Biostatistics Commons^™

Earthquake Exposures And Mental Health Outcomes In Children And Adolescents From Phulpingdanda Village, Nepal: A Cross-Sectional Study, Jessica S. Schwind, Clara B. Formby, Susan L. Santangelo, Stephanie A. Norman, Rebecca Brown, Rebecca Hoffman Frances, Elisabeth Koss, Dibesh Karmacharya

Biostatistics, Epidemiology & Environmental Health Sciences: Faculty Publications

Background

Mental health issues can reach epidemic proportions in developed countries after natural disasters, but research is needed to better understand the impact on children and adolescents in developing nations.

Methods

A cross-sectional study was performed to examine the relationship between earthquake exposures and depression, PTSD, and resilience among children and adolescents in Phulpingdanda village in Nepal, 1 year after the 2015 earthquakes, using the Depression Self-Rating Scale for Children, Child PTSD Symptom Scale, and the Child and Youth Resilience Measure, respectively. To quantify exposure, a basic demographic and household questionnaire, including an earthquake exposure assessment tool for children and …

Large-Scale Genome-Wide Meta-Analysis Of Polycystic Ovary Syndrome Suggests Shared Genetic Architecture For Different Diagnosis Criteria, Felix Day, Tugce Karaderi, Michelle R. Jones, Cindy Meun, Chunyan He, Alex Drong, Peter Kraft, Nan Lin, Hongyan Huang, Linda Broer, Reedik Magi, Richa Saxena, Triin Laisk, Margrit Urbanek, M. Geoffrey Hayes, Gudmar Thorleifsson, Juan Fernandez-Tajes, Anubha Mahajan, Benjamin H. Mullin, Bronwyn G. A. Stuckey, Timothy D. Spector, Scott G. Wilson, Mark O. Goodarzi, Lea Davis, Barbara Obermayer-Pietsch, André G. Uitterlinden, Verneri Anttila, Benjamin M. Neale, Marjo-Riitta Jarvelin, Bart Fauser

Internal Medicine Faculty Publications

Polycystic ovary syndrome (PCOS) is a disorder characterized by hyperandrogenism, ovulatory dysfunction and polycystic ovarian morphology. Affected women frequently have metabolic disturbances including insulin resistance and dysregulation of glucose homeostasis. PCOS is diagnosed with two different sets of diagnostic criteria, resulting in a phenotypic spectrum of PCOS cases. The genetic similarities between cases diagnosed based on the two criteria have been largely unknown. Previous studies in Chinese and European subjects have identified 16 loci associated with risk of PCOS. We report a fixed-effect, inverse-weighted-variance meta-analysis from 10,074 PCOS cases and 103,164 controls of European ancestry and characterisation of PCOS related …

Dichotomous Scoring Of Tdp-43 Proteinopathy From Specific Brain Regions In 27 Academic Research Centers: Associations With Alzheimer's Disease And Cerebrovascular Disease Pathologies, Yuriko Katsumata, David W. Fardo, Walter A. Kukull, Peter T. Nelson

Biostatistics Faculty Publications

TAR-DNA binding protein 43 (TDP-43) proteinopathy is a common brain pathology in elderly persons, but much remains to be learned about this high-morbidity condition. Published stage-based systems for operationalizing disease severity rely on the involvement (presence/absence) of pathology in specific anatomic regions. To examine the comorbidities associated with TDP-43 pathology in aged individuals, we studied data from the National Alzheimer’s Coordinating Center (NACC) Neuropathology Data Set. Data were analyzed from 929 included subjects with available TDP-43 pathology information, sourced from 27 different American Alzheimer’s Disease Centers (ADCs). Cases with relatively unusual diseases including autopsy-proven frontotemporal lobar degeneration (FTLD-TDP or FTLD-tau) …

Positive Association Between Dietary Inflammatory Index And The Risk Of Osteoporosis: Results From The Koges_Health Examinee (Hexa) Cohort Study, Hye Sun Kim, Cheongmin Sohn, Minji Kwon, Woori Na, Nitin Shivappa, James R. Hébert, Mi Kyung Kim

