Statistics and Probability Commons^™

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

Uncovering Local Trends In Genetic Effects Of Multiple Phenotypes Via Functional Linear Models, Olga A. Vsevolozhskaya, Dmitri V. Zaykin, David A. Barondess, Xiaoren Tong, Sneha Jadhav, Qing Lu

Biostatistics Faculty Publications

Recent technological advances equipped researchers with capabilities that go beyond traditional genotyping of loci known to be polymorphic in a general population. Genetic sequences of study participants can now be assessed directly. This capability removed technology-driven bias toward scoring predominantly common polymorphisms and let researchers reveal a wealth of rare and sample-specific variants. Although the relative contributions of rare and common polymorphisms to trait variation are being debated, researchers are faced with the need for new statistical tools for simultaneous evaluation of all variants within a region. Several research groups demonstrated flexibility and good statistical power of the functional linear …

One-Step Targeted Minimum Loss-Based Estimation Based On Universal Least Favorable One-Dimensional Submodels, Mark J. Van Der Laan, Susan Gruber

U.C. Berkeley Division of Biostatistics Working Paper Series

Consider a study in which one observes n independent and identically distributed random variables whose probability distribution is known to be an element of a particular statistical model, and one is concerned with estimation of a particular real valued pathwise differentiable target parameter of this data probability distribution. The targeted maximum likelihood estimator (TMLE) is an asymptotically efficient substitution estimator obtained by constructing a so called least favorable parametric submodel through an initial estimator with score, at zero fluctuation of the initial estimator, that spans the efficient influence curve, and iteratively maximizing the corresponding parametric likelihood till no more updates …

Modeling And Survival Analysis Of Breast Cancer: A Statistical, Artificial Neural Network, And Decision Tree Approach, Venkateswara Rao Mudunuru

USF Tampa Graduate Theses and Dissertations

Survival analysis today is widely implemented in the fields of medical and biological sciences, social sciences, econometrics, and engineering. The basic principle behind the survival analysis implies to a statistical approach designed to take into account the amount of time utilized for a study period, or the study of time between entry into observation and a subsequent event. The event of interest pertains to death and the analysis consists of following the subject until death. Events or outcomes are defined by a transition from one discrete state to another at an instantaneous moment in time. In the recent years, research …

Maximum Likelihood Based Analysis Of Equally Spaced Longitudinal Count Data With Specified Marginal Means, First-Order Antedependence, And Linear Conditional Expectations, Victoria Gamerman, Matthew Guerra, Justine Shults

UPenn Biostatistics Working Papers

This manuscript implements a maximum likelihood based approach that is appropriate for equally spaced longitudinal count data with over-dispersion, so that the variance of the outcome variable is larger than expected for the assumed Poisson distribution. We implement the proposed method in the analysis of two data sets and make comparisons with the semi-parametric generalized estimating equations (GEE) approach that incorrectly ignores the over-dispersion. The simulations demonstrate that the proposed method has better small sample efficiency than GEE. We also provide code in R that can be used to recreate the analysis results that we provide in this manuscript.

Marginal Structural Models With Counterfactual Effect Modifiers, Wenjing Zheng, Zhehui Luo, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

In health and social sciences, research questions often involve systematic assessment of the modification of treatment causal effect by patient characteristics, in longitudinal settings with time-varying or post-intervention effect modifiers of interest. In this work, we investigate the robust and efficient estimation of the so-called Counterfactual-History-Adjusted Marginal Structural Model (van der Laan and Petersen (2007)), which models the conditional intervention-specific mean outcome given modifier history in an ideal experiment where, possible contrary to fact, the subject was assigned the intervention of interest, including the treatment sequence in the conditioning history. We establish the semiparametric efficiency theory for these models, and …

Conditional Screening For Ultra-High Dimensional Covariates With Survival Outcomes, Hyokyoung Grace Hong, Jian Kang, Yi Li

