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2022

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Advances In Head And Neck Cancer Pain, Y Ye, D D Jensen, C T Viet, H L Pan, W M Campana, M Amit, M D Boada Aug 2022

Advances In Head And Neck Cancer Pain, Y Ye, D D Jensen, C T Viet, H L Pan, W M Campana, M Amit, M D Boada

Faculty, Staff and Student Publications

Head and neck cancer (HNC) affects over 890,000 people annually worldwide and has a mortality rate of 50%. Aside from poor survival, HNC pain impairs eating, drinking, and talking in patients, severely reducing quality of life. Different pain phenotype in patients (allodynia, hyperalgesia, and spontaneous pain) results from a combination of anatomical, histopathological, and molecular differences between cancers. Poor pathologic features (e.g., perineural invasion, lymph node metastasis) are associated with increased pain. The use of syngeneic/immunocompetent animal models, as well as a new mouse model of perineural invasion, provides novel insights into the pathobiology of HNC pain. Glial and immune …


Microbiome Dynamics During Chemoradiation Therapy For Anal Cancer, Daniel Lin, Molly B El Alam, Joseph Abi Jaoude, Ramez Kouzy, Jae L Phan, Jacob H Elnaggar, Brianna Resendiz, Andrea Y Delgado Medrano, Erica J Lynn, Nicholas D Nguyen, Sonal S Noticewala, Geena G Mathew, Emma B Holliday, Bruce D Minsky, Prajnan Das, Van K Morris, Cathy Eng, Melissa P Mezzari, Joseph F Petrosino, Nadim J Ajami, Ann H Klopp, Cullen M Taniguchi, Lauren E Colbert Aug 2022

Microbiome Dynamics During Chemoradiation Therapy For Anal Cancer, Daniel Lin, Molly B El Alam, Joseph Abi Jaoude, Ramez Kouzy, Jae L Phan, Jacob H Elnaggar, Brianna Resendiz, Andrea Y Delgado Medrano, Erica J Lynn, Nicholas D Nguyen, Sonal S Noticewala, Geena G Mathew, Emma B Holliday, Bruce D Minsky, Prajnan Das, Van K Morris, Cathy Eng, Melissa P Mezzari, Joseph F Petrosino, Nadim J Ajami, Ann H Klopp, Cullen M Taniguchi, Lauren E Colbert

Faculty, Staff and Student Publications

Purpose: Patients with localized squamous cell carcinoma of the anus (SCCA) who experience treatment toxicity or recurrences have few therapeutic options. Investigation into the microbiome's influence on treatment toxicity and its potential use as a predictive biomarker could improve these patients' outcomes. Our study presents the first longitudinal characterization of the SCCA tumor microbiome and its associations with treatment-related toxicities.

Methods and materials: This prospective cohort study included patients with nonmetastatic SCCA receiving standard-of-care chemoradiation therapy. Anorectal swabs of the tumor site were collected before, during, and after treatment. Patient-reported quality-of-life metrics were collected at similar time points. 16S rRNA …


Artificial Intelligence-Assisted Mapping Of Proliferation Centers Allows The Distinction Of Accelerated Phase From Large Cell Transformation In Chronic Lymphocytic Leukemia, Siba El Hussein, Pingjun Chen, L Jeffrey Medeiros, John D Hazle, Jia Wu, Joseph D Khoury Aug 2022

Artificial Intelligence-Assisted Mapping Of Proliferation Centers Allows The Distinction Of Accelerated Phase From Large Cell Transformation In Chronic Lymphocytic Leukemia, Siba El Hussein, Pingjun Chen, L Jeffrey Medeiros, John D Hazle, Jia Wu, Joseph D Khoury

Faculty, Staff and Student Publications

Chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL) is characterized morphologically by numerous small lymphocytes and pale nodules composed of prolymphocytes and paraimmunoblasts known as proliferation centers (PCs). Patients with CLL can undergo transformation to a more aggressive lymphoma, most often diffuse large B-cell lymphoma (DLBCL), known as Richter transformation (RT). An accelerated phase of CLL (aCLL) also may be observed which correlates with subsequent transformation to DLBCL, and may represent an early stage of transformation. Distinguishing PCs in CLL from aCLL or RT can be diagnostically challenging, particularly in small needle biopsy specimens. Available guidelines pertaining to distinguishing CLL from its' …


Plasma Metabolomics Analysis Of Aspirin Treatment And Risk Of Colorectal Adenomas, Elizabeth L Barry, Veronika Fedirko, Yutong Jin, Ken Liu, Leila A Mott, Janet L Peacock, Michael N Passarelli, John A Baron, Dean P Jones Aug 2022

Plasma Metabolomics Analysis Of Aspirin Treatment And Risk Of Colorectal Adenomas, Elizabeth L Barry, Veronika Fedirko, Yutong Jin, Ken Liu, Leila A Mott, Janet L Peacock, Michael N Passarelli, John A Baron, Dean P Jones