Faculty Publications

Previous studies have found that diet’s inflammatory potential is related to various diseases. However, little is known about its relationship with osteoporosis. The aim of this study was to investigate the association between the dietary inflammatory index (DII®) and osteoporosis risk in a large-scale prospective cohort study in Korea. This prospective cohort study included 159,846 participants (men 57,740; women 102,106) from South Korea with a mean follow-up of 7.9 years. The DII was calculated through a validated semi-quantitative FFQ (SQFFQ), and information on osteoporosis was self-reported by the participants. Analyses were performed by using a multivariable Cox proportional hazard model. …

Serum Nutrient Levels And Aging Effects On Periodontitis, Jeffrey L Ebersole, Joshua Lambert, Heather Bush, Pinar Emecen Huja, Arpita Basu

Biostatistics Faculty Publications

Periodontal disease damages tissues as a result of dysregulated host responses against the chronic bacterial biofilm insult and approximately 50% of US adults > 30 years old exhibit periodontitis. The association of five blood nutrients and periodontitis were evaluated due to our previous findings regarding a potential protective effect for these nutrients in periodontal disease derived from the US population sampled as part of the National Health and Nutrition Examination Survey (1999–2004). Data from over 15,000 subjects was analyzed for blood levels of cis-β-carotene, β-cryptoxanthin, folate, vitamin D, and vitamin E, linked with analysis of the presence and severity of periodontitis. …

Subject Level Clustering Using A Negative Binomial Model For Small Transcriptomic Studies., Qian Li, Janelle R. Noel-Macdonnell, Devin C. Koestler, Ellen L. Goode, Brooke L. Fridley

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Unsupervised clustering represents one of the most widely applied methods in analysis of high-throughput 'omics data. A variety of unsupervised model-based or parametric clustering methods and non-parametric clustering methods have been proposed for RNA-seq count data, most of which perform well for large samples, e.g. N ≥ 500. A common issue when analyzing limited samples of RNA-seq count data is that the data follows an over-dispersed distribution, and thus a Negative Binomial likelihood model is often used. Thus, we have developed a Negative Binomial model-based (NBMB) clustering approach for application to RNA-seq studies.

RESULTS: We have developed a Negative …

A Logitudinal Feature Selection Method Identifies Relevant Genes To Distinguish Complicated Injury And Uncomplicated Injury Over Time, Suyan Tian, Chi Wang, Howard H. Chang

Biostatistics Faculty Publications

Background: Feature selection and gene set analysis are of increasing interest in the field of bioinformatics. While these two approaches have been developed for different purposes, we describe how some gene set analysis methods can be utilized to conduct feature selection.

Methods: We adopted a gene set analysis method, the significance analysis of microarray gene set reduction (SAMGSR) algorithm, to carry out feature selection for longitudinal gene expression data.

Results: Using a real-world application and simulated data, it is demonstrated that the proposed SAMGSR extension outperforms other relevant methods. In this study, we illustrate that a gene’s expression profiles over …

Instances Of Influenza In The United States Visualized, Parth Patel

Publications and Research

The Tycho Project collects large data sets related to healthcare and in particular, instances and geographical information of diseases. We look at the instance counts and locations of Influenza from 1919-1951 across the United States. We hope to find seasonal and geographical insight to the spread of the disease.

A Generative Statistical Approach For Data Classification In A Biologically Inspired Design Tool, Marvin Manuel Arroyo Rujano

Graduate Theses and Dissertations

The objective of the research this thesis describes is to find a way to classify text-based descriptions of biological adaption to support Biologically Inspired design. Biologically inspired design is a fairly new field with ongoing research. There are different tools to assist designers and biologists in bio-inspired design. Some of the most common are BioTRIZ and AskNature. In recent years, more tools have been proposed to aid and make research in the field easier, for example, the Biologically Inspired Adaptive System Design (BIASD) tool. This tool was designed with the goal of helping designers in early design stages generate more …

Innate Immunity, The Hepatic Extracellular Matrix, And Liver Injury: Mathematical Modeling Of Metastatic Potential And Tumor Development In Alcoholic Liver Disease., Shanice V. Hudson

