Digital Commons Network^™

Impact Of Impaired Glucose Metabolism On Periodontitis Progression Over Three Years, Oelisoa M. Andriankaja, Kaumudi Joshipura, Francisco Muñoz, Bruce A. Dye, Frank B. Hu, Cynthia M. Pérez

Center for Oral Health Research Faculty Publications

We evaluated the relationship between glucose abnormalities and periodontitis in overweight/obese individuals. Eight hundred and seventy (870) diabetes-free participants aged 40–65 years completed the three-year follow-up in the San Juan Overweight Adults Longitudinal Study. The ADA thresholds for fasting and 2-h post-load glucose and HbA1c were used to define prediabetes. The NHANES methods were used to assess periodontitis. Multivariable linear regression was used to evaluate the relationship between baseline glucose metabolism measures and periodontitis at follow-up, adjusting for potential confounders. There was no association between impaired glucose measures and mean pocket depth (PD), mean clinical attachment loss (CAL), or mean …

The Human Disease Ontology 2022 Update., Lynn M Schriml, James B Munro, Mike Schor, Dustin Olley, Carrie Mccracken, Victor Felix, J Allen Baron, Rebecca Jackson, Susan M. Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion Dialo, Michelle Giglio, Carol Greene

Faculty Research 2022

The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO's 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years. The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational research projects and …

How Data Visualization Can Facilitate Active Learning And Undergraduate Research In An Online Class, Kari Goin Kono, Shawn Smallman

Office of Academic Innovation Publications

This assignment describes how a data visualization assignment can aid students in developing research skills in an online course.

How Does Lc/Ms Compare To Uv In Coffee Authentication And Determination Of Antioxidant Effects? Brazilian And Middle Eastern Coffee As Case Studies, Enas A. El-Hawary, Ahmed Zayed, Annegret Laub, Luzia V. Modolo

Faculty Journal Articles

Coffee is a popular beverage owing to its unique flavor and diverse health benefits. The current study aimed at investigating the antioxidant activity, in relation to the phytochemical composition, of authenticated Brazilian green and roasted Coffea arabica and C. robusta, along with 15 commercial specimens collected from the Middle East. Ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-ESI–HRMS) and UV spectrometry were employed for profiling and fingerprinting, respectively. With the aid of global natural product social molecular networking (GNPS), a total of 88 peaks were annotated as belonging to different chemical classes, of which 11 metabolites are reported for …

Plant Canopy May Promote Seed Dispersal By Wind, Xuanping Qin, Wei Liang, Zhimin Liu, Minghu Liu, Carol C. Baskin, Jerry M. Baskin, Zhiming Xin, Zhigang Wang, Quanlai Zhou

Biology Faculty Publications

Seed dispersal has received much research attention. The plant canopy can intercept diaspores, but the effect of the plant canopy (the aboveground portion of a plant consisting of branches and leaves) on dispersal distance has not been explored empirically. To determine the effect of plant canopy on seed dispersal distance, a comparison of diaspores falling through open air and through plant canopy was made in a wind tunnel using three wind speeds and diaspores with various traits. Compared with diaspores falling through open air, the dispersal distance of diaspores falling through plant canopy was decreased or increased, depending on wind …

Plga/Peg Nanoparticles Loaded With Cyclodextrin-Peganum Harmala Alkaloid Complex And Ascorbic Acid With Promising Antimicrobial Activities, Sherif Ashraf Fahmy, Noha Khalil Mahdy, Hadeer Al Mulla, Hassan Mohamed El Said Azzazy

Faculty Journal Articles

Antimicrobial drugs face numerous challenges, including drug resistance, systemic toxic effects, and poor bioavailability. To date, treatment choices are limited, which warrants the search for novel potent antivirals, including those extracted from natural products. The seeds of Peganum harmala L. (Zygophyllaceae family) have been reported to have antimicrobial, antifungal, and anticancer activities. In the present study, a 2-hydroxy propyl-β-cyclodextrin (HPβCD)/harmala alkaloid-rich fraction (HARF) host–guest complex was prepared using a thin-film hydration method to improve the water solubility and bioavailability of HARF. The designed complex was then co-encapsulated with ascorbic acid into PLGA nanoparticles coated with polyethylene glycol (HARF–HPßCD/AA@PLGA-PEG NPs) using …