The University of Michigan Department of Biostatistics Working Paper Series

Identifying important biomarkers that are predictive for cancer patients' prognosis is key in gaining better insights into the biological influences on the disease and has become a critical component of precision medicine. The emergence of large-scale biomedical survival studies, which typically involve excessive number of biomarkers, has brought high demand in designing efficient screening tools for selecting predictive biomarkers. The vast amount of biomarkers defies any existing variable selection methods via regularization. The recently developed variable screening methods, though powerful in many practical setting, fail to incorporate prior information on the importance of each biomarker and are less powerful in …

Correlation Of Maximal Inspiratory Pressure To Transdiaphragmatic Twitch Pressure In Intensive Care Unit Patients, Gerald S. Supinski, Philip M. Westgate, Leigh Ann Callahan

Internal Medicine Faculty Publications

Background: Respiratory muscle weakness contributes to respiratory failure in ICU patients. Unfortunately, assessment of weakness is difficult since the most objective test, transdiaphragmatic pressure in response to phrenic nerve stimulation (PdiTw), is difficult to perform. While most clinicians utilize maximum inspiratory pressure (Pimax) to assess strength, the relationship of this index to PdiTw has not been evaluated in a large ICU population. The purpose of the present study was to assess both PdiTw and Pimax in ICU patients to determine how these indices correlate with each other, what factors influence these indices, and how well these indices predict outcomes.

Methods: …

On The Dynamics Of Boolean Gene Regulatory Networks With Stochasticity, Yuezhe Li

Theses and Dissertations

Genes are responsible for producing proteins that are essential to the construction of complex biological systems. The mechanisms by which this production is regulated have long been the center of wide spread research efforts. Deterministic Boolean gene regulatory models have been a particularly effective avenue of research in this field. However these models fall short of accounting for variations in the gene functionality due to the uncertain internal or external environmental conditions. One of the recent attempts to overcome this weakness is by (Murrugarra, 2012), in which a probabilistic component is introduced as the fixed activation/degradation propensities at the cellular …

Simulating Longer Vectors Of Correlated Binary Random Variables Via Multinomial Sampling, Justine Shults

UPenn Biostatistics Working Papers

The ability to simulate correlated binary data is important for sample size calculation and comparison of methods for analysis of clustered and longitudinal data with dichotomous outcomes. One available approach for simulating length n vectors of dichotomous random variables is to sample from the multinomial distribution of all possible length n permutations of zeros and ones. However, the multinomial sampling method has only been implemented in general form (without first making restrictive assumptions) for vectors of length 2 and 3, because specifying the multinomial distribution is very challenging for longer vectors. I overcome this difficulty by presenting an algorithm for …

Strengthening Instrumental Variables Through Weighting, Douglas Lehmann, Yun Li, Rajiv Saran, Yi Li

The University of Michigan Department of Biostatistics Working Paper Series

Instrumental variable (IV) methods are widely used to deal with the issue of unmeasured confounding and are becoming popular in health and medical research. IV models are able to obtain consistent estimates in the presence of unmeasured confounding, but rely on assumptions that are hard to verify and often criticized. An instrument is a variable that influences or encourages individuals toward a particular treatment without directly affecting the outcome. Estimates obtained using instruments with a weak influence over the treatment are known to have larger small-sample bias and to be less robust to the critical IV assumption that the instrument …

Motorcycle Helmet Effectiveness In Reducing Head, Face And Brain Injuries By State And Helmet Law, Cody S. Olsen, Andrea M. Thomas, Michael Singleton, Anna M. Gaichas, Tracy J. Smith, Gary A. Smith, Justin Peng, Michael J. Bauer, Ming Qu, Denise Yeager, Timothy Kerns, Cynthia Burch, Lawrence J. Cook

Biostatistics Faculty Publications

Background: Despite evidence that motorcycle helmets reduce morbidity and mortality, helmet laws and rates of helmet use vary by state in the U.S.

