Medicine and Health Sciences Commons^™

Developmental Patterning Of Peptide Transcription In The Central Circadian Clock In Both Sexes, Vania Carmona-Alcocer, Lindsey S. Brown, Aisha Anchan, Kayla E. Rohr, Jennifer A. Evans

Biomedical Sciences Faculty Research and Publications

Introduction: Neuropeptide signaling modulates the function of central clock neurons in the suprachiasmatic nucleus (SCN) during development and adulthood. Arginine vasopressin (AVP) and vasoactive intestinal peptide (VIP) are expressed early in SCN development, but the precise timing of transcriptional onset has been difficult to establish due to age-related changes in the rhythmic expression of each peptide.

Methods: To provide insight into spatial patterning of peptide transcription during SCN development, we used a transgenic approach to define the onset of Avp and Vip transcription. Avp-Cre or Vip-Cre males were crossed to Ai9^+/+ females, producing offspring in which the fluorescent protein …

Structural And Solution Speciation Studies On Selected [Cu(Nn)(Oo)] Complexes And An Investigation Of Their Biomimetic Activity, Ros Generation And Their Cytotoxicity In Normoxic, Hypoxic And Anoxic Environments In Mcf-7 Breast Cancer-Derived Cells, Hollie Jenkins

Articles

Reactive oxygen species(ROS) generation with subsequent DNA damage is one of the principle mechanisms of action assigned to copper-based anticancer complexes. The efficacy of this type of chemotherapeutic may be reduced in the low oxygen environment of tumours. In this study the cytotoxicity of three complexes, [Cu(dips)(phen)] (1), [Cu(ph)(phen)]·2H2O (2) and [Cu(ph)(bpy)]·H2O (3) (disp: 3,5-diisopropylsalicylate, phen: 1,10- phenanthroline, ph: phthalate, bpy: 2,2′-bipyridyl) were assessed for anticancer activity in the breast-cancer derived MCF-7 line under normoxic, hypoxic and anoxic conditions. In an immortalised keratinocyte HaCaT cell line, the cytotoxicity of complexes 2 and 3 was significantly reduced under both normoxic and …

Peptidases Are Potential Targets Of Copper(Ii)-1,10-Phenanthroline-5,6-Dione Complex, A Promising And Potent New Drug Against Trichomonas Vaginalis, Graziela Vargas Rigo, Fernanda Gomes Cardoso, Matheus Mendonca Pereira, Michael Devereux, Malachy Mccann, Andre L.S. Santos, Tiana Tasca

Articles

Trichomonas vaginalis is responsible for 156 million new cases per year worldwide. When present asymptomatically, the parasite can lead to serious complications, such as development of cervical and prostate cancer. As infection increases the acquisition and transmission of HIV, the control of trichomoniasis represents an important niche for the discovery and development of new antiparasitic molecules. This urogenital parasite synthesizes several molecules that allow the establishment and pathogenesis of infection. Among them, peptidases occupy key roles as virulence factors, and the inhibition of these enzymes has become an important mechanism for modulating pathogenesis. Based on these premises, our group recently …

Meeting The Client Halfway: A Relational Revision To Account For Intra-Actions In Psychotherapeutic Space, Lara Pirro Jancetic

Antioch University Dissertations & Theses

This post-qualitative study branching from new-materialist, post-humanist epistemology and ontology examines relationality through the lens of three different theories: agential realism, John Shotter’s communication theory, and relational mindfulness. These theories each describe the dynamics involved in relationships, how they each make sense of these dynamics, and what they entail for human relations. Using a post-qualitative diffractive methodology, this study examines these theories and how they intersect to bring about new insights in our understanding of relationships and how this information can support therapy practice. The results are a series of nine principles of orientation, which were applied to marriage and …

What Does It Look Like For Mental Healthcare Organizations To Be Healthy Places To Work? An Action Research Study, Stephanie L. Fox

Antioch University Dissertations & Theses

Mental healthcare organizations have a reputation for being unhealthy places to work. The irony of this reputation is keenly felt by its workforce who report unsustainable workloads, high levels of stress, and lack of support or engagement from higher-level leadership. As a mental healthcare provider now in a position of leadership, who has worked across all levels of care within the sector, it was of interest to me to explore how a mental health organization can become a healthier and more sustainable place to work. I approached this study with the assumption that if an organization was healthy and intentional …