Faculty, Staff and Student Publications

Despite substantial observational and experimental evidence that aspirin use can provide protection against the development of colorectal neoplasia, our understanding of the molecular mechanisms involved is inadequate and limits our ability to use this drug effectively and safely for chemoprevention. We employed an untargeted plasma metabolomics approach using liquid chromatography with high-resolution mass spectroscopy to explore novel metabolites that may contribute to the chemopreventive effects of aspirin. Associations between levels of metabolic features in plasma and aspirin treatment were investigated among 523 participants in a randomized placebo-controlled clinical trial of two doses of aspirin (81 or 325 mg/day) and were …


Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support A Root Of The Eukaryotic Tree Of Life Between Opisthokonts And All Other Lineages, Mario A. Cerón-Romero, Miguel M. Fonseca, Leonardo De Oliveira Martins, David Posada, Laura A. Katz Aug 2022

Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support A Root Of The Eukaryotic Tree Of Life Between Opisthokonts And All Other Lineages, Mario A. Cerón-Romero, Miguel M. Fonseca, Leonardo De Oliveira Martins, David Posada, Laura A. Katz

Biological Sciences: Faculty Publications

Advances in phylogenomics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single-gene fusion. Subsequent, highly cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes does not consider phylogenetically-informative events like gene duplications and losses. A recent study using gene tree …


Preventing Cholesterol-Induced Perk (Protein Kinase Rna-Like Endoplasmic Reticulum Kinase) Signaling In Smooth Muscle Cells Blocks Atherosclerotic Plaque Formation, Abhijnan Chattopadhyay, Pujun Guan, Suravi Majumder, Kaveeta Kaw, Zhen Zhou, Chen Zhang, Siddharth K Prakash, Anita Kaw, L Maximillian Buja, Callie S Kwartler, Dianna M Milewicz Aug 2022

Preventing Cholesterol-Induced Perk (Protein Kinase Rna-Like Endoplasmic Reticulum Kinase) Signaling In Smooth Muscle Cells Blocks Atherosclerotic Plaque Formation, Abhijnan Chattopadhyay, Pujun Guan, Suravi Majumder, Kaveeta Kaw, Zhen Zhou, Chen Zhang, Siddharth K Prakash, Anita Kaw, L Maximillian Buja, Callie S Kwartler, Dianna M Milewicz

Faculty, Staff and Student Publications

BACKGROUND: Vascular smooth muscle cells (SMCs) undergo complex phenotypic modulation with atherosclerotic plaque formation in hyperlipidemic mice, which is characterized by de-differentiation and heterogeneous increases in the expression of macrophage, fibroblast, osteogenic, and stem cell markers. An increase of cellular cholesterol in SMCs triggers similar phenotypic changes in vitro with exposure to free cholesterol due to cholesterol entering the endoplasmic reticulum, triggering endoplasmic reticulum stress and activating Perk (protein kinase RNA-like endoplasmic reticulum kinase) signaling.

METHODS: We generated an SMC-specific

RESULTS: SMC-specific deletion of Perk reduces atherosclerotic plaque formation in male hyperlipidemic mice by 80%. Single-cell transcriptomic data identify 2 …


Saliva Cortisol Diurnal Variation And Stress Responses In Term And Preterm Infants, David Q. Stoye, James P. Boardman, Clive Osmond, Gemma Sullivan, Gillian Lamb, Gill S. Black, Natalie Z. M. Homer, Nina Nelson, Elvar Theodorsson, Evalotte Mörelius, Rebecca M. Reynolds Aug 2022

Saliva Cortisol Diurnal Variation And Stress Responses In Term And Preterm Infants, David Q. Stoye, James P. Boardman, Clive Osmond, Gemma Sullivan, Gillian Lamb, Gill S. Black, Natalie Z. M. Homer, Nina Nelson, Elvar Theodorsson, Evalotte Mörelius, Rebecca M. Reynolds

Research outputs 2022 to 2026

Objective:

To determine if preterm birth is associated with adaptation of the hypothalamic–pituitary–adrenal (HPA) axis and whether HPA axis programming relates to the degree of prematurity (defined as extremely preterm birth at < 28 weeks or very preterm birth at 28–32 weeks gestation).

Design:

This study reports findings from a prospective birth cohort. Saliva cortisol concentrations were measured prevaccination and postvaccination, and in the morning and evening, at 4 months chronological age.

Setting:

Infants born at a single Scottish hospital.

Participants:

45 term-born, 42 very preterm and 16 extremely preterm infants.

