Biostatistics Commons^™

Developing Statistical Methods For Data From Platforms Measuring Gene Expression, Gaoxiang Jia

Statistical Science Theses and Dissertations

This research contains two topics: (1) PBNPA: a permutation-based non-parametric analysis of CRISPR screen data; (2) RCRnorm: an integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data from FFPE samples.

Clustered regularly-interspaced short palindromic repeats (CRISPR) screens are usually implemented in cultured cells to identify genes with critical functions. Although several methods have been developed or adapted to analyze CRISPR screening data, no single spe- cific algorithm has gained popularity. Thus, rigorous procedures are needed to overcome the shortcomings of existing algorithms. We developed a Permutation-Based Non-Parametric Analysis (PBNPA) algorithm, which computes p-values at the gene level …

Robust Estimation Of The Average Treatment Effect In Alzheimer's Disease Clinical Trials, Michael Rosenblum, Aidan Mcdermont, Elizabeth Colantuoni

Johns Hopkins University, Dept. of Biostatistics Working Papers

The primary analysis of Alzheimer's disease clinical trials often involves a mixed-model repeated measure (MMRM) approach. We consider another estimator of the average treatment effect, called targeted minimum loss based estimation (TMLE). This estimator is more robust to violations of assumptions about missing data than MMRM.

We compare TMLE versus MMRM by analyzing data from a completed Alzheimer's disease trial data set and by simulation studies. The simulations involved different missing data distributions, where loss to followup at a given visit could depend on baseline variables, treatment assignment, and the outcome measured at previous visits. The TMLE generally has improved …

Apolipoprotein-Defined Lipoprotein Subclasses, Serum Apolipoproteins, And Carotid Intima-Media Thickness In T1d, Arpita Basu, Alicia J. Jenkins, Julie A. Stoner, Ying Zhang, Richrd L. Klein

Kinesiology and Nutrition Sciences Faculty Research

Circulating apolipoprotein-defined lipoprotein subclasses (ADLS) and apolipoproteins predict vascular events in the general and type 2 diabetes populations, but data in T1D are limited. We examined associations of ADLS, serum apolipoproteins, and conventional lipids with carotid intima-media thickness (IMT) measured contemporaneously and 6 years later in 417 T1D participants [men: n = 269, age 42 +/- 6 y (mean +/- SD); women: n = 148, age 39 +/- 8 y] in the Epidemiology of Diabetes Interventions and Complications study, the follow-up of the Diabetes Control and Complications Trial (DCCT). Date were analyzed by multiple linear regression stratified by sex, and …

Dietary Inflammatory Index And Type 2 Diabetes Mellitus In Adults: The Diabetes Mellitus Survey Of Mexico City, Edgar Denova-Gutiérrez, Paloma Muñoz-Aguirre, Nitin Shivappa, James R. Hébert, Lizbeth Tolentino-Mayo, Carolina Batis, Simón Barquera

Faculty Publications

Diet and inflammation are both associated with type 2 diabetes mellitus (T2DM). In the present study, we aimed to assess the relation between the dietary inflammatory index (DII) and the presence of T2DM in Mexican adults participating in the Diabetes Mellitus Survey administered in Mexico City (DMS-MC). The study involved 1174 subjects (48.5% men) between 20–69 years of age. A validated semi-quantitative food frequency questionnaire was employed to evaluate dietary intake and to compute DII. The DII is based on scientific evidence about the association between dietary compounds and six established inflammatory biomarkers. Multivariate logistic regression models were used to …

Perceived Access And Barriers To Care Among Illicit Drug Users And Hazardous Drinkers: Findings From The Seek, Test, Treat, And Retain Data Harmonization Initiative (Sttr)., Mika Matsuzaki, Quan M Vu, Marya Gwadz, Joseph A C Delaney, Irene Kuo, Maria Esther Perez Trejo, William E Cunningham, Chinazo O Cunningham, Katerina Christopoulos

Epidemiology Faculty Publications

BACKGROUND: Illicit drug use (DU) and hazardous drinking (HD) among marginalized populations may be associated with greater barriers to care.

METHODS: We used baseline data on the participants of the Seek, Test, Treat, and Retain data harmonization initiative. DU includes use of any illicit drugs within the past 6 months. HD was defined as scores ≥8 for men and ≥ 7 for women on Alcohol Use Disorders Identification Test within the past 12 months. Social support scores were assigned by summing scores from individual questions related to social support. Two outcomes for multivariable regression models and mediation analysis were perceived …

Defining Care Patterns And Outcomes Among Persons Living With Hiv In Washington, Dc: Linkage Of Clinical Cohort And Surveillance Data., Amanda D Castel, Arpi Terzian, Jenevieve Opoku, Lindsey Powers Happ, Naji Younes, Michael Kharfen, Alan Greenberg, Dc Cohort Executive Committee

Epidemiology Faculty Publications

BACKGROUND: Triangulation of data from multiple sources such as clinical cohort and surveillance data can help improve our ability to describe care patterns, service utilization, comorbidities, and ultimately measure and monitor clinical outcomes among persons living with HIV infection.