Connecting Antibiotic Resistance To The Environment (Care): Introducing A Novel Framework Integrating Chemical Cross-Resistance And Place-Based Engagement To The Blue Marsh Watershed In Reading, Pennsylvania, Jill Felker

Antioch University Dissertations & Theses

Antibiotic resistance is a serious health threat around the world. Millions of individuals are infected with antibiotic-resistant bacteria yearly, and thousands die from previously curable illnesses. Although antibiotic resistance occurs naturally, misuse of antibiotics accelerates the loss of their effectiveness. Public health campaigns focusing on antibiotic awareness have not effectively communicated and educated the public on this health crisis. New efforts to combat antibiotic resistance are urgently needed. This dissertation focuses on the ecological and public health components of antibiotic resistance research that must be addressed to decelerate antibiotic resistance. A new interdisciplinary theoretical framework was developed to Connect Antibiotic …

A Case Study On Factors Influencing Retention Of Mental Health Clinicians In A New Hampshire Community Mental Health Center, William E. Keating

Antioch University Dissertations & Theses

This study examined the perspectives of master-level clinical mental health providers and members of leadership at a Community Mental Health Center (CMHC) in New Hampshire, to understand clinician and leadership perspectives as to why master-level providers choose to continue working at CMHCs. Most prior research on turnover in such organizations has focused on why so many leave their positions, however this study instead focuses on factors related to the decision to stay at a specific CMHC in an urban area of New Hampshire. A single case study method was utilized to focus on masters-level mental health care providers with additional …

Relationship Goals: How Do Relational Therapists Conceptualize Cases And Treatment Plan When Working With Consensually Non-Monogamous Clients?, Caitlyn Burns

Antioch University Dissertations & Theses

This study aimed to explore how relational therapists in the United States conceptualize cases and treatment plan when working with consensually non-monogamous clients and how dominant discourses about relationships (mononormativity) influence relational therapists during this process through a queer theory lens. This was a grounded theory study and surveyed a sample of thirty relational therapists or therapists-in- training. Results showed relational therapists conduct conceptualization and treatment planning through a two-part process. Therapists intend to treat CNM clients the same as any other client, but are unable to do so due to dominant discourses of mononormativity. Furthermore, mononormative discourses influenced relational …

Black Mental Health Clinicians' Experiences And Lessons From The Intersecting Crises Of Black Mental Health, Covid-19, And Racial Trauma: An Interpretive Phenomenological Study, Chanté Meadows

Antioch University Dissertations & Theses

This study explored the experiences of African American mental health clinicians’ during the intersecting crises of the Black mental health crisis, the highly publicized racial tension tied to extrajudicial violence and over-policing of Black Americans, and the COVID-19 pandemic. The pandemic started a global crisis that affected millions of people’s physical and mental health and overall well-being. Shared trauma explores the duality of mental health clinicians’ personal and professional experiences. Grounded in critical race theory and models of trauma, this study explores Black mental health clinicians’ lived experiences and lessons. This is an interpretive phenomenological study with narrative interviews of …

Black Marriage, Attachment And Connecting In Relationships: An Observational Multi-Method Study Investigating The Effects Of The Getting The Love You Want Workshop On Black Couples’ In-Session Attachment, Interactions, Marital Satisfaction And Communication, Paula Smith

Antioch University Dissertations & Theses

The focus of this dissertation is examining the impact of Imago Relationship Therapy (IRT), more specifically the “Getting the Love You Want” workshop (GTLYW), on five Black/African American couples’ attachment, interactions, marital satisfaction and communication. This study examines Black couples’ lived experiences through a modified version of a quantitative measure, called the Patient Attachment Client System (PACS), the Marital Satisfaction Questionnaire-Revised (MSQ-R), semi-structured questionnaires to measure qualitative data as well as direct observation of participants’ interactions. PACS analyzes how patients’ in-session discourse enables them to share present experiences and link these processes with their attachment structure. In this view, attachment …

Counselors’ Lived Experience Treating Patients Utilizing Methadone: The Intersection Of Culture, Policy, And Stigma, Kathryn Floyd Eggert

Antioch University Dissertations & Theses

The United States continues to experience unprecedented deaths related to the opioid epidemic. Efforts to address the epidemic remain hampered by war-on-drugs policies that stigmatize people who use drugs and create barriers to accessing evidence-based treatments, particularly methadone maintenance treatments (MMT). Despite 50 years of research regarding MMT, it remains highly regulated, and arguably the most stigmatized treatment. The punitive regulatory structure of MMT remained unchanged until emergency waivers were initiated during the COVID-19 pandemic. The study used an exploratory, critical phenomenological approach to examine the intersection of culture and regulation on the lived experiences of 26 addiction counselors who …