Outcomes:

Cortisol stress response to vaccination (postvaccination minus prevaccination cortisol concentrations), diurnal slope (log-transformed morning minus log-transformed evening cortisol values) …


Revised Draft Final Solid Media Management Program Plan, Pioneer Technical Services, Inc. Aug 2022

Revised Draft Final Solid Media Management Program Plan, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.


Determinants Of Blood Acylcarnitine Concentrations In Healthy Individuals Of The European Prospective Investigation Into Cancer And Nutrition, Roland Wedekind, Joseph A. Rothwell, Vivian Viallon, Pekka Keski-Rahkonen, Julie A. Schmidt, Veronique Chajes, Vna Katzke, Theron Johnson, Maria Santucci De Magistris, Vittorio Krogh, Pilar Amiano, Carlotta Sacerdote, Daniel Redondo-Sánchez, José María Huerta, Anne Tjønneland, Pratik Pokharel, Paula Jakszyn, Rosario Tumino, Eva Ardanaz, Torkjel M. Sandanger, Anna Winkvist, Johan Hultdin, Matthias B. Schulze, Elisabete Weiderpass, Marc J. Gunter, Inge Huybrechts Aug 2022

Determinants Of Blood Acylcarnitine Concentrations In Healthy Individuals Of The European Prospective Investigation Into Cancer And Nutrition, Roland Wedekind, Joseph A. Rothwell, Vivian Viallon, Pekka Keski-Rahkonen, Julie A. Schmidt, Veronique Chajes, Vna Katzke, Theron Johnson, Maria Santucci De Magistris, Vittorio Krogh, Pilar Amiano, Carlotta Sacerdote, Daniel Redondo-Sánchez, José María Huerta, Anne Tjønneland, Pratik Pokharel, Paula Jakszyn, Rosario Tumino, Eva Ardanaz, Torkjel M. Sandanger, Anna Winkvist, Johan Hultdin, Matthias B. Schulze, Elisabete Weiderpass, Marc J. Gunter, Inge Huybrechts

Research outputs 2022 to 2026

Background & aims: Circulating levels of acylcarnitines (ACs) have been associated with the risk of various diseases such as cancer and type 2 diabetes. Diet and lifestyle factors have been shown to influence AC concentrations but a better understanding of their biological, lifestyle and metabolic determinants is needed. Methods: Circulating ACs were measured in blood by targeted (15 ACs) and untargeted metabolomics (50 ACs) in 7770 and 395 healthy participants of the European Prospective Investigation into Cancer and Nutrition (EPIC), respectively. Associations with biological and lifestyle characteristics, dietary patterns, self-reported intake of individual foods, estimated intake of carnitine and fatty …


Guidelines For Model Adaptation: A Study Of The Transferability Of A General Seagrass Ecosystem Dynamic Bayesian Networks Model, Paula Sobenko Hatum, Kathryn Mcmahon, Kerrie Mengersen, Paul Pao Yen Wu Aug 2022

Guidelines For Model Adaptation: A Study Of The Transferability Of A General Seagrass Ecosystem Dynamic Bayesian Networks Model, Paula Sobenko Hatum, Kathryn Mcmahon, Kerrie Mengersen, Paul Pao Yen Wu

Research outputs 2022 to 2026

In general, it is not feasible to collect enough empirical data to capture the entire range of processes that define a complex system, either intrinsically or when viewing the system from a different geographical or temporal perspective. In this context, an alternative approach is to consider model transferability, which is the act of translating a model built for one environment to another less well-known situation. Model transferability and adaptability may be extremely beneficial—approaches that aid in the reuse and adaption of models, particularly for sites with limited data, would benefit from widespread model uptake. Besides the reduced effort required to …


Survivor Bond Models For Securitizing Longevity Risk, Priscilla Mansah Codjoe Aug 2022

Survivor Bond Models For Securitizing Longevity Risk, Priscilla Mansah Codjoe

Doctoral Dissertations

"Longevity risk is the risk that a reference population’s mortality rates deviate from what is projected from prior life tables. This is due to discoveries in biological sciences, improved public health measures, and nutrition, which have dramatically increased life expectancy. Longevity risk raises life insurers’ liability, increasing product costs and reserves. Securitization through longevity derivatives is a way of dealing with this risk.

To enhance the pricing of life contingent products, we present an additive type mortality model in the style of the Lee-Carter. This model incorporates policyholder covariates. By using counting processes and martingale machinery, we obtain close form …


Machine Learning Applications In Plant Identification, Wireless Channel Estimation, And Gain Estimation For Multi-User Software-Defined Radio, Viraj K. Gajjar Aug 2022

Machine Learning Applications In Plant Identification, Wireless Channel Estimation, And Gain Estimation For Multi-User Software-Defined Radio, Viraj K. Gajjar

Doctoral Dissertations

"This work applies machine learning (ML) techniques to selected computer vision and digital communication problems. Machine learning algorithms can be trained to perform a specific task without explicit programming. This research applies ML to the problems of: plant identification from images of leaves, channel state information (CSI) estimation for wireless multiple-input-multiple-output (MIMO) systems, and gain estimation for a multi-user software-defined radio (SDR) application.