Electronic Theses and Dissertations

The overarching goals of the current work are to fill key gaps in the current understanding of alcohol consumption and the risk of metastasis to the liver. Considering the evidence this research group has compiled confirming that the hepatic matrisome responds dynamically to injury, an altered extracellular matrix (ECM) profile appears to be a key feature of pre-fibrotic inflammatory injury in the liver. This group has demonstrated that the hepatic ECM responds dynamically to alcohol exposure, in particular, sensitizing the liver to LPS-induced inflammatory damage. Although the study of alcohol in its role as a contributing factor to oncogenesis and …

Quantitative Microbial Risk Assessment For Parts, Ground, And Msc Poultry Product Including Intervention Analysis And Exploration Of Enterobacteriaceae As An Indicator Organism In Poultry Processing, Leigh Ann Parette

Graduate Theses and Dissertations

Samples collected at five different large bird poultry processing facilities over a period of 7 months from prescald to post debone locations were enumerated for Enterobacteriaceae, Salmonella spp., and Campylobacter spp. and the results were used to create Quantitative Microbial Risk Analyses (QMRA) models for parts, ground, and mechanically separated chicken (MSC) products. Sensitivity analyses indicated the points in the process at which reductions would be most advantageous to the endpoint and simulation models were run to test reductions required to meet the current USDA performance standards.

These data were analyzed to determine the reductions from one node (location) to …

Spatio-Temporal Reconstruction Of Remote Sensing Observations, Kamrul Khan

Graduate Theses and Dissertations

The USDA Forest Service aims to use satellite imagery for monitoring and predicting changes in forest conditions over time within the country. We specifically focus on a 230, 400 hectares region in north-central Wisconsin between 2003 - 2012. The auxiliary data collected from the satellite imagery of this region are relatively dense in space and time and can be used to efficiently predict how the forest condition changed over that decade. However, these records have a significant proportion of missing values due to weather conditions and system failures. To fill in these missing values, we build spaciotemporal models based on …

Concentrations Of Criteria Pollutants In The Contiguous U.S., 1979 – 2015: Role Of Model Parsimony In Integrated Empirical Geographic Regression, Sun-Young Kim, Matthew Bechle, Steve Hankey, Elizabeth (Lianne) A. Sheppard, Adam A. Szpiro, Julian D. Marshall

UW Biostatistics Working Paper Series

BACKGROUND: National- or regional-scale prediction models that estimate individual-level air pollution concentrations commonly include hundreds of geographic variables. However, these many variables may not be necessary and parsimonious approach including small numbers of variables may achieve sufficient prediction ability. This parsimonious approach can also be applied to most criteria pollutants. This approach will be powerful when generating publicly available datasets of model predictions that support research in environmental health and other fields. OBJECTIVES: We aim to (1) build annual-average integrated empirical geographic (IEG) regression models for the contiguous U.S. for six criteria pollutants, for all years with regulatory monitoring data …

Risk Factors Associated With Low Birth Weight, Mohammad Zen Rahfiludin, Yudhy Dharmawan

Kesmas

Neonatal deaths are associated with preterm birth complications. The aim of this study was to analyze risk factors associated with LBW. This was a crosssectional study held in Bulu Primary Health Care, Temanggung, Central Java, Indonesia. The sample size required for this study was 69 based on the Slovin formula. Data were collected using questionnaires and semi-quantitative Food Frequency Questionnaire forms. Data on infant birth weight was taken from midwives’ delivery cohort records. Mid upper arm circumference (MUAC), hemoglobin level, blood pressure, maternal age, parity, nutritional intake, and serum transferrin receptor data were taken from the infant’s mother using a …

Family Perception Towards Health Role In Filariasis Countermeasures Using The Health Belief Model Approach In Aceh Besar District, Said Devi Elvin, Mutia Yusuf, Wirda Hayati, Teuku Alamsyah

Kesmas

Aceh Besar District is a filariasis endemic area. This endemic state is strongly influenced by people’s perception of filariasis countermeasures. This study aimed to determine relation between family perceptions towards health role in filariasis countermeasures using the Health Belief Model. An analytical survey was applied with a cross-sectional study approach. The study population was families at three villages that are Lambaro Bileu, Lambaet, and Cot Preh of Kuta Baro Primary Health Care. This represents 1,113 families with a sample of 92 families that were selected using a proportionate stratified random sampling technique. The study instrument was a questionnaire and data …