OBJECTIVES: The objective of this study was to determine whether linkage of clinical cohort data and routinely collected HIV surveillance data would enhance the completeness and accuracy of each database and improve the understanding of care patterns and clinical outcomes.

METHODS: We linked data from the District of Columbia (DC) Cohort, a large HIV observational clinical cohort, with Washington, DC, Department …

Biomarker And Clinical Trial Design Support For Disease-Modifying Therapies: Report Of A Survey Of The Eu/Us: Alzheimer's Disease Task Force, Jeffrey Cummings, Nick Fox, Bruno Vellas, Paul Aisen, Guogen Shan

Environmental & Global Health Faculty Research

BACKGROUND: Disease-modifying therapies are urgently needed for the treatment of Alzheimer’s disease (AD). The European Union/United States (EU/US) Task Force represents a broad range of stakeholders including biopharma industry personnel, academicians, and regulatory authorities. OBJECTIVES: The EU/US Task Force represents a community of knowledgeable individuals who can inform views of evidence supporting disease modification and the development of disease-modifying therapies (DMTs). We queried their attitudes toward clinical trial design and biomarkers in support of DMTs. DESIGN/SETTING/PARTICIANTS: A survey of members of the EU/US Alzheimer’s Disease Task Force was conducted. Ninety-three members (87%) responded. The details were analyzed to understand what …

Incorporating Historical Models With Adaptive Bayesian Updates, Philip S. Boonstra, Ryan P. Barbaro

The University of Michigan Department of Biostatistics Working Paper Series

This paper considers Bayesian approaches for incorporating information from a historical model into a current analysis when the historical model includes only a subset of covariates currently of interest. The statistical challenge is two-fold. First, the parameters in the nested historical model are not generally equal to their counterparts in the larger current model, neither in value nor interpretation. Second, because the historical information will not be equally informative for all parameters in the current analysis, additional regularization may be required beyond that provided by the historical information. We propose several novel extensions of the so-called power prior that adaptively …

A Spline-Assisted Semiparametric Approach To Nonparametric Measurement Error Models, Fei Jiang, Yanyuan Ma

COBRA Preprint Series

Nonparametric estimation of the probability density function of a random variable measured with error is considered to be a difficult problem, in the sense that depending on the measurement error prop- erty, the estimation rate can be as slow as the logarithm of the sample size. Likewise, nonparametric estimation of the regression function with errors in the covariate suffers the same possibly slow rate. The traditional methods for both problems are based on deconvolution, where the slow convergence rate is caused by the quick convergence to zero of the Fourier transform of the measurement error density, which, unfortunately, appears in …

Angiostrongylus Cantonensis: Epidemiologic Review, Location-Specific Habitat Modelling, And Surveillance In Hillsborough County, Florida, U.S.A., Brad Christian Perich

USF Tampa Graduate Theses and Dissertations

Angiostrongylus cantonensis is a parasitic nematode endemic to tropical and subtropical regions and is the leading cause of human eosinophilic meningitis. The parasite is commonly known as rat lungworm because the primary host in its lifecycle is the rat. A clinical overview of rat lungworm infection is presented, followed by a literature review of rat lungworm epidemiology, risk factors, and surveillance projects. Data collected from previous snail surveys in Florida was considered alongside elevation, population per square kilometer, median household income by zip code territory, and normalized difference vegetation index specific to the geographic coordinates from which the snail samples …

Antenatal Care Provider And Cesarean Section In Urban Areas In Indonesia, Terry Yuliana Rahadian Pristya, Milla Herdayati, Besral Besral, Dheni Fidyah Fika

Kesmas

Tren persalinan sesar di Indonesia (2007-2012) mengalami peningkatan dua kali lipat berisiko pada munculnya masalah kesehatan jangka panjang maupun pendek. Penelitian ini bertujuan mengetahui hubungan tenaga kesehatan pemeriksa kehamilan dengan persalinan sesar. Penelitian kuantitatif ini menggunakan desain potong lintang dengan sampel penelitian 5143 wanita usia subur berusia 15-49 tahun yang melahirkan anak terakhirnya, baik melahirkan sesar maupun tidak di wilayah perkotaan yang terpilih dalam sampel Survei Demografi Kesehatan Indonesia tahun 2012. Analisis multivariat regresi logistik digunakan untuk mengetahui hubungan tenaga pemeriksa kehamilan dengan persalinan sesar, dikontrol oleh usia ibu, tempat periksa kehamilan, paritas, dan tempat melahirkan. Hasil penelitian menunjukkan bahwa …