In the first task, two methods for plant species identification from leaf images are developed. One of the methods uses hand-crafted features extracted from leaf images to train a support vector machine classifier. The other method combines …


Development Of Flood Prediction Models Using Machine Learning Techniques, Bhanu Kanwar Aug 2022

Development Of Flood Prediction Models Using Machine Learning Techniques, Bhanu Kanwar

Doctoral Dissertations

"Flooding and flash flooding events damage infrastructure elements and pose a significant threat to the safety of the people residing in susceptible regions. There are some methods that government authorities rely on to assist in predicting these events in advance to provide warning, but such methodologies have not kept pace with modern machine learning. To leverage these algorithms, new models must be developed to efficiently capture the relationships among the variables that influence these events in a given region. These models can be used by emergency management personnel to develop more robust flood management plans for susceptible areas. The research …


Defining The Current Distribution Of The Imperiled Black-Spotted Newt Across South Texas, Usa, Padraic S. Robinson, Drew R. Davis, Sean M. Collins, Richard Kline Aug 2022

Defining The Current Distribution Of The Imperiled Black-Spotted Newt Across South Texas, Usa, Padraic S. Robinson, Drew R. Davis, Sean M. Collins, Richard Kline

School of Earth, Environmental, & Marine Sciences Faculty Publications

The Black-spotted Newt (Notophthalmus meridionalis) is a chronically understudied salamander species, with many aspects of its natural history, ecology, and distribution poorly known. Previous studies using traditional methodologies have had limited success documenting N. meridionalis on the landscape, detecting individuals at 6% (7 of 114) and 1% (2 of 221) of sites surveyed. A novel environmental DNA (eDNA) assay was designed and implemented with the goals of assessing the current distribution of N. meridionalis across south Texas, USA, and better understanding the conditions for positive eDNA detections. We conducted eDNA sampling and traditional surveys at 80 sites throughout …


Assessing Stress In College Students After Breathing Meditation With And Without Music, Joshua L. Le Clerg Aug 2022

Assessing Stress In College Students After Breathing Meditation With And Without Music, Joshua L. Le Clerg

Graduate Theses

College students face increased levels of stress due to the COVID-19 pandemic, which can adversely affect their academic performance. Therefore, it is critical for students to have access to practices that reduce stress, such as breathing meditations and listening to calming music, which are cost effective and require minimal time commitment. This study aimed to examine the efficacy of combining breathing meditation and listening to music for five minutes a day, five days a week, for two weeks. Fifteen undergraduate students completed the study and were randomly assigned to a control group who completed the breathing meditation without music (n=8) …


Sex-Specific Phenotypes In The Aging Mouse Heart And Consequences For Chronic Fibrosis, Aude Angelini, Jesus Ortiz-Urbina, Joann Trial, Anilkumar K Reddy, Anna Malovannaya, Antrix Jain, Mark L Entman, George E Taffet, Katarzyna A Cieslik Aug 2022

Sex-Specific Phenotypes In The Aging Mouse Heart And Consequences For Chronic Fibrosis, Aude Angelini, Jesus Ortiz-Urbina, Joann Trial, Anilkumar K Reddy, Anna Malovannaya, Antrix Jain, Mark L Entman, George E Taffet, Katarzyna A Cieslik

Faculty, Staff and Students Publications

The incidence of diastolic dysfunction increases with age in both humans and mice. This is characterized by increased passive stiffness and slower relaxation of the left ventricle. The stiffness arises at least partially from progressively increased interstitial collagen deposition because of highly secretory fibroblasts. In the past, we demonstrated that AMPK activation via the drug 5-aminoimidazole-4-carboxamide riboside (AICAR) in middle-aged mice reduced adverse remodeling after myocardial infarction. Therefore, as an attempt to normalize the fibroblast phenotype, we used 21-mo-old male and female mice and treated them with AICAR (0.166 mg/g body wt) where each mouse was followed in a functional …


Randomized Placebo-Controlled Trial Of Losartan For Pediatric Nafld, Miriam B Vos, Mark L Van Natta, Niviann M Blondet, Srinivasan Dasarathy, Mark Fishbein, Paula Hertel, Ajay K Jain, Saul J Karpen, Joel E Lavine, Saeed Mohammad, Laura A Miriel, Jean P Molleston, Marialena Mouzaki, Arun Sanyal, Emily P Sharkey, Jeffrey B Schwimmer, James Tonascia, Laura A Wilson, Stavra A Xanthakos, Nash Clinical Research Network Aug 2022