Work-Related Skin Diseases Among Workers In The Sewing Section At Pt. X Shoe Company In West Java, Hendra Hendra, Eva Nirwana, Marzuki Isahak

Kesmas

Occupational skin diseases are the most common work-related diseases in many countries. Shoe industry workers are potential to be affected by work-related skin diseases (WRSDs). This study aimed to analyze the risk factors associated with WRSDs among workers in the sewing section at a shoe company in West Java. A total of 477 workers were examined and interviewed using the modified Nordic Occupational Skin Questionnaire-2002/LONG from May 2016 to July 2016. Chi-square test and logistic regression were used to analyze the risk factors related to WRSDs. The results showed that 57.7% of the workers suffered from WRSDs. Most of the …

Pizza And Hamburger Consumption To Overweight Among Adolescents In Jambi City, Ummi Kalsum, Sahridayanti Nainggolan, Nawi Ng

Kesmas

Junk food is unhealthy and poor in nutrient quality, and may result in weight gain, obesity, and coronary heart disease, if consumed regularly. The prevalence of overweight in adolescents is 5-10% higher in urban areas. Adolescents undergo lifestyle changes, including in food consumption behavior. This study aimed to determine relation between junk food consumption patterns and overweight in adolescents. This study was conducted based on a cross-sectional design. A total of 137 high school students in Jambi City were involved in this study. Patterns of junk food consumption were assessed using food frequency questionnaires that examined the eating habits of …

Adolescents' Attitude Toward Hiv/Aids Prevention In Yogyakarta, Meysa Tiranda, Nanik Setiyawati, Anita Rahmawati

Kesmas

Acquired immunodeficiency syndrome (AIDS) is the second leading cause of death in adolescent groups in the world. In Indonesia, the rate of human immunodeficiency virus (HIV)-infected adolescents increases annually. Yogyakarta, well-known as the education city, has the highest number of HIV/AIDS cases in the productive age group of 20–29 years old, which means that they have been already infected with HIV since teen age. This study aimed to determine influential factors that affect adolescents' attitude toward HIV/AIDS prevention. The study was an analytic survey research with a cross-sectional design. Stratified random sampling was applied to select a sample size of …

Role Stress, Personality Type, Burnout, And Performance Of Midwives Towards Postnatal Care Program Achievement In Surabaya City, Elita Halimsetiono, Thinni Nurul Rochmah, Dewi Retno Suminar

Kesmas

The coverage of postnatal care program in Surabaya City had declined since 2011–2013 and could not reach the target. This analytic observational study used a cross-sectional design and was conducted during April–May 2015 to analyze the effect of role stress, personality type, and burnout on midwives’ performance towards postnatal care program achievement in Surabaya City. A total sample of 45 midwives was collected from eight primary health care centers in Surabaya City with basic emergency obstetric and neonatal care services. Accidental sampling was used for sample selection. This study indicated that most of the midwives were aged 20–30 years and …

Impact Of Budget Increase On Primary Health Care Performance In The Era Of National Health Insurance: Case Study In Buleleng District, Kadek Suranugraha, Ni Made Sri Nopiyani, Pande Putu Januraga

Kesmas

Since 2014, there has been an increase in funds for primary health care (PHC) coming from the National Health Insurance program capitation funds and the Health Operational Assistance Fund. This study aimed to explore the effect of this budget increase on the health care services at PHC. The case study used a qualitative approach and interviews from 19 PHC health workers with the highest and lowest budget. Data were analyzed using thematic analysis and supported by quantitative data. The positive impact of the increasing PHC budget was felt by PHC staff due to the addition of operational equipment and incentives …

Utilization Of Styrofoam As Soundproofing Material With Auditory Frequency Range, Sjahrul Meizar Nasri, Iting Shofwati