Methods: We pooled data from eleven states: five with universal laws requiring all motorcyclists to wear a helmet, and six with partial laws requiring only a subset of motorcyclists to wear a helmet. Data were combined in the Crash Outcome Data Evaluation System's General Use Model and included motorcycle crash records probabilistically linked to emergency department and inpatient discharges for years 2005-2008. Medical outcomes were compared between partial and universal helmet law settings. We estimated adjusted relative …

Evaluating The Impact Of A Hiv Low-Risk Express Care Task-Shifting Program: A Case Study Of The Targeted Learning Roadmap, Linh Tran, Constantin T. Yiannoutsos, Beverly S. Musick, Kara K. Wools-Kaloustian, Abraham Siika, Sylvester Kimaiyo, Mark J. Van Der Laan, Maya L. Petersen

U.C. Berkeley Division of Biostatistics Working Paper Series

In conducting studies on an exposure of interest, a systematic roadmap should be applied for translating causal questions into statistical analyses and interpreting the results. In this paper we describe an application of one such roadmap applied to estimating the joint effect of both time to availability of a nurse-based triage system (low risk express care (LREC)) and individual enrollment in the program among HIV patients in East Africa. Our study population is comprised of 16;513 subjects found eligible for this task-shifting program within 15 clinics in Kenya between 2006 and 2009, with each clinic starting the LREC program between …

Progression Of Electrocardiographic Abnormalities In Type 1 Diabetes During 16 Years Of Follow‐Up: The Epidemiology Of Diabetes Interventions And Complications (Edic) Study, Elsayed Soliman, Jye-Yu Backlund, Ionut Bebu, Yabing Li, Zhu-Ming Zhang, Patricia A. Cleary, John M. Lachin

GW Biostatistics Center

Background The electrocardiogram (ECG) is an objective tool for cardiovascular disease (CVD) risk assessment.

Methods and Results We evaluated distribution of ECG abnormalities and risk factors for developing new abnormalities in 1314 patients with type 1 diabetes (T1D) from the Epidemiology of Diabetes Interventions and Complications (EDIC) study. Annual ECGs were centrally read. ECG abnormalities were classified as major and minor according to the Minnesota ECG Classification. At EDIC year 1 (baseline), 356 (27.1%) of the participants had at least 1 ECG abnormality (major or minor) whereas 26 (2%) had at least one major abnormality. During 16 years of follow‐up, …

Knowledge And Behavior Change Of People Living With Hiv Through Nutrition Education And Counseling, Fitri Hudayani, Ratu Ayu Dewi Sartika

Kesmas

HIV, AIDS, dan gizi saling berhubungan. Pada Unit Pelayanan Terpadu HIV Rumah Sakit Umum Pusat Nasional Dr. Cipto Mangunkusumo, layanan edukasi dan konseling gizi disediakan secara kolaboratif untuk orang yang hidup dengan HIV. Penelitian ini bertujuan untuk mengetahui pengaruh pendidikan dan konseling gizi terhadap pengetahuan dan perilaku orang yang hidup dengan HIV. Penelitian ini dilakukan dengan desain kuasi eksperimental menggunakan kelompok perlakuan dan kontrol. Kelompok perlakuan terdiri dari 25 sampel dan 29 sampel untuk kelompok kontrol, dilakukan sebelum dan setelah perlakuan. Sampel berusia dewasa antara 18 – 50 tahun dipilih dengan menerapkan kriteria inklusi dan eksklusi. Sampel uji-t berpasangan digunakan …

Influence Of Household Environment And Maternal Behaviors To Upper Respiratory Infection Among Toddlers, Reny Fahdiyani, Ardini S. Raksanagara, Hadyana Sukandar