Randomized Placebo-Controlled Trial Of Losartan For Pediatric Nafld, Miriam B Vos, Mark L Van Natta, Niviann M Blondet, Srinivasan Dasarathy, Mark Fishbein, Paula Hertel, Ajay K Jain, Saul J Karpen, Joel E Lavine, Saeed Mohammad, Laura A Miriel, Jean P Molleston, Marialena Mouzaki, Arun Sanyal, Emily P Sharkey, Jeffrey B Schwimmer, James Tonascia, Laura A Wilson, Stavra A Xanthakos, Nash Clinical Research Network

Faculty, Staff and Students Publications

BACKGROUND AND AIMS: To date, no pharmacotherapy exists for pediatric NAFLD. Losartan, an angiotensin II receptor blocker, has been proposed as a treatment due to its antifibrotic effects.

APPROACH AND RESULTS: The Nonalcoholic Steatohepatitis Clinical Research Network conducted a multicenter, double-masked, placebo-controlled, randomized clinical trial in children with histologically confirmed NAFLD at 10 sites (September 2018 to April 2020). Inclusion criteria were age 8-17 years, histologic NAFLD activity score ≥ 3, and serum alanine aminotransferase (ALT) ≥ 50 U/l. Children received 100 mg of losartan or placebo orally once daily for 24 weeks. The primary outcome was change in ALT …


Cross-Ancestry Genome-Wide Meta-Analysis Of 61,047 Cases And 947,237 Controls Identifies New Susceptibility Loci Contributing To Lung Cancer, Jinyoung Byun, Younghun Han, Yafang Li, Jun Xia, Erping Long, Jiyeon Choi, Xiangjun Xiao, Meng Zhu, Wen Zhou, Ryan Sun, Yohan Bossé, Zhuoyi Song, Ann Schwartz, Christine Lusk, Thorunn Rafnar, Kari Stefansson, Tongwu Zhang, Wei Zhao, Rowland W Pettit, Yanhong Liu, Xihao Li, Hufeng Zhou, Kyle M Walsh, Ivan Gorlov, Olga Gorlova, Dakai Zhu, Susan M Rosenberg, Susan Pinney, Joan E Bailey-Wilson, Diptasri Mandal, Mariza De Andrade, Colette Gaba, James C Willey, Ming You, Marshall Anderson, John K Wiencke, Demetrius Albanes, Stephan Lam, Adonina Tardon, Chu Chen, Gary Goodman, Stig Bojeson, Hermann Brenner, Maria Teresa Landi, Stephen J Chanock, Mattias Johansson, Thomas Muley, Angela Risch, H-Erich Wichmann, Heike Bickeböller, David C Christiani, Gad Rennert, Susanne Arnold, John K Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Angeline S Andrew, Lambertus A Kiemeney, Hongbing Shen, Shanbeh Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Angela Cox, Yun-Chul Hong, Jian-Min Yuan, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Alpa Patel, Qing Lan, Nathaniel Rothman, Fiona Taylor, Linda Kachuri, John S Witte, Lori C Sakoda, Margaret Spitz, Paul Brennan, Xihong Lin, James Mckay, Rayjean J Hung, Christopher I Amos Aug 2022

Cross-Ancestry Genome-Wide Meta-Analysis Of 61,047 Cases And 947,237 Controls Identifies New Susceptibility Loci Contributing To Lung Cancer, Jinyoung Byun, Younghun Han, Yafang Li, Jun Xia, Erping Long, Jiyeon Choi, Xiangjun Xiao, Meng Zhu, Wen Zhou, Ryan Sun, Yohan Bossé, Zhuoyi Song, Ann Schwartz, Christine Lusk, Thorunn Rafnar, Kari Stefansson, Tongwu Zhang, Wei Zhao, Rowland W Pettit, Yanhong Liu, Xihao Li, Hufeng Zhou, Kyle M Walsh, Ivan Gorlov, Olga Gorlova, Dakai Zhu, Susan M Rosenberg, Susan Pinney, Joan E Bailey-Wilson, Diptasri Mandal, Mariza De Andrade, Colette Gaba, James C Willey, Ming You, Marshall Anderson, John K Wiencke, Demetrius Albanes, Stephan Lam, Adonina Tardon, Chu Chen, Gary Goodman, Stig Bojeson, Hermann Brenner, Maria Teresa Landi, Stephen J Chanock, Mattias Johansson, Thomas Muley, Angela Risch, H-Erich Wichmann, Heike Bickeböller, David C Christiani, Gad Rennert, Susanne Arnold, John K Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Angeline S Andrew, Lambertus A Kiemeney, Hongbing Shen, Shanbeh Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Angela Cox, Yun-Chul Hong, Jian-Min Yuan, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Alpa Patel, Qing Lan, Nathaniel Rothman, Fiona Taylor, Linda Kachuri, John S Witte, Lori C Sakoda, Margaret Spitz, Paul Brennan, Xihong Lin, James Mckay, Rayjean J Hung, Christopher I Amos