Incidents Of Snake Fungal Disease Caused By The Fungal Pathogen Ophidiomyces Ophidiicola In Texas, Alan Lizarraga, Lezley Hart, Michele Nolen, Lance R. Williams, Joseph S. Glavy

Pharmacy Faculty Publications and Presentations

The pathogen Ophidiomyces ophidiicola, widely known as the primary cause of snake fungal disease (SFD), has been detected in Texas’s naïve snakes. Our team set out to characterize O. ophidiicola’s spread in eastern Texas. From December 2018 until November 2021, we sampled and screened with ultraviolet (UV) light 176 snakes across eastern Texas and detected 27. O. ophidiicola’s positive snakes using qPCR and one snake in which SFD was confirmed via additional histological examination. Upon finding the ribbon snake with a clear clinical display, we isolated and cultured what we believe to be the first culture from Texas. This cultured …

Feasibility Of And Experience Using A Portable Mri Scanner In The Neonatal Intensive Care Unit., Maura Sien, Amie L. Robinson, Houchun H. Hu, Christopher R. Nitkin, Ara Hall, Marcie G. Files, Nathan S. Artz, John T. Pitts, Sherwin S. Chan

Manuscripts, Articles, Book Chapters and Other Papers

OBJECTIVE: A portable, low-field MRI system is now Food and Drug Administration cleared and has been shown to be safe and useful in adult intensive care unit settings. No neonatal studies have been performed. The objective is to assess our preliminary experience and assess feasibility of using the portable MRI system at the bedside in a neonatal intensive care unit (NICU) at a quaternary children's hospital.

STUDY DESIGN: This was a single-site prospective cohort study in neonates ≥2 kg conducted between October and December 2020. All parents provided informed consent. Neonates underwent portable MRI examination in the NICU with support …

Behavioral Health Grants Overview 2022, Parkview Health

Health Services and Informatics Research

2022 List of Externally and Internally Funded Research for our Behavioral Health Outreach Initiatives.

Our Mission: To strengthen awareness around mental health, support needs in our community, reduce stigma, and encourage people to connect with care.

Conceptualizing Care Partners' Burden, Stress, And Support For Reintegrating Veterans: A Mixed Methods Study., Nicholas A Rattray, Mindy Flanagan, Allison Mann, Leah Danson, Ai-Nghia Do, Diana Natividad, Katrina Spontak, Gala True

Health Services and Informatics Research

BACKGROUND: People who support Veterans as they transition from their military service into civilian life may be at an increased risk of psychological distress. Existing studies focus primarily on paid family caregivers, but few studies include spouses and informal non-family "care partners." We sought to identify key challenges faced by care partners of Veterans with invisible injuries.

METHODS: Semi-structured interviews were conducted with 36 individuals involved in supporting a recently separated US military Veteran enrolled in a 2-year longitudinal study. CPs completed validated measures on perceived stress, caregiving burden, quality of their relationship, life satisfaction, and flourishing. Independent

RESULTS: Care …

Do Physiological Variables Predict The Need For Transport To Hospital From Music Festivals? An Analysis Of Australian Festival Data, Ned Douglas, Jake Donovan, James Carew, Kayla Brouwer, Ebony Edwards, Mitchell Gibson, Jacqueline Leverett, Joseph Paul, Lachlan Holbery-Morgan, Jessica Pritchard, Elyssia Bourke, Erin Smith

Research outputs 2022 to 2026

Objective:

Using physiological markers to detect patients at risk of deterioration is common. Deaths at music festivals in Australia prompted scrutiny of tools to identify critically unwell patients for transport to hospital. This study evaluated initial physiological parameters to identify patients selected for transport to hospital from a music festival.

Methods:

A retrospective audit of 2045 presentations at music festivals in Victoria, Australia, was performed. Presentation heart rate, systolic blood pressure, respiratory rate, oxygen saturation, temperature, and Glasgow Coma Scale were assessed using area under the receiver operating characteristic curve (AUROC) analysis, with a prespecified threshold of 0.7.