Early Inititation Of Breastfeeding And Vitamin A Supplementation With Nutritional Status Of Children Aged 6-59 Months, Betty Yosephin Simanjuntak, Miratul Haya, Desri Suryani, Che An Ahmad

Kesmas

Masa balita, khususnya dua tahun pertama kehidupan merupakan usia emas bagi anak karena pertumbuhan dan perkembangannya yang cepat. Oleh karena itu, terjadinya gangguan nutrisi pada masa itu bisa bersifat permanen dan tidak dapat diubah. Penelitian ini mengkaji hubungan antara inisiasi dini pemberian air susu ibu dan vitamin A dengan status gizi. Total sampel yang dianalisis dalam penelitian ini adalah 1.592 anak di bawah lima tahun (balita) berusia 6-59 bulan yang diambil dari Pemantauan Status Gizi Indonesia 2015 di Bengkulu. Data termasuk usia, jenis kelamin, inisiasi menyusui dini, panjang kelahiran, berat lahir, suplementasi vitamin Adikumpulkan dengan menggunakan kuesioner. Berat dan tinggi …

Family Support As A Factor Influencing The Provision Of Exclusive Breastfeeding Among Adolescent Mothers In Bantul, Yogyakarta, Maulida Lailatussu’Da, Niken Meilani, Nanik Setiyawati, Sammy Onyapidi Barasa

Kesmas

Kehamilan remaja di Indonesia cukup tinggi. Kecamatan Sewon memiliki angka persalinan remaja tertinggi di Kabupaten Bantul pada tahun 2015-2016. Penelitian ini bertujuan untuk mengetahui faktor-faktor yang memengaruhi pemberian ASI eksklusif pada ibu usia remaja di Kecamatan Sewon, Kabupaten Bantul. Penelitian ini menggunakan desain potong lintang dan sampel penelitian berjumlah 45 orang ibu usia remaja yang mempunyai bayi usia 6-24 bulan. Pengumpulan data menggunakan kuesioner terstruktur. Analisis bivariat menggunakan kai kuadrat dan fisher’s exact test, sedangkan analisis multivariat menggunakan regresi logistik. Hasil penelitian menunjukkan bahwa 53.3% ibu usia remaja tidak memberikan ASI eksklusif. Analisis bivariat menunjukkan faktor status kehamilan (nilai p …

Effect Of Nutrition Counseling Knowledge And Attitude Toward Mother Breastfeeding And Baby Growth In Sub Lubuk Pakam, Herta Masthalina, Zein Agustina

Kesmas

Untuk dapat menjalankan program ASI eksklusif, ibu menyusui harus memiliki pengetahuan yang baik. Salah satu cara dalam menambah pengetahuan yaitu dengan memberikan konseling gizi. Penelitian ini bertujuan untuk mengetahui pengaruh konseling gizi tentang ASI eksklusif dan status gizi terhadap pengetahuan dan sikap ibu menyusui di wilayah Puskesmas Kecamatan Lubuk Pakam. Jenis penelitian ini adalah quasi experimental non-equivalent control group design. Sampel sejumlah 60 ibu dibagi ke dalam dua kelompok, yaitu 30 ibu yang diberikan konseling gizi intensif pada kelompok intervensi di wilayah kerja Puskesmas Lubuk Pakam dan 30 ibu pada kelompok kontrol di wilayah kerja Puskesmas Tanjung Morawa. Kelompok perlakuan …

The Effect Of Health Insurance On Institutional Delivery In Indonesia, Mazda Novi Mukhlisa, Pujiyanto Pujiyanto

Kesmas

Pemanfaatan pelayanan persalinan di fasilitas kesehatan berdampak pada menurunnya angka kematian ibu (AKI). Di Indonesia, persalinan di fasilitas kesehatan mengalami peningkatan setiap tahunnya, tetapi masih terdapat sekitar 30% ibu yang bersalin di rumah. Sayangnya, peningkatan pemanfaatan pelayanan persalinan di fasilitas kesehatan tersebut tidak diimbangi dengan penurunan AKI, sehingga Indonesia tidak berhasil mencapai target MDGs. Untuk mencapai Universal Health Coverage, Indonesia mengimplementasikan program Jaminan Kesehatan Nasional (JKN) yang mengintegrasikan empat jaminan kesehatan, yaitu Askes/ASABRI, Jamsostek, Jamkesmas, dan Jamkesda. Jaminan kesehatan dapat mengatasi kendala biaya pada persalinan di fasilitas kesehatan. Dengan menggunakan data Riset Kesehatan Dasar 2013 dan data Potensi Desa 2011 …