Faculty, Staff and Students Publications

To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung …


Pathological Implication Of Protein Post-Translational Modifications In Cancer, Sheng Pan, Ru Chen Aug 2022

Pathological Implication Of Protein Post-Translational Modifications In Cancer, Sheng Pan, Ru Chen

Faculty, Staff and Students Publications

Protein post-translational modifications (PTMs) profoundly influence protein functions and play crucial roles in essentially all cell biological processes. The diverse realm of PTMs and their crosstalk is linked to many critical signaling events involved in neoplastic transformation, carcinogenesis and metastasis. The pathological roles of various PTMs are implicated in all aspects of cancer hallmark functions, cancer metabolism and regulation of tumor microenvironment. Study of PTMs has become an important area in cancer research to understand cancer biology and discover novel biomarkers and therapeutic targets. With a limited scope, this review attempts to discuss some PTMs of high frequency with recognized …


A Telemedicine Alternative To The 6-Minute Walk Test Using Personal Activity Trackers In Liver Transplant Candidates, Andres Duarte-Rojo, Rebecca A Brown, Pamela M Bloomer, Marie Nunez Duarte, Rachel K Grubbs, Ruben Hernaez Aug 2022

A Telemedicine Alternative To The 6-Minute Walk Test Using Personal Activity Trackers In Liver Transplant Candidates, Andres Duarte-Rojo, Rebecca A Brown, Pamela M Bloomer, Marie Nunez Duarte, Rachel K Grubbs, Ruben Hernaez

Faculty, Staff and Students Publications

The COVID-19 pandemic has limited liver transplant (LT) candidates access to clinics. Telehealth methods to assess frailty are needed. We developed a method to estimate the step length of LT candidates, which would permit remotely obtaining the 6-min walk test (6MWT) distance with a personal activity tracker (PAT).

METHODS: 6MWT was performed while candidates wore a PAT. On first 21 subjects (stride cohort), the step length was measured and compared with calculated one (6MWT-distance/6MWT steps). On a second cohort (PAT-6MWT; n = 116), we collected the 6MWT step count and used multivariable models to generate formulas estimating step length. We …


Cell Plasticity In Regeneration In The Stomach And Beyond, Mahliyah Adkins-Threats, Jason C Mills Aug 2022

Cell Plasticity In Regeneration In The Stomach And Beyond, Mahliyah Adkins-Threats, Jason C Mills

Faculty, Staff and Students Publications

Recent studies using cell lineage-tracing techniques, organoids, and single-cell RNA sequencing analyses have revealed: 1) adult organs use cell plasticity programs to recruit progenitor cells to regenerate tissues after injury, and 2) plasticity is far more common than previously thought, even in homeostasis. Here, we focus on the complex interplay of normal stem cell differentiation and plasticity in homeostasis and after injury, using the gastric epithelium as a touchstone. We also examine common features of regenerative programs and discuss the evolutionarily conserved, stepwise process of paligenosis which reprograms mature cells into progenitors that can repair damaged tissue. Finally, we discuss …


Intergrader Agreement Of Foveal Cone Topography Measured Using Adaptive Optics Scanning Light Ophthalmoscopy, Niamh Wynne, Jenna A. Cava, Mina Gaffney, Heather Heitkotter, Abigail Scheidt, Jenny L. Reiniger, Jenna Grieshop, Kai Yang, Wolf M. Harmening, Robert F. Cooper, Joseph Carroll Aug 2022

Intergrader Agreement Of Foveal Cone Topography Measured Using Adaptive Optics Scanning Light Ophthalmoscopy, Niamh Wynne, Jenna A. Cava, Mina Gaffney, Heather Heitkotter, Abigail Scheidt, Jenny L. Reiniger, Jenna Grieshop, Kai Yang, Wolf M. Harmening, Robert F. Cooper, Joseph Carroll

Biomedical Engineering Faculty Research and Publications

The foveal cone mosaic can be directly visualized using adaptive optics scanning light ophthalmoscopy (AOSLO). Previous studies in individuals with normal vision report wide variability in the topography of the foveal cone mosaic, especially the value of peak cone density (PCD). While these studies often involve a human grader, there have been no studies examining intergrader reproducibility of foveal cone mosaic metrics. Here we re-analyzed published AOSLO foveal cone images from 44 individuals to assess the relationship between the cone density centroid (CDC) location and the location of PCD. Across 5 graders with variable experience, we found a measurement error …


Building Communities Of Teaching Practice And Data-Driven Open Education Resources With Neon Faculty Mentoring Networks, Kusum Naithani, Megan Jones, Kristine L. Richmond Aug 2022