Results:

The …

Powering Single-Cell Genomics To Unravel Circulating Tumour Cell Subpopulations In Non-Small Cell Lung Cancer Patients, Emmanuel Acheampong, Michael Morici, Afaf Abed, Samantha Bowyer, Du-Bois Asante, Weitao Lin, Michael Millward, Elin S. Gray, Aaron Beasley

Research outputs 2022 to 2026

Background

Circulating tumour cells (CTCs) are attractive “liquid biopsy” candidates that could provide insights into the different phenotypes of tumours present within a patient. The epithelial-to-mesenchymal transition (EMT) of CTCs is considered a critical step in tumour metastasis; however, it may confound traditional epithelial feature-based CTC isolation and detection. We applied single-cell copy number alteration (CNA) analysis for the identification of genomic alterations to confirm the neoplastic nature of circulating cells with only mesenchymal phenotypes.

Methods

We isolated CTCs from blood samples collected from 46 NSCLC patients using the Parsortix system. Enriched cells were subjected to immunofluorescent staining for CTC …

Law Enforcement Recruit Health Database, Myles C. Murphy, Simone Radavelli-Bagatini, Garth Allen, Nicolas Hart, Andrea Mosler

Research Datasets

Our study established clear demographic, mental health/physical injury, and physical performance data to be collected in a law enforcement recruit training program for injury surveillance and performance monitoring. Furthermore, we identified several items that were classified as relevant, but unlikely to be reported truthfully. These items which can help inform current practice and assist clinicians to determine the trustfulness of information received by patients when working within law enforcement environments.

Principles And Philosophies For Speech And Language Therapists Working With People With Primary Progressive Aphasia: An International Expert Consensus, A. Volkmer, J. Cartwright, L. Ruggero, A. Beales, J. Gallée, S. Grasso, M. Henry, R. Jokel, J. Kindell, R. Khayum, M. Pozzebon, E. Rochon, C. Taylor-Rubin, R. Townsend, F. Walker, S. Beeke, Deborah Hersh

Research outputs 2022 to 2026

Purpose:

Primary progressive aphasia (PPA) is a language-led dementia associated with Alzheimer’s pathology and fronto-temporal lobar degeneration. Multiple tailored speech and language interventions have been developed for people with PPA. Speech and language therapists/speech-language pathologists (SLT/Ps) report lacking confidence in identifying the most pertinent interventions options relevant to their clients living with PPA during their illness trajectory.

Materials and methods:

The aim of this study was to establish a consensus amongst 15 clinical-academic SLT/Ps on best practice in selection and delivery of speech and language therapy interventions for people with PPA. An online nominal group technique (NGT) and consequent focus …

Injury Profiles Of Police Recruits Undergoing Basic Physical Training: A Prospective Cohort Study, Nicole Merrick, Nicolas H. Hart, Andrea B. Mosler, Garth Allen, Myles C. Murphy

Research outputs 2022 to 2026

Purpose:

A lack of published epidemiological data among police recruits presents a major challenge when designing appropriate prevention programs to reduce injury burden. We aimed to report the injury epidemiology of Western Australian (WA) Police Force recruits and examine sex and age as injury risk factors

Methods:

Retrospective analyses were conducted of prospectively collected injury data from WA Police Force recruits between 2018–2021. Injury was defined as ‘time-loss’ and injury incidence rate per 1000 training days (Poisson exact 95% confidence intervals) was calculated. For each region and type of injury, the incidence, severity, and burden were calculated. The association between …

Autonomy Versus Support: Self-Reliance And Help-Seeking For Mental Health Problems In Young People, Amelia Ishikawa, Debra Rickwood, Emily Bariola, Navjot Bhullar

Research outputs 2022 to 2026

Purpose:

Many young people with mental ill-health do not seek support, and developmental growth in self-reliance may be a barrier to help-seeking. Increasing autonomy is a positive developmental task for youth and a key aspect of resilience. This study examined the influence of perceived social support and resilience on the previously unexamined relationship between self-reliance and intentions to seek help from informal, professional, and self-help sources for mental health problems.

Methods:

An online survey was completed by a representative Australian community sample of 5,203 young people aged 12–25 years (half female), in May–June 2020.