Risk Of Adolescent Pregnancy Toward Maternal And Infant Health, Analisis Of Idhs 2012, Anni Fithriyatul Mas'udah, Besral Besral, Bimandra Adiputra Djaafara

Kesmas

Dampak kehamilan pada remaja erat kaitannya dengan risiko kesehatan ibu dan bayi. Penelitian ini bertujuan untuk mengembangkan komposit indeks kesehatan ibu, indeks kesehatan bayi dan untuk menelaah pengaruh kehamilan remaja terhadap kesehatan ibu dan bayi. Penelitian ini menggunakan data Survei Demografi Kesehatan Indonesia tahun 2012, dengan sampel 2.167 responden yang memenuhi syarat inklusi (wanita usia subur yang pernah melahirkan anak pertama sejak Januari 2007 sampai survei dilaksanakan). Analisis menggunakan Polychoric Principal Component Analysis untuk menentukan komposit indeks kesehatan ibu dan bayi, serta regresi logistik untuk mengetahui besar hubungan kehamilan remaja terhadap kesehatan ibu dan bayi. Kesehatan ibu dapat ditentukan melalui …

Exclusive Breastfeeding Intention Among Pregnant Women, Tria Astika Endah Permatasari, Ratu Ayu Dewi Sartika, Endang Laksminingsih Achadi, Urip Purwono, Anies Irawati, Dwiana Ocviyanti, Evi Martha

Kesmas

Intensi pemberian ASI eksklusif adalah intensi ibu untuk memberikan hanya ASI pada bayinya sejak dilahirkan hingga berusia enam bulan. Intensi pada periode prenatal merupakan penentu langsung pemberian ASI eksklusif. Penelitian ini bertujuan mengetahui faktor paling dominan berhubungan dengan intensi pemberian ASI eksklusif pada ibu hamil di sebuah rumah sakit ibu dan anak di Kota Tangerang Selatan. Penelitian dengan desain studi potong lintang dilakukan secara primer. Sampel berjumlah 143 ibu hamil trimester ketiga dipilih secara purposive sampling. Intensi pemberian ASI eksklusif diukur menggunakan kuesioner the Infant Feeding Intentions scale. Sedangkan sikap, norma subjektif dan persepsi kontrol perilaku dinilai menggunakan modifikasi kuesioner …

Technical Considerations In The Use Of The E-Value, Tyler J. Vanderweele, Peng Ding, Maya Mathur

Harvard University Biostatistics Working Paper Series

The E-value is defined as the minimum strength of association on the risk ratio scale that an unmeasured confounder would have to have with both the exposure and the outcome, conditional on the measured covariates, to explain away the observed exposure-outcome association. We have elsewhere proposed that the reporting of E-values for estimates and for the limit of the confidence interval closest to the null become routine whenever causal effects are of interest. A number of questions have arisen about the use of E-value including questions concerning the interpretation of the relevant confounding association parameters, the nature of the transformation …

Strategies To Adjust For Response Bias In Clinical Trials: A Simulation Study, Victoria R. Swaidan

USF Tampa Graduate Theses and Dissertations

Background: Response bias can distort treatment effect estimates and inferences in clinical trials. Although prevention, quantification, and adjustments have been developed, current methods are not applicable when subject-level reliability is used as the measure of response bias. Thus, the objective of the current study is to develop, test, and recommend a series of bias correction strategies for use in these cases. Methods: Monte Carlo simulation and logistic regression modeling were used to develop the strategies, examining the collective impact of sample size (N), effect size (ES), reliability distribution, and response style on estimating the treatment effect size in a series …

The Association Of Long-Term Exposure To Particulate Matter Air Pollution With Brain Mri Findings: The Aric Study., Melinda C Power, Archana P Lamichhane, Duanping Liao, Xiaohui Xu, Clifford R Jack, Rebecca F Gottesman, Thomas Mosley, James D Stewart, Jeff D Yanosky, Eric A Whitsel

Epidemiology Faculty Publications

BACKGROUND: Increasing evidence links higher particulate matter (PM) air pollution exposure to late-life cognitive impairment. However, few studies have considered associations between direct estimates of long-term past exposures and brain MRI findings indicative of neurodegeneration or cerebrovascular disease.

OBJECTIVE: Our objective was to quantify the association between brain MRI findings and PM exposures approximately 5 to 20 y prior to MRI in the Atherosclerosis Risk in Communities (ARIC) study.

METHODS: ARIC is based in four U.S. sites: Washington County, Maryland; Minneapolis suburbs, Minnesota; Forsyth County, North Carolina; and Jackson, Mississippi. A subset of ARIC participants underwent 3T brain MRI in …