Building Communities Of Teaching Practice And Data-Driven Open Education Resources With Neon Faculty Mentoring Networks, Kusum Naithani, Megan Jones, Kristine L. Richmond

Biological Sciences Faculty Publications and Presentations

With the growing availability and accessibility of big data in ecology, we face an urgent need to train the next generation of scientists in data science practices and tools. One of the biggest barriers for implementing a data-driven curriculum in undergraduate classrooms is the lack of training and support for educators to develop their own skills and time to incorporate these principles into existing courses or develop new ones. Alongside the research goals of the NEON, providing education and training are key components for building a community of scientists and users equipped to utilize large-scale ecological and environmental data. To …


Early Growth Response 1 Transcription Factor Is Essential For The Pathogenic Properties Of Human Endometriotic Epithelial Cells, Vineet K Maurya, Maria M Szwarc, Rodrigo Fernandez-Valdivia, David M Lonard, Song Yong, Niraj Joshi, Asgerally T Fazleabas, John P Lydon Aug 2022

Early Growth Response 1 Transcription Factor Is Essential For The Pathogenic Properties Of Human Endometriotic Epithelial Cells, Vineet K Maurya, Maria M Szwarc, Rodrigo Fernandez-Valdivia, David M Lonard, Song Yong, Niraj Joshi, Asgerally T Fazleabas, John P Lydon

Faculty, Staff and Students Publications

Although a non-malignant gynecological disorder, endometriosis displays some pathogenic features of malignancy, such as cell proliferation, migration, invasion and adaptation to hypoxia. Current treatments of endometriosis include pharmacotherapy and/or surgery, which are of limited efficacy and often associated with adverse side effects. Therefore, to develop more effective therapies to treat this disease, a broader understanding of the underlying molecular mechanisms that underpin endometriosis needs to be attained. Using immortalized human endometriotic epithelial and stromal cell lines, we demonstrate that the early growth response 1 (EGR1) transcription factor is essential for cell proliferation, migration and invasion, which represent some of the …


Salivary Biomarker Evaluation Of Chronic Pancreatitis Patients Reveals Alterations In Human Proteins, Cytokines, Prostaglandin E2 Levels, And Bacterial Diversity, Richard T Waldron, Elaina K Jones, Vincent I Anani, Jolaine M Hines, Jing Zhao, Aurelia Lugea, Marcio A Diniz, Sungjin Kim, Aida Habtezion, Kristi L Hoffman, Joseph F Petrosino, William E Fisher, Liang Li, Ryan J Lennon, Ravinder Jit Singh, Santhi Swaroop Vege, Stephen J Pandol, Mark D Topazian Aug 2022

Salivary Biomarker Evaluation Of Chronic Pancreatitis Patients Reveals Alterations In Human Proteins, Cytokines, Prostaglandin E2 Levels, And Bacterial Diversity, Richard T Waldron, Elaina K Jones, Vincent I Anani, Jolaine M Hines, Jing Zhao, Aurelia Lugea, Marcio A Diniz, Sungjin Kim, Aida Habtezion, Kristi L Hoffman, Joseph F Petrosino, William E Fisher, Liang Li, Ryan J Lennon, Ravinder Jit Singh, Santhi Swaroop Vege, Stephen J Pandol, Mark D Topazian

Faculty, Staff and Students Publications

OBJECTIVES: Chronic pancreatitis (CP) is a chronic fibroinflammatory condition of the pancreas difficult to diagnose in early stages. Novel biomarkers useful to facilitate early diagnosis or treatment responses may be found in biofluids. Although saliva can be easily and noninvasively collected from patients, useful salivary biomarkers from CP patients have not yet been identified.

METHODS: Here, we analyzed the proteome by quantitative proteomics, cytokine/chemokine levels by Luminex analysis, prostaglandin E2 (PGE2) levels by a mass spectrometry-based assay, and bacterial species diversity by 16S ribosomal ribonucleic acid sequencing in saliva samples from confirmed CP patients and healthy controls.

RESULTS: Our results …


Identifying Bone Matrix Impairments In A Mouse Model Of Neurofibromatosis Type 1 (Nf1) By Clinically Translatable Techniques, Rafay Ahmed, Sasidhar Uppuganti, Shrey Derasari, Joshua Meyer, Jacquelyn S Pennings, Florent Elefteriou, Jeffry S Nyman Aug 2022

Identifying Bone Matrix Impairments In A Mouse Model Of Neurofibromatosis Type 1 (Nf1) By Clinically Translatable Techniques, Rafay Ahmed, Sasidhar Uppuganti, Shrey Derasari, Joshua Meyer, Jacquelyn S Pennings, Florent Elefteriou, Jeffry S Nyman