Kesmas

Infeksi saluran pernapasan akut atas (ISPA atas) di negara berkembang menyebabkan morbiditas tinggi pada anak bawah usia lima tahun (balita). Kementerian Kesehatan Republik Indonesia melaporkan bahwa ISPAnonpneumonia meningkat 2,6% dari tahun 2007 ke 2011. Faktor risiko yang dapat berkontribusi termasuk lingkungan dan perilaku. Penelitian ini bertujuan untuk menyelidiki faktor perilaku dan lingkungan dengan ISPA atas pada balita. Studi kasus kontrol ini dilakukan dari Februari-April 2015 pada balita di Tamansari yang merupakan daerah kumuh di Kota Bandung. Kasus adalah 55 ibu dengan balita menderita ISPA atas yang datang ke puskesmas, sedangkan kontrol dua kali lebih besar dari kasus dipilih dari lingkungan …

Predisposing Factors With Complementary Feeding Practices Among 9-11 Month-Old Infants In Jakarta Urban Slum Area, Septriana Septriana, Gita Ardelia Suhartono

Kesmas

Penyebab utama kekurangan gizi selain dari penyakit infeksi adalah pola asuh yang tidak sesuai dan pemberian makan yang optimal menjadi salah satu cara untuk mengatasi konsekuensi jangka panjang dari kekurangan zat gizi. Penelitian ini bertujuan untuk mengetahui hubungan antara faktor pendukung praktik pemberian makanan pendamping air susu ibu (MPASI) pada bayi usia 9 - 11 bulan di daerah kumuh perkotaan Jakarta. Penelitian potong lintang ini melibatkan 50 orang pengasuh bayi usia 9 – 11 bulan. Data dikumpulkan melalui wawancara menggunakan kuesioner. Tidak terdapat hubungan yang bermakna antara usia pengasuh dengan praktik pemberian makan (nilai p = 0,645). Demikian juga dengan …

Residential Density, Parents’ Sexual Activity And Teenage Sexual Behavior In Yogyakarta, Luluk Rosida, Evi Martha, Besral Besral

Kesmas

Pada daerah kumuh dan padat, orangtua sering terpaksa harus berbagi ruang tidur dengan anak-anaknya sehingga anak-anaknya sudah terpapar dengan aktivitas seksual sejak dini. Penelitian ini bertujuan mengetahui kepadatan hunian, aktivitas seksual orangtua, dan efeknya terhadap perilaku seksual remaja di Yogyakarta. Penelitian ini menggunakan desain potong lintang dengan mewawancarai 268 keluarga yang memiliki anak remaja yang dipilih secara acak di daerah kumuh perkotaan dan daerah pedesaan pada bulan Maret – Mei 2015. Analisis data dilakukan menggunakan uji kai kuadrat dan regresi-cox multivariat. Hasil penelitian ini menunjukkan bahwa orangtua yang tinggal di hunian padat memiliki risiko dua kali lebih besar untuk melakukan …

Effects Of Mothers’ Attitude As Breeders And Distance Of Stockyard Toward Diarrhea Incidence Among Toddlers, Yarmaliza Yarmaliza, Sugito Sugito, Teuku Reza Ferasyi, Nurliana Nurliana, Razali Razali

Kesmas

Diare merupakan penyakit dengan perubahan bentuk dan konsentrasi tinja yang melembek sampai mencair, dan bertambahnya frekuensi buang air besar lebih dari biasanya (tiga kali atau lebih dalam sehari). Di Provinsi Aceh, terdapat kasus diare sebanyak 48/1.000 kelahiran hidup pada 2013. Di Kabupaten Aceh Barat, pada tahun 2014 terdapat 1.071 kasus, sedangkan di Kecamatan Meureubo terdapat sebanyak 70 kasus pada anak bawah lima tahun (balita). Penelitian ini bertujuan untuk mengetahui hubungan sikap ibu sebagai peternak dan jarak kandang ternak terhadap kejadian diare pada balita di wilayah kerja Puskesmas Kecamatan Meureubo. Penelitian ini dilakukan secara potong lintang pada bulan Juli – September …