Results:

Path analysis showed the hypothesised …

Patterns And Implications Of Neurological Examination Findings In Autosomal Dominant Alzheimer Disease, Jonathan Vöglein, Nicolai Franzmeier, John C. Morris, Marianne Dieterich, Eric Mcdade, Mikael Simons, Oliver Preische, Anna Hofmann, Jason Hassenstab, Tammie L. Benzinger, Anne Fagan, James M. Noble, Sarah B. Berman, Neill R. Graff-Radford, Bernardino Ghetti, Martin R. Farlow, Jasmeer P. Chhatwal, Stephen Salloway, Chengjie Xiong, Celeste M. Karch, Nigel Cairns, Richard J. Perrin, Gregory Day, Ralph Martins, Raquel Sanchez-Valle, Hiroshi Mori, Hiroyuki Shimada, Takeshi Ikeuchi, Kazushi Suzuki, Peter R. Schofield, Colin L. Masters, Alison Goate, Virginia Buckles, Nick C. Fox, Patricio Chrem, Ricardo Allegri, John M. Ringman, Igor Yakushev, Christoph Laske, Mathias Jucker, Günter Höglinger, Randall L. Bateman, Adrian Danek, Johannes Levin, Dominantly Inherited Alzheimer Network

Research outputs 2022 to 2026

Introduction:

As knowledge about neurological examination findings in autosomal dominant Alzheimer disease (ADAD) is incomplete, we aimed to determine the frequency and significance of neurological examination findings in ADAD.

Methods:

Frequencies of neurological examination findings were compared between symptomatic mutation carriers and non mutation carriers from the Dominantly Inherited Alzheimer Network (DIAN) to define AD neurological examination findings. AD neurological examination findings were analyzed regarding frequency, association with and predictive value regarding cognitive decline, and association with brain atrophy in symptomatic mutation carriers.

Results:

AD neurological examination findings included abnormal deep tendon reflexes, gait disturbance, pathological cranial nerve examination findings, …

Identifying The Serious Clinical Outcomes Of Adverse Reactions To Drugs By A Multi-Task Deep Learning Framework, Haochen Zhao, Peng Ni, Qichang Zhao, Xiao Liang, Di Ai, Shannon Erhardt, Jun Wang, Yaohang Li, Jiianxin Wang

Computer Science Faculty Publications

Adverse Drug Reactions (ADRs) have a direct impact on human health. As continuous pharmacovigilance and drug monitoring prove to be costly and time-consuming, computational methods have emerged as promising alternatives. However, most existing computational methods primarily focus on predicting whether or not the drug is associated with an adverse reaction and do not consider the core issue of drug benefit-risk assessment-whether the treatment outcome is serious when adverse drug reactions occur. To this end, we categorize serious clinical outcomes caused by adverse reactions to drugs into seven distinct classes and present a deep learning framework, so-called GCAP, for predicting the …

Consensus Guidelines For Sarcopenia Prevention, Diagnosis And Management In Australia And New Zealand, Jesse Zanker, Marc Sim, Kate Anderson, Saliu Balogun, Sharon L. Brennan-Olsen, Elsa Dent, Gustavo Duque, Christian M. Girgis, Mathis Grossmann, Alan Hayes, Tim Henwood, Vasant Hirani, Charles Inderjeeth, Sandra Iuliano, Justin Keogh, Joshua R. Lewis, Gordon S. Lynch, Julie A. Pasco, Steven Phu, Esmee M. Reijnierse, Nicholas Russell, Lara Vlietstra, Renuka Visvanathan, Troy Walker, Debra L. Waters, Solomon Yu, Andrea B. Maier, Robin M. Daly, David Scott

Research outputs 2022 to 2026

Background:

Sarcopenia is an age-associated skeletal muscle condition characterized by low muscle mass, strength, and physical performance. There is no international consensus on a sarcopenia definition and no contemporaneous clinical and research guidelines specific to Australia and New Zealand. The Australian and New Zealand Society for Sarcopenia and Frailty Research (ANZSSFR) Sarcopenia Diagnosis and Management Task Force aimed to develop consensus guidelines for sarcopenia prevention, assessment, management and research, informed by evidence, consumer opinion, and expert consensus, for use by health professionals and researchers in Australia and New Zealand.

Methods:

A four-phase modified Delphi process involving topic experts and informed …

Cellbrf: A Feature Selection Method For Single-Cell Clustering Using Cell Balance And Random Forest, Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang

Computer Science Faculty Publications

Motivation

Single-cell RNA sequencing (scRNA-seq) offers a powerful tool to dissect the complexity of biological tissues through cell sub-population identification in combination with clustering approaches. Feature selection is a critical step for improving the accuracy and interpretability of single-cell clustering. Existing feature selection methods underutilize the discriminatory potential of genes across distinct cell types. We hypothesize that incorporating such information could further boost the performance of single cell clustering. Results

We develop CellBRF, a feature selection method that considers genes’ relevance to cell types for single-cell clustering. The key idea is to identify genes that are most important for discriminating …