Kesmas

The utilization of bricks made of styrofoam is expectedly able to be a soundproof for noise control and as a preventive action to reduce the steadily increasing prevalence of hearing loss. This study aimed to assess the use of sound absorption material in which styrofoam was utilized to reduce the noise exposure. In this study, fine aggregates (sand and styrofoam) were made with a mixture of cement with a composition of 1:4 and 1:6, also the addition of polystyrene waste with a percentage of 0%, 20%, 40%, 60%, and 80%. Determination of acoustical property of the mixture was done by …

Health Promotion Toward Knowledge And Intention For Early Detection Of Cervical Cancer In Commercial Sex Workers, Desi Rusmiati, Tiurlan Yunetty Silitonga, Warendi Warendi

Kesmas

Cervical cancer is one of the cancer types that become a haunting danger for many women in the world. In Indonesia, the prevalence rate reached 0.8% or an estimated 98,692 patients. Its prevalence increased to 10% in the commercial sex worker group. This study aimed to explain the effect of health promotion on knowledge and intention for early detection of cervical cancer using the inspection of visual acetate method in the commercial sex workers. This study was quantitative with a quasi-experimental type, one group of pretest and posttest design. The population sample included the commercial sex workers at Genteng Subvillage, …

Inpatient And Outpatient Infection As A Trigger Of Cardiovascular Disease: The Aric Study, Logan Cowan, Pamela L. Lutsey, James S. Pankow, Kunihiro Matsushita, Junichi Ishigami, Kamakshi Lakshminarayan

Biostatistics, Epidemiology & Environmental Health Sciences: Faculty Publications

Background

Acute infections are known cardiovascular disease (CVD) triggers, but little is known regarding how CVD risk varies following inpatient versus outpatient infections. We hypothesized that in‐ and outpatient infections are associated with CVD risk and that the association is stronger for inpatient infections.

Methods and Results

Coronary heart disease (CHD) and ischemic stroke cases were identified and adjudicated in the ARIC (Atherosclerosis Risk in Communities Study). Hospital discharge diagnosis codes and Medicare claims data were used to identify infections diagnosed in in‐ and outpatient settings. A case‐crossover design and conditional logistic regression were used to compare in‐ and outpatient …

Flowgraph Models For Clustered Multistate Time To Event Data, Kristin Hall

USF Tampa Graduate Theses and Dissertations

Healthcare systems have multistate processes. Such processes may be modeled using flowgraphs, which are directed graphs. Flowgraph models support a variety of transition time distributions, easily handle reversibility between states and allow alternate paths to the event or state of interest to be taken. However, estimation of flowgraph and first passage time distribution parameters can lead to incorrect inferences when interdependent data are treated as independent.

In this dissertation, we expand the flowgraph model to accommodate nested and correlated data structures. We develop a framework to incorporate random effects into transition probability and transition time components of a flowgraph model. …

Genome-Wide Analysis Of Alternative Rna Splicing In Children With Acute Myeloid Leukemia (Aml), Xichen Li

Shared Knowledge Conference

The pediatric Acute Myeloid Leukemia (AML) is a high-risk and hard-to-treat childhood cancer that originates in the bone marrow from immature white blood cells. Recently, more and more evidence indicates that aberrant splicing of genes is a common characteristic for AML. Gene expression profiles have proved extremely useful for identifying genes that are associated with clinical characteristics and survival outcome of cancer patients. However, conventional gene expression profiles do not account for the differences observed in expressed isoforms when alternative RNA splicing is analyzed. Alternative RNA splicing can generate dozens of distinct transcripts from individual genes and the expressions of …

Analysis Of Ranked Gene Tree Probability Distributions Under The Coalescent Process For Detecting Anomaly Zones, Anastasiia Kim

Shared Knowledge Conference

In phylogenetic studies, gene trees are used to reconstruct species tree. Under the multispecies coalescent model, gene trees topologies may differ from that of species trees. The incorrect gene tree topology (one that does not match the species tree) that is more probable than the correct one is termed anomalous gene tree (AGT). Species trees that can generate such AGTs are said to be in the anomaly zone (AZ). In this region, the method of choosing the most common gene tree as the estimate of the species tree will be inconsistent and will converge to an incorrect species tree when …