Cadmium Contamination In Farmland Soil And Water Near Zinc Mining Site, Kanitta Jiraungkoorskul, Sara Arphorn, Mathuros Tipayamongholgul, Wattasit Siriwong

Kesmas

Penelitian ini merupakan penelitian potong lintang yang dilakukan di Kecamatan Phatadpaeng, Kota Mae Sod, Provinsi Tak, Thailand. Penelitian ini bertujuan untuk mengetahui konsentrasi kadmium pada air dan tanah pertanian serta pada pemukiman petani dan rumah tangga. Konsentrasi kadmium pada 48 sampel tanah dan air pemukiman petani, 12 sampel rumah tangga, enam sampel tanah pertanian, dan delapan sampel air pertanian ditelusuri menggunakan Graphite Furnace Atomic Absorption Spectrophotometer. Uji Mann-Whitney U digunakan untuk analisis perbedaan konsentrasi kadmium antara tanah pertanian dan tanah pemukiman, air pertanian dan air pemukiman. Hasil penelitian menunjukkan tidak terdapat perbedaan secara statistik pada seluruh matriks, namun air dan …

Study On Clinical, Histopathological Features And Evaluation Results Of Skin Cancer Treatment In Can Tho Oncology Hospital, Nguyen Van Qui, Phan Nguyen Ngoc

Kesmas

Kanker kulit, diagnosis kanker paling umum, cenderung mengalami peningkatan. Kondisi ini secara khusus merupakan isu penting di negara-negara maju. Penelitian ini bertujuan untuk mendeskripsikan fitur klinis, fitur hispatologis, komplikasi dan hasil pengobatan bedah awal kanker kulit di Rumah Sakit Onkologi Can Tho dari tahun 2014 sampai 2015. Penelitian deskriptif prospektif ini melibatkan seluruh pasien dengan kanker kulit nonmelanoma yang diuji dan diobati di Rumah Sakit Onkologi Can Tho dari Juli 2014 sampai Maret 2015. Terdapat 78 kasus terpilih. Kanker kulit ditemukan lebih umum pada pasien yang lebih tua. Prevalensi karsinoma sel basal ditemukan lebih tinggi dibandingkan karsinoma sel skuamosa dengan …

Communication Of Parents, Sexual Content Intake And Teenage Sexual Behavior At Senior High School In Banjarmasin City, Rusmilawaty Rusmilawaty, Yuniarti Yuniarti, Tri Tunggal

Kesmas

Perilaku seks bebas di kalangan remaja Kota Banjarmasin belakangan ini semakin mengkhawatirkan para orangtua. Kurangnya pendidikan seksologi berdampak para remaja cenderung melakukan hubungan seksual pranikah yang akan berakibat pada kehamilan yang tidak diinginkan dan pernikahan dini. Komunikasi orangtua-anak dan paparan media baik media cetak maupun elektronik merupakan cara untuk mengurangi perilaku seksual berisiko. Tujuan penelitian ini untuk mengetahui hubungan komunikasi orangtua dan asupan muatan seksual dengan perilaku seksual remaja sekolah menengah atas (SMA) di Kota Banjarmasin. Untuk mencapai tujuan tersebut, penelitian survei analitik dengan pendekatan potong lintang dilakukan pada bulan Juli – Oktober 2015 di dua sekolah negeri dan satu …

Crtgeedr: An R Package For Doubly Robust Generalized Estimating Equations Estimations In Cluster Randomized Trials With Missing Data, Melanie Prague, Rui Wang, Victor De Gruttola

Harvard University Biostatistics Working Paper Series

No abstract provided.

Statistical Interpretation Including The Appropriate Statistical Tests, Olga A. Vsevolozhskaya

Biostatistics Presentations

Outline:

1. Evaluation of treatment’s therapeutic potential after experimental stroke.
2. Post-stroke behavioral testing and functional recovery.