Vimentin Intermediate Filaments Mediate Cell Morphology On Viscoelastic Substrates, Maxx Swoger, Sarthak Gupta, Elisabeth E. Charrier, Michael Bates, Heidi Hehnly, Alison E. Patteson

Physics - All Scholarship

The ability of cells to take and change shape is a fundamental feature underlying development, wound repair, and tissue maintenance. Central to this process is physical and signaling interactions between the three cytoskeletal polymeric networks: F-actin, microtubules, and intermediate filaments (IFs). Vimentin is an IF protein that is essential to the mechanical resilience of cells and regulates cross-talk among the cytoskeleton, but its role in how cells sense and respond to the surrounding extracellular matrix is largely unclear. To investigate vimentin’s role in substrate sensing, we designed polyacrylamide hydrogels that mimic the elastic and viscoelastic nature of in vivo tissues. …

Targeting Dnmts To Overcome Enzalutamide Resistance In Prostate Cancer, Elia Farah, Zhuangzhuang Zhang, Sagar M. Utturkar, Jinpeng Liu, Timothy L. Ratliff, Xiaoqi Liu

Toxicology and Cancer Biology Faculty Publications

Prostate cancer is the second leading cause of cancer death among men in the United States. The androgen receptor (AR) antagonist enzalutamide is an FDA-approved drug for treatment of patients with late-stage prostate cancer and is currently under clinical study for early-stage prostate cancer treatment. After a short positive response period to enzalutamide, tumors will develop drug resistance. In this study, we uncovered that DNA methylation was deregulated in enzalutamide-resistant cells. DNMT activity and DNMT3B expression were upregulated in resistant cell lines. Enzalutamide induced the expression of DNMT3A and DNMT3B in prostate cancer cells with a potential role of p53 …

Exploratory Content Analysis Of Direct-To-Consumer Pet Genomics: What Is Being Marketed And What Are Consumers Saying?, Nikki E. Bennett, Silvio Ernesto Mirabal Torres, Peter B. Gray

Anthropology Faculty Research

Mars Petcare introduced the first direct-to-consumer domestic dog genetic test in 2009 and Basepaws introduced the first direct-to-consumer cat genetic test in 2016. Social science research has evaluated numerous aspects of the human direct-to-consumer market, yet no such exploration has evaluated the occurrence of pet owners pursuing pet genetic tests. Using a mixed methods approach, we conducted an exploratory content analysis of direct-to-consumer pet genetic company webpages and consumer reviews shared on Amazon. Initial data reviews indicated some companies may be key industry players, relative to others. Our results present content frequency for each group (key industry players, all other …

Lncrnafunc: A Knowledgebase Of Lncrna Function In Human Cancer, Mengyuan Yang, Huifen Lu, Jiajia Liu, Sijia Wu, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. …

Fusiongdb 20: Fusion Gene Annotation Updates Aided By Deep Learning, Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou

Faculty, Staff and Student Publications

A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies. FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims. In this study, we report fusion gene annotation updates aided by deep learning (FusionGDB 2.0) available at https://compbio.uth.edu/FusionGDB2/. FusionGDB 2.0 has substantial updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with 44 human …

Morphological And Molecular Assessment Of Lithophyllum Okamurae With The Description Of L. Neo-Okamurae Sp. Nov. (Corallinales, Rhodophyta), Aki Kato, Daniela Basso, Annalisa Caragnano, Graziella Rodondi, Gall L Le, Viviana Peña, Jason M. Hall-Spencer, Masasuke Baba

School of Biological and Marine Sciences

No abstract provided.

Gender Equality Redux, Ratna Kapur, Brenda Cossman

National Law School Journal

This article offers a broad review of gender justice jurisprudence in India between 1993 and 2022. In analysing some of the landmark judgements on women's rights in the intervening years, the authors find the judicial approach to gender equality uneven and at times, conflicting. Despite the significant advancements in the jurisprudence of gender equality and dignity, discrimination and inequality persist on a staggering scale. The article argues for the continued importance of subjecting equality jurisprudence to feminist critical inquiry, which pays attention to the deeper structural and systemic issues that impact gender equality.