Safety, Tolerability, And Pharmacokinetics Of Long-Acting Injectable Cabotegravir In Low-Risk Hiv-Uninfected Individuals: Hptn 077, A Phase 2a Randomized Controlled Trial., Raphael J Landovitz, Sue Li, Beatriz Grinsztejn, Halima Dawood, Albert Y Liu, Manya Magnus, Mina C Hosseinipour, Ravindre Panchia, Leslie Cottle, Gordon Chau, Paul Richardson, Mark A Marzinke, Craig W Hendrix, Susan H Eshleman, Yinfeng Zhang, Elizabeth Tolley, Jeremy Sugarman, Ryan Kofron, Adeola Adeyeye, David Burns, Alex R Rinehart, David Margolis, William R Spreen, Myron S Cohen, Marybeth Mccauley, Joseph J Eron

Epidemiology Faculty Publications

BACKGROUND: Cabotegravir (CAB) is a novel strand-transfer integrase inhibitor being developed for HIV treatment and prevention. CAB is formulated both as an immediate-release oral tablet for daily administration and as a long-acting injectable suspension (long-acting CAB [CAB LA]) for intramuscular (IM) administration, which delivers prolonged plasma exposure to the drug after IM injection. HIV Prevention Trials Network study 077 (HPTN 077) evaluated the safety, tolerability, and pharmacokinetics of CAB LA in HIV-uninfected males and females at 8 sites in Brazil, Malawi, South Africa, and the United States.

METHODS AND FINDINGS: HPTN 077 was a double-blind, placebo-controlled phase 2a trial. Healthy …

Trends In Obesity And Multimorbidity In Canada., Michael Lebenbaum, Gregory S Zaric, Amardeep Thind, Sisira Sarma

Epidemiology and Biostatistics Publications

Very few studies have examined trends in multimorbidity over time and even fewer have examined trends over time across different body mass index (BMI) groups. Given a general decline in death rates but increased cardiovascular risk factors among individuals with obesity, the trend in the association between obesity and multimorbidity is hypothesized to be increasing over time. The data for our study came from the 1996-97 National Population Health Survey and the 2005 and 2012-13 Canadian Community Health Surveys (N = 277,366 across all 3 surveys). We examined trends in the association between BMI groups and multimorbidity using a logistic …

Blood Transfusions In Preterm Infants: Changes On Perfusion Index And Intermittent Hypoxemia, Katrina T. Ibonia, Henrietta S. Bada, Philip M. Westgate, Enrique Gomez Pomar, Prasad Bhandary, Abhijit R. Patwardhan, Elie G. Abu Jawdeh

Pediatrics Faculty Publications

BACKGROUND

Red blood cell (RBC) transfusion decreases intermittent hypoxemia (IH) events beyond the first week of life. This benefit may be related to improved perfusion to the respiratory control network. Perfusion index (PI) is a perfusion measure provided by the pulse oximeter. We hypothesized that the benefit in IH after RBC transfusion is associated with an increase in PI. In addition, we assessed the value of PI and clinical measures in predicting the effect of RBC transfusion on IH.

STUDY DESIGN AND METHODS

We prospectively enrolled infants less than 30 weeks' gestation age. PI and oxygen saturation (SpO₂) …

Modification Of Asphalt Rubber With Nanoclay Towards Enhanced Storage Stability, Song-Yi Park, Minji Kang, Lynne Wilkens, Yurii Shvetsov, Brook Harmon, Nitin Shivappa, Michael Wirth, James R. Hébert, Christopher Haiman, Loïc Le Marchand, Carol Boushey

Faculty Publications

Asphalt rubber (AR), which is prepared by blending crumb rubber and bitumen, provides various advantages, including superior rutting resistance, lower road-tire noise and longer service life. However, contractors have expressed concerns regarding its poor storage stability, which in turn limits its wider application. This study aims to address the storage stability concern by incorporating nano-montmorillonite (nanoclay). Three types of nanoclay were dispersed into hot AR binder by high shear blending. The rheological properties of nanoclay-crumb rubber modifier (CRM)-modified bitumen were evaluated through Superpave performance grade (PG) tests and the storage stability was characterized by measuring the difference in softening points …