Faculty, Staff and Students Publications

Three-to-four percent of children with neurofibromatosis type 1 (NF1) present with unilateral tibia bowing, fracture, and recalcitrant healing. Alkaline phosphatase enzyme therapy prevented poor bone mineralization and poor mechanical properties in mouse models of NF1 skeletal dysplasia; but transition to clinical trials is hampered by the lack of a technique that i) identifies NF1 patients at risk of tibia bowing and fracture making them eligible for trial enrollment and ii) monitors treatment effects on matrix characteristics related to bone strength. Therefore, we assessed the ability of matrix-sensitive techniques to provide characteristics that differentiate between cortical bone from mice characterized by …


Combined Laryngeal Cleft Injection Laryngoplasty And Salivary Botulinum Toxin For Saliva Aspiration, Justin Nguyen, Julina Ongkasuwan, Grace Anand, Elton M Lambert Aug 2022

Combined Laryngeal Cleft Injection Laryngoplasty And Salivary Botulinum Toxin For Saliva Aspiration, Justin Nguyen, Julina Ongkasuwan, Grace Anand, Elton M Lambert

Faculty, Staff and Students Publications

OBJECTIVES: Children with type I laryngeal clefts and sialorrhea can have posterior drooling, aspiration of oral secretions, and respiratory complications. Laryngeal cleft injection laryngoplasty (LCIL) and salivary botulinum injections (Sal-Bot) have been used separately for short-term treatment of type I laryngeal clefts and sialorrhea. Our goal was to evaluate combined LCIL and Sal-Bot and create recommendations for further treatment based on response to initial treatment.

METHODS: Retrospective chart review of nine patients who underwent direct laryngoscopy and bronchoscopy with combined LCIL and Sal-Bot from 2012 to 2019. Charts were reviewed for patient characteristics, response to treatment, and pre and post-op …


Differentiated Instruction And Kindergarten Through 5th Grade Teachers, Aslihan Unal, Zafer Unal, Yasar Bodur Aug 2022

Differentiated Instruction And Kindergarten Through 5th Grade Teachers, Aslihan Unal, Zafer Unal, Yasar Bodur

Georgia Educational Researcher

The purpose of this article is to examine Kindergarten through 5th-grade teachers’ understanding of differentiated instruction and perception of their ability to implement differentiated instruction in their classrooms. Differentiated instruction is a critical factor for children’s success. Thirty-one K-5 teachers from the state of Georgia participated in this study. The teacher survey on differentiated instruction developed by Tomlinson (2001) and modified by Page (2007) was used in this study. The researchers also included two open-ended, differentiated instruction questions and seven demographic questions. Study results suggested that while teachers mostly agree that differentiation is an important instructional strategy, they are faced …


A Review Of Heat Stress In Chickens. Part Ii: Insights Into Protein And Energy Utilization And Feeding, Jean-Remi Teyssier, Giorgio Brugaletta, Federico Sirri, Sami Dridi, Samuel J. Rochell Aug 2022

A Review Of Heat Stress In Chickens. Part Ii: Insights Into Protein And Energy Utilization And Feeding, Jean-Remi Teyssier, Giorgio Brugaletta, Federico Sirri, Sami Dridi, Samuel J. Rochell

Poultry Science Faculty Publications and Presentations

With the growing global demand for animal protein and rising temperatures caused by climate change, heat stress (HS) is one of the main emerging environmental challenges for the poultry industry. Commercially-reared birds are particularly sensitive to hot temperatures, so adopting production systems that mitigate the adverse effects of HS on bird performance is essential and requires a holistic approach. Feeding and nutrition can play important roles in limiting the heat load on birds; therefore, this review aims to describe the effects of HS on feed intake (FI) and nutrient digestibility and to highlight feeding strategies and nutritional solutions to potentially …


Cyclic Di-Gmp Regulates Motility, Biofilm Formation, And Desiccation Tolerance In Acinetobacter Baumannii, Garrett Reynolds Aug 2022

Cyclic Di-Gmp Regulates Motility, Biofilm Formation, And Desiccation Tolerance In Acinetobacter Baumannii, Garrett Reynolds

Electronic Theses and Dissertations

Acinetobacter baumannii is an increasingly multidrug-resistant pathogen contributing to hospital-acquired infections necessitating the discovery of novel treatments. A bacterial second messenger, cyclic diguanosine monophosphate (cyclic di-GMP), can regulate various persistence factors that are potentially advantageous for survival in hospital environments. Cyclic di-GMP–modulating enzymes and cyclic di-GMP–binding effectors predictively are encoded in the Acinetobacter baumannii genome. I hypothesized that cyclic di-GMP controls motility, biofilm formation, and desiccation tolerance in Acinetobacter baumannii. Disrupting cyclic di-GMP–modulating enzymes or cyclic di-GMP–binding effectors should alter the regulatory effectiveness of these phenotypes. I tested the multidrug-resistant isolate Acinetobacter baumannii strain AB5075 and identified several transposon …