Shades Of Life In Indian Abortion Law, Gauri Pillai

National Law School Journal

This case comment analyses the recent Kerala High Court decision in Cry of Life Society v Union of India, where a petition was filed to declare India's law on abortion unconstitutional for violating the right to life of the foetus. The High Court dismissed the petition, upholding the constitutionality of the legislation as protecting women's right to life. The author discusses the High Court's order, narrowing in on the right to life argument used by the Court, and the right to life argument that the Court missed. This analysis distils and responds to the 'shades of life' underlying abortion law …

Book Review: Properties Of Rent: Community, Capital And Politics In Globalising Delhi, Aniket Nandan

National Law School Journal

No abstract provided.

The Epiphytic Diatom Community Of An Invasive Macroalga, Starry Stonewort (Charales: Nitellopsis Obtusa) And Its Native Relative, Chara Contraria (Charales) From Two Drowned River Mouth Lakes, Kelsey Inman-Carter

Student Summer Scholars Manuscripts

Epiphytic diatoms are essential primary producers in aquatic environments, but the relationship between them and their hosts is not well understood. The purpose of this project is to understand the specificity of a macroalgal host-epiphytic diatom relationship in Pentwater and Muskegon Lakes, and compare the epiphytic diatom communities of the invasive Nitellopsis obtusa to its close native relative, Chara contraria, using a metabarcoding approach. To these ends, host samples were collected monthly from July to September in 2020 (90 samples) and in June 2021 (55 samples). DNA was extracted from each sample and the plastid RUBISCO (rbcL) barcoding region of …

Water Use Characteristics Of Weeds: A Global Review, Best Practices, And Future Directions, Mandeep Singh, Meetpal Singh Kukal, Suat Irmak, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Weeds usually penalize crop yields by competing for resources, such as water, light, nutrients, and space. Most of the studies on the crop-weed competition domain are limited to assessing crop-yield losses due to weed pressure and other crop-weed interactions, overlooking the significant uptake of soil-water by weeds that exacerbates global water constraints and threatens the productivity and profitability. The objective of this review was to synthesize globally available quantitative data on weed water use (WU) sourced from 23 peer-reviewed publications (filtered from 233 publications via a multi-step protocol of inclusion criteria) with experimental investigations across space (3 continents), time (1927–2018), …

Future Orientation Among Children Affected By Parental Hiv In China: An Exploratory Analysis Of Complex Interactions, Heather L. Mcdaniel, Sayward E. Harrison, Amanda J. Fairchild, Xiaoming Li Ph.D.

Faculty Publications

We utilized an exploratory analytic approach to examine predictors of children's future beliefs, an internal asset associated with resilience among children affected by HIV, with emphasis on complex interactions among multisystem factors. Children (N = 1221) affected by parental HIV in China reported on psychosocial functioning, as well as internal, familial, and community resilience assets. Exploratory data analysis was conducted using a binary segmentation program. Six binary splits on predictors accounted for 22.78% of the variance in future expectation, suggesting interactions between children's perceived control of their future, loneliness, caregiver trust, and social support. Four binary splits accounted for …

Emergence Of Clinical Clostridioides Difficile Isolates With Decreased Susceptibility To Vancomycin, Charles Darkoh, Kadiatou Keita, Chioma Odo, Micah Oyaro, Eric L Brown, Cesar A Arias, Blake M Hanson, Herbert L Dupont

Faculty, Staff and Student Publications

BACKGROUND: Clostridioides difficile infection (CDI) is a leading cause of hospital-associated antibiotic-related diarrhea and deaths worldwide. Vancomycin is one of the few antibiotics recommended for both nonsevere and severe CDI cases. We sought to determine whether vancomycin nonsusceptible C. difficile strains are circulating in the patient population.

METHODS: Stool samples from patients with CDI were collected from 438 and 98 patients at a large university hospital in Houston, Texas, and Nairobi, Kenya, respectively. The stools were examined for the presence of vancomycin and metronidazole nonsusceptible C. difficile using broth dilution culture, Etest (BioMérieux, France), polymerase chain reaction (PCR), whole-genome sequencing, …

Association Between Exposure To Radioactive Iodine After The Chernobyl Accident And Thyroid Volume In Belarus 10-15 Years Later, Ekaterina Chirikova, Robert J Mcconnell, Patrick O'Kane, Vasilina Yauseyenka, Mark P Little, Victor Minenko, Vladimir Drozdovitch, Ilya Veyalkin, Maureen Hatch, June M Chan, Chiung-Yu Huang, Kiyohiko Mabuchi, Elizabeth K Cahoon, Alexander Rozhko, Lydia B Zablotska

Department of Radiology Faculty Papers

Background: While there is a robust literature on environmental exposure to iodine-131 (131I) in childhood and adolescence and the risk of thyroid cancer and benign nodules, little is known about its effects on thyroid volume.

