed using GC-MS, Fourier transform infrared spectroscopy, and ultraviolet-visible spectroscopy to identify the active components. Zinc nanoparticles were created using an alcoholic extract. FTIR, UV-Vis, SEM, EDX, and TEM are used to characterize zinc nanoparticles. Using a continuous processing procedure, zinc nanoparticles with apricot extract and powder were employed to clean polluted water. Firstly, 2 g of zinc nanoparticles were used with 20 ml of polluted …


Study Of The Anticancer And Antimicrobial Biological Activity Of A New Series Of Thiohydantoin Derivatives, Qusay Hussein Hays, Dakhil Zughayir Mutlaq Jan 2024

Study Of The Anticancer And Antimicrobial Biological Activity Of A New Series Of Thiohydantoin Derivatives, Qusay Hussein Hays, Dakhil Zughayir Mutlaq

Baghdad Science Journal

Recently, some prostate cancer patients have acquired resistance to the second -generation drugs (anzalutamide and apalutamide) prescribed for the treatment of this disease due to the emergence of the F876L mutation, which represents a challenge to modern medicine. In this study, a new series of 2-thiohydantoin derivatives were prepared through the reaction of different derivatives of maleimide (1c-4c) with isothiocyanate derivatives. The prepared compounds were diagnosed using FT-IR,1H-NMR ,13C-NMR, Mass spectra. The prepared series compounds has been studied against prostate cancer cells. The MTT assay was used to determine the activity of the prepared compounds against prostate cancer cells. The …


Can Large Language Models Discern Evidence For Scientific Hypotheses? Case Studies In The Social Sciences, Sai Koneru, Jian Wu, Sarah Rajtmajer Jan 2024

Can Large Language Models Discern Evidence For Scientific Hypotheses? Case Studies In The Social Sciences, Sai Koneru, Jian Wu, Sarah Rajtmajer

Computer Science Faculty Publications

Hypothesis formulation and testing are central to empirical research. A strong hypothesis is a best guess based on existing evidence and informed by a comprehensive view of relevant literature. However, with exponential increase in the number of scientific articles published annually, manual aggregation and synthesis of evidence related to a given hypothesis is a challenge. Our work explores the ability of current large language models (LLMs) to discern evidence in support or refute of specific hypotheses based on the text of scientific abstracts. We share a novel dataset for the task of scientific hypothesis evidencing using community-driven annotations of studies …


Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang Jan 2024

Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation

Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited.

Results

Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of …


Hite: A Fast And Accurate Dynamic Boundary Adjustment Approach For Full-Length Transposable Element Detection And Annotation, Kang Hu, Peng Ning, Minghua Xu, You Zou, Jianye Chang, Xin Gao, Yaohang Li, Jue Ruan, Bin Hu, Jianxin Wang Jan 2024

Hite: A Fast And Accurate Dynamic Boundary Adjustment Approach For Full-Length Transposable Element Detection And Annotation, Kang Hu, Peng Ning, Minghua Xu, You Zou, Jianye Chang, Xin Gao, Yaohang Li, Jue Ruan, Bin Hu, Jianxin Wang

Computer Science Faculty Publications

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, …


The Combined Focal Loss And Dice Loss Function Improves The Segmentation Of Beta-Sheets In Medium-Resolution Cryo-Electron-Microscopy Density Maps, Yongcheng Mu, Thu Nguyen, Bryan Hawickhorst, Willy Wriggers, Jiangwen Sun, Jing He Jan 2024

The Combined Focal Loss And Dice Loss Function Improves The Segmentation Of Beta-Sheets In Medium-Resolution Cryo-Electron-Microscopy Density Maps, Yongcheng Mu, Thu Nguyen, Bryan Hawickhorst, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Although multiple neural networks have been proposed for detecting secondary structures from medium-resolution (5–10 Å) cryo-electron microscopy (cryo-EM) maps, the loss functions used in the existing deep learning networks are primarily based on cross-entropy loss, which is known to be sensitive to class imbalances. To monitor and tune the performance of various loss functions for the secondary structure detection problem, we investigated five loss functions: cross-entropy, Focal loss, Dice loss, and two combined loss functions. Using a U-Net architecture in our DeepSSETracer method and a dataset composed of 1,355 box-cropped atomic-structure/density-map pairs, we found that a newly designed loss function …


Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers Jan 2024

Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers

Computer Science Faculty Publications

Motivation: This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results: We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 …