Enabling Customization Of Discussion Forums For Blind Users, Mohan Sunkara, Yash Prakash, Hae-Na Lee, Sampath Jayarathna, Vikas Ashok

Computer Science Faculty Publications

Online discussion forums have become an integral component of news, entertainment, information, and video-streaming websites, where people all over the world actively engage in discussions on a wide range of topics including politics, sports, music, business, health, and world affairs. Yet, little is known about their usability for blind users, who aurally interact with the forum conversations using screen reader assistive technology. In an interview study, blind users stated that they often had an arduous and frustrating interaction experience while consuming conversation threads, mainly due to the highly redundant content and the absence of customization options to selectively view portions …

The Impact Of Acute Calcium Intake On Bone Turnover Markers During A Training Day In Elite Male Rowers, Bronwen Lundy, Alannah K. A. Mckay, Nikita C. Fensham, Fensham, Nicolin Tee, Bryce Anderson, Aimee Morabito, Megan L. R. Ross, Marc Sim, Kathryn Ackerman, Louise M. Burke

Research outputs 2022 to 2026

Introduction: While an acute exercise session typically increases bone turnover markers (BTM), the impact of subsequent sessions and the interaction with pre-exercise calcium intake remains unclear despite the application to the ‘real life’ training of many competitive athletes. Methods: Using a randomized crossover design, elite male rowers (n = 16) completed two trials, a week apart, consisting of two 90-minute rowing ergometer sessions (Ex1, Ex2) separated by 150 minutes. Prior to each trial, participants consumed a high (CAL: ~1000 mg) or isocaloric low (CON: < 10 mg) calcium meal. Biochemical markers including parathyroid hormone: PTH; serum ionised calcium (iCa) and bone turnover markers (C-terminal telopeptide of type I collagen: β-CTX-I; osteocalcin: OC) were monitored from baseline to 3 hours post Ex2. Results: While each session caused perturbances of serum iCa, CAL maintained calcium concentrations above those of CON for most time points, 4.5 and 2.4 % higher post EX1 and EX2 respectively. The decrease in iCa in CON was associated with an elevation of blood PTH (p < 0.05) and β-CTX-I (p < 0.0001) over this period of repeated training sessions and their recovery, particularly during and after Ex2. Pre-exercise intake of calcium-rich foods lowered BTM over the course of a day with several training sessions. Conclusions: Pre-exercise intake of a calcium-rich meal prior to training sessions undertaken within the same day had a cumulative and prolonged effect on the stabilisation of blood iCa during exercise. In turn, this reduced the post-exercise PTH response, potentially attenuating the increase in markers of bone resorption. Such practical strategies may be integrated into the athlete’s overall sports nutrition plan, with the potential to safeguard long term bone health and reduce the risk of bone stress injuries.

Msdrp: A Deep Learning Model Based On Multisource Data For Predicting Drug Response, Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Cancer heterogeneity drastically affects cancer therapeutic outcomes. Predicting drug response in vitro is expected to help formulate personalized therapy regimens. In recent years, several computational models based on machine learning and deep learning have been proposed to predict drug response in vitro. However, most of these methods capture drug features based on a single drug description (e.g. drug structure), without considering the relationships between drugs and biological entities (e.g. target, diseases, and side effects). Moreover, most of these methods collect features separately for drugs and cell lines but fail to consider the pairwise interactions between drugs and cell …

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …

Progenitor Cell Isolation From Mouse Epididymal Adipose Tissue And Sequencing Library Construction, Qianglin Liu, Chaoyang Li, Yuxia Li, Leshan Wang, Xujia Zhang, Buhao Deng, Peidong Gao, Mohammad Shiri, Fozi Alkaifi, Junxing Zhao, Jacqueline M. Stephens, Constantine A. Simintiras, Joseph Francis, Jiangwen Sun, Xing Fu

Computer Science Faculty Publications

Here, we present a protocol to isolate progenitor cells from mouse epididymal visceral adipose tissue and construct bulk RNA and assay for transposase-accessible chromatin with sequencing (ATAC-seq) libraries. We describe steps for adipose tissue collection, cell isolation, and cell staining and sorting. We then detail procedures for both ATAC-seq and RNA sequencing library construction. This protocol can also be applied to other tissues and cell types directly or with minor modifications.

For complete details on the use and execution of this protocol, please refer to Liu et al. (2023).¹

*¹ Liu, Q., Li, C., Deng, B., Gao, P., …