Methods: To assess the effect of 131I dose to the thyroid on the volume of the thyroid gland, we examined the data from the baseline screening of the Belarusian-American Cohort Study of residents of Belarus who were exposed to the Chernobyl fallout at ages ≤18 years. Thyroid dose estimates were based on individual thyroid activity measurements made shortly after the accident and dosimetric data from …

Transcriptomes Of Peripheral Blood Mononuclear Cells From Juvenile Dermatomyositis Patients Show Elevated Inflammation Even When Clinically Inactive, Elisha D O Roberson, Rosana A Mesa, Gabrielle A Morgan, Li Cao, Wilfredo Marin, Lauren M Pachman

Open Access Publications

In juvenile dermatomyositis (JDM), the most common pediatric inflammatory myopathy, weakness is accompanied by a characteristic rash that often becomes chronic and is associated with vascular damage. We hoped to understand the molecular underpinnings of JDM, particularly when untreated, which would facilitate the identification of novel mechanisms and clinical targets that might disrupt disease progression. We studied the RNA-Seq data from untreated JDM peripheral blood mononuclear cells (PBMCs; n = 11), PBMCs from a subset of the same patients when clinically inactive (n = 8/11), and separate samples of untreated JDM skin and muscle (n = 4 each). All JDM …

Neonatal Sepsis: A Systematic Review Of Core Outcomes From Randomised Clinical Trials, Cían J. Henry, Gergana Semova, Ellen Barnes, Isabel Cotter, Tara Devers, Aisyah Rafaee, Andreea Slavescu, Niamh O. Cathain, Danielle Mccollum, Edna Roche, David Mockler, John Allen, Judith Meehan, Claus Klingenberg, Jos M. Latour, Den Hoogen A Van, Tobias Strunk, Eric Giannoni, Luregn J. Schlapbach, Marina Degtyareva, Frans B. Plötz, Boode Wp De, Lars Naver, James L. Wynn, Helmut Küster, Jan Janota, Fleur M. Keij, Irwin K.M. Reiss, Joseph M. Bliss, Joseph M. Bliss, Joyce M. Koenig, Mark A. Turner, Christopher Gale, Eleanor J. Molloy

School of Nursing and Midwifery

Abstract Background The lack of a consensus definition of neonatal sepsis and a core outcome set (COS) proves a substantial impediment to research that influences policy and practice relevant to key stakeholders, patients and parents. Methods A systematic review of the literature was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. In the included studies, the described outcomes were extracted in accordance with the provisions of the Core Outcome Measures in Effectiveness Trials (COMET) handbook and registered. Results Among 884 abstracts identified, 90 randomised controlled trials (RCTs) were included in this review. Only 30 …

Associations Between Resources And Practices Of Ild Centers And Outcomes In Patients With Idiopathic Pulmonary Fibrosis: Data From The Ipf-Pro Registry, Joao A De Andrade, Tejaswini Kulkarni, Megan L Neely, Anne S Hellkamp, Amy Hajari Case, Daniel A Culver, Kalpalatha Guntupalli, Shaun Bender, Craig S Conoscenti, Laurie D Snyder, Ipf-Pro Registry Investigators

Faculty, Staff and Students Publications

BACKGROUND: Performance benchmarks for the management of idiopathic pulmonary fibrosis (IPF) have not been established. We used data from the IPF-PRO Registry, an observational registry of patients with IPF managed at sites across the US, to examine associations between the characteristics of the enrolling sites and patient outcomes.