Alzheimer's Biomarkers Are Correlated With Brain Connectivity In Older Adults Differentially During Resting And Task States, Yang Jiang, Haiqing Huang, Erin Abner, Lucas S. Broster, Gregory A. Jicha, Frederick A. Schmitt, Richard Kryscio, Anders H. Andersen, David Powell, Linda J. Van Eldik, Brian T. Gold, Peter T. Nelson, Charles D. Smith, Mingzhou Ding

Behavioral Science Faculty Publications

β-amyloid (Aβ) plaques and tau-related neurodegeneration are pathologic hallmarks of Alzheimer’s disease (AD). The utility of AD biomarkers, including those measured in cerebrospinal fluid (CSF), in predicting future AD risk and cognitive decline is still being refined. Here, we explored potential relationships between functional connectivity (FC) patterns within the default-mode network (DMN), age, CSF biomarkers (Aβ₄₂ and pTau₁₈₁), and cognitive status in older adults. Multiple measures of FC were explored, including a novel time series-based measure [total interdependence (TI)]. In our sample of 27 cognitively normal older adults, no significant associations were found between levels of Aβ …

Hpcnmf: A High-Performance Toolbox For Non-Negative Matrix Factorization, Karthik Devarajan, Guoli Wang

COBRA Preprint Series

Non-negative matrix factorization (NMF) is a widely used machine learning algorithm for dimension reduction of large-scale data. It has found successful applications in a variety of fields such as computational biology, neuroscience, natural language processing, information retrieval, image processing and speech recognition. In bioinformatics, for example, it has been used to extract patterns and profiles from genomic and text-mining data as well as in protein sequence and structure analysis. While the scientific performance of NMF is very promising in dealing with high dimensional data sets and complex data structures, its computational cost is high and sometimes could be critical for …

A Test Of Symmetry Based On The Kernel Kullback-Leibler Information With Application To Base Deficit Data, Hani M. Samawi, Robert L. Vogel

Biostatistics: Faculty Publications

The assumption of the symmetry of the underlying distribution is important to many statistical inference and modeling procedures. This paper provides a test of symmetry using kernel density estimation and the Kullback-Leibler information. Based on simulation studies, the new test procedure outperforms other tests of symmetry found in the literature, including the Runs Test of Symmetry. We illustrate our new procedure using real data.

Accounting For Interactions And Complex Inter-Subject Dependency In Estimating Treatment Effect In Cluster Randomized Trials With Missing Outcomes, Melanie Prague, Rui Wang, Alisa Stephens, Eric Tchetgen Tchetgen, Victor Degruttola

Harvard University Biostatistics Working Paper Series

No abstract provided.

Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret

UW Biostatistics Working Paper Series

We have frequently implemented crossover studies to evaluate new therapeutic interventions for genital herpes simplex virus infection. The outcome measured to assess the efficacy of interventions on herpes disease severity is the viral shedding rate, defined as the frequency of detection of HSV on the genital skin and mucosa. We performed a simulation study to ascertain whether our standard model, which we have used previously, was appropriately considering all the necessary features of the shedding data to provide correct inference. We simulated shedding data under our standard, validated assumptions and assessed the ability of 5 different models to reproduce the …

An Efficient Basket Trial Design, Kristen Cunanan, Alexia Iasonos, Ronglai Shen, Colin B. Begg, Mithat Gonen

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

The landscape for early phase cancer clinical trials is changing dramatically due to the advent of targeted therapy. Increasingly, new drugs are designed to work against a target such as the presence of a specific tumor mutation. Since typically only a small proportion of cancer patients will possess the mutational target, but the mutation is present in many different cancers, a new class of basket trials is emerging, whereby the drug is tested simultaneously in different baskets, i.e., sub-groups of different tumor types. Investigators not only desire to test whether the drug works, but also to determine which types of …