METHODS: An online survey was used to collect information on the resources, operations, and self-assessment practices of IPF-PRO Registry sites that enrolled ≥ 10 patients. Site variability in 1-year event rates of clinically relevant outcomes, including death, death or lung transplant, and hospitalization, was assessed. Models were adjusted for differences in patient …

Adipose Tissue Uses In Peripheral Nerve Surgery, Allison Podsednik, Raysa Cabrejo, Joseph Rosen

School of Medicine Publications

Currently, many different techniques exist for the surgical repair of peripheral nerves. The degree of injury dictates the repair and, depending on the defect or injury of the peripheral nerve, plastic surgeons can perform nerve repairs, grafts, and transfers. All the previously listed techniques are routinely performed in human patients, but a novel addition to these peripheral nerve surgeries involves concomitant fat grafting to the repair site at the time of surgery. Fat grafting provides adipose-derived stem cells to the injury site. Though fat grafting is performed as an adjunct to some peripheral nerve surgeries, there is no clear evidence …

Receipt Of Help By People With Cognitive Impairment: Results From The English Longitudinal Study Of Ageing, S Read, B Hu, J Dixon, N Brimblecombe, Et Al

Peninsula Medical School

OBJECTIVES: We investigated whether people with dementia or low memory/orientation reported more help misaligned with needs - more unmet need and/or more unrequired help - than other people with similar levels of functional limitation, and examined associations with quality of life. METHODS: From pooled English Longitudinal Study of Ageing data from waves 6, 7, and 8, we identified community-dwelling people aged 50+ with: dementia (n= 405); low memory/orientation but no dementia (n= 4520); and intact memory/orientation (n= 10,264). Unmet need (not receiving help for the functional limitation) and unrequired help (receipt of help without the respective functional limitation) were used …

Information Needs And Information-Seeking Behavior Of Undergraduate Students: A Remote Area Perspective, Shahzadi Humbhi, Shabbir Ahmed Tareen, Alia Humbhi

Library Philosophy and Practice (e-journal)

Nowadays it is the prerequisite of the libraries to know the information-seeking behavior of the users and provide the services according to their needs. The prime purpose of the current study is to examine the information needs, information sources, information-seeking behaviors. As well as find out the challenges the undergraduate face while using the library. The survey research method was used to collect the data. With the help of a structured questionnaire, the data was collected and a random sampling method was used for this purpose. The results of the study revealed that 220(62%) undergraduates need information for their semester …

3’Aqtl-Atlas: An Atlas Of 3’Utr Alternative Polyadenylation Quantitative Trait Loci Across Human Normal Tissues, Ya Cui, Fanglue Peng, Dan Wang, Yumei Li, Jason Sheng Li, Lei Li, Wei Li

Faculty, Staff and Students Publications

Genome-wide association studies (GWAS) have identified thousands of non-coding single-nucleotide polymorphisms (SNPs) associated with human traits and diseases. However, functional interpretation of these SNPs remains a significant challenge. Our recent study established the concept of 3' untranslated region (3'UTR) alternative polyadenylation (APA) quantitative trait loci (3'aQTLs), which can be used to interpret ∼16.1% of GWAS SNPs and are distinct from gene expression QTLs and splicing QTLs. Despite the growing interest in 3'aQTLs, there is no comprehensive database for users to search and visualize them across human normal tissues. In the 3'aQTL-atlas (https://wlcb.oit.uci.edu/3aQTLatlas), we provide a comprehensive list of 3'aQTLs containing …

Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related To Alzheimer's Disease, Evan E Hubbard, Randall J Bateman, Richard J Perrin, Et Al.

2020-Current year OA Pubs

One of the potential benefits of using data-independent acquisition (DIA) proteomics protocols is that information not originally targeted by the study may be present and discovered by subsequent analysis. Herein, we reanalyzed DIA data originally recorded for global proteomic analysis to look for isomerized peptides, which occur as a result of spontaneous chemical modifications to long-lived proteins. Examination of a large set of human brain samples revealed a striking relationship between Alzheimer's disease (AD) status and isomerization of aspartic acid in a peptide from tau. Relative to controls, a surprising increase in isomer abundance was found in both autosomal dominant …

Expert In Biomedicine To Speak At Founders’ Day Convocation, Julia Perez

News and Events (Discontinued Series)

No abstract provided.

Grassland Landscape Design: Working With Land-Managers, C. J. Pearson, R. K. Mann, I. G. Mann

IGC Proceedings (1977-2023)

We are entering an era of landscape design in order to simultaneously tackle largescale issues such as salinity and rising water tables, whole-farm profitability and the maintenance or enhancement of rural communities. In Australia, an important element of landscape design will be the reintroduction or broadening of the base of perennial grasses within farm systems. The goal of this project was to accelerate awareness and adoption of perennial grasses in a large but ecologically-specific area, namely the already-cleared steep uplands in the high rainfall recharge areas of the Murray-Darling Basin. We used a participatory model, in which land-managers made monthly …