Physical Sciences and Mathematics Commons^™

Dna Cyclization And Looping In The Wormlike Limit: Normal Modes And The Validity Of The Harmonic Approximation, Stefan M. Giovan, Andreas Hanke, Stephen D. Levene

Physics and Astronomy Faculty Publications and Presentations

For much of the last three decades, Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, J, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last 10 years approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly …

Revision-Polyurethane-Graphene Nanocomposites For Corrosion-Resistant Coatings, Alexandra Rose Stevenson

Master's Theses

Corrosion is a prevalent concern throughout the world, causing significant monetary and safety concerns. Research has been dedicated to developing cost-effective solutions for corrosion that will also meet increasingly stringent environmental regulations. The recently discovered nanomaterial graphene has been proposed as a potential component in anticorrosion technology due to its strong air and water barrier properties. However, graphene is a relatively expensive, difficult to synthesize material. By incorporating it into nanocomposites, its properties can be exploited even at low concentrations. Previous work has been conducted involving the preparation of anticorrosive polystyrene-graphene nanocomposites; these materials were found to be effective long-term …

Woodstocc: Extracting Latent Parallelism From A Dna Sequence Aligner On A Gpu, Stephen V. Cole, Jacob R. Gardner, Jeremy D. Buhler

All Computer Science and Engineering Research

An exponential increase in the speed of DNA sequencing over the past decade has driven demand for fast, space-efficient algorithms to process the resultant data. The first step in processing is alignment of many short DNA sequences, or reads, against a large reference sequence. This work presents WOODSTOCC, an implementation of short-read alignment designed for Graphics Processing Unit (GPU) architectures. WOODSTOCC translates a novel CPU implementation of gapped short-read alignment, which has guaranteed optimal and complete results, to the GPU. Our implementation combines an irregular trie search with dynamic programming to expose regularly structured parallelism. We first describe this implementation, …

Design, Synthesis And Evaluation Of Bivalent Inhibitors Of Trehalose-6-Phosphate Phosphatase, Chunliang Liu

Chemistry and Chemical Biology ETDs

The D-glucose disaccharide α, α-D-trehalose is synthesized by a variety of bacteria, fungi, plants and invertebrates to support cell survival by functioning as a fuel, a metabolic regulator or a protectant against environmental stress. Five different trehalose biosynthetic pathways are known to exist, one of which, the OtsA/OtsB pathway is common among pathogenic bacteria and fungi and is also found in parasitic nematodes. Previously reported otsA and otsB gene knockout (or knockdown) experiments have shown that both pathway enzymes are essential for M. tuberculosis cell growth and host colonization. RNAi gene silencing carried out in the nematode model system Caenohabditis …

Mining Public Databases For Discovery Of Structure And Function Within The Hotdog-Fold Thioesterase And Had Phosphatase Enzyme Families, Sarah Toews Keating

Chemistry and Chemical Biology ETDs

For my doctoral work, I have developed strategies to mine public databases for data that can be used to infer structural and functional information for the hotdog-fold and HADSF superfamilies. For the hotdog-fold superfamily, I used curated and automatically applied annotations of structure, taxonomic lineage, function, and subfamily membership from the UniProtKB, gene context and taxonomic information from the NCBI, and the results of several in-depth explorations of subfamily/function and structural class membership. Based on the distribution of the aforementioned annotations mapped onto a sequence similarity network (SSN), I applied structural assignments to sequences and/or specific function/subfamily assignments to ~143,000 …

Construction Of Nonlinear Expression For Recursive Number Sequences, Tian-Xiao He

Tian-Xiao He

Bps Brane Cosmology In N=2 Supergravity, Moataz Emam

Moataz Emam

We study the embedding of flat BPS 3-branes in five dimensional N=2 supergravity theory. We derive the branes' dynamical equations as well as general expressions for the hypermultiplet fields then focus on a single brane and study its time evolution. It is shown that the brane's Hubble parameter correlates with the moduli of the underlying manifold's complex structure. For certain particular solutions, the moduli seem to exhibit an instability; being large valued at early times then rapidly decaying to either zero or some convergent constant value. The possibility of extending these results to the cosmology of our universe is implied …

Impact Of Biofield Treatment On Spectroscopic And Physicochemical Properties Of P-Nitroaniline, Mahendra Kumar Trivedi, Alice Branton, Dahryn Trivedi, Gopal Nayak, Khemraj Bairwa, Snehasis Jana

Mahendra Kumar Trivedi

Collaboration And Health Care Diagnostics: An Agent Based Model Simulation, Sebastian Linde, George K. Thiruvathukal

George K. Thiruvathukal

This paper presents a simple ABM simulation that seeks to provide insight into the public health benefits that derive from greater collaboration among health care professionals. In particular, the paper compares the efficiency, delivery and timeliness of health care diagnostics under two contrasting paradigms–one in which collaboration is encouraged, and an- other where it is not. The preliminary results of this study suggest that while the effect of cooperation on aggregate public health depends on the patient search algorithm employed, its effect on overall efficiency and timeliness of health care diagnostics and treatment is significant and pos- itive. Since the …

The Quasi-Static Deformation, Failure, And Fracture Behavior Of Titanium Alloy Gusset Plates Containing Bolt Holes, Therese Hurtuk, Craig Menzemer, Anil Patnaik, Tirumalai Srivatsan, Kannan Manigandan, T. Quick

Anil Patnaik

In this article, the influence of bolt holes, specifically their number and layout on strength, deformation, and final fracture behavior of titanium alloy gusset plates under the influence of an external load is presented and discussed. Several plates having differences in both the number and layout of the bolt holes were precision machined and then deformed under quasi-static loading. The specific influence of number of bolt holes and their layout on maximum load-carrying capability and even fracture load was determined. The conjoint influence of bolt number, bolt layout pattern, nature of loading, contribution from local stress concentration, and intrinsic microstructural …

Late Quaternary Speleogenesis And Landscape Evolution In A Tropical Carbonate Island: Pango La Kuumbi (Kuumbi Cave), Zanzibar, Nikos Kourampas, Ceri Shipton, William Mills, Ruth Tibesasa, Henrietta Horton, Mark Horton, Mary Prendergast, Alison Crowther, Katerina Douka, Patrick Faulkner, Llorenç Picornell, Nicole Boivin

International Journal of Speleology

Kuumbi Cave is one of a group of caves that underlie a flight of marine terraces in Pleistocene limestone in eastern Zanzibar (Indian Ocean). Drawing on the findings of geoarchaeological field survey and archaeological excavation, we discuss the formation and evolution of Kuumbi Cave and its wider littoral landscape. In the later part of the Quaternary (last ca. 250,000 years?), speleogenesis and terrace formation were driven by the interplay between glacioeustatic sea level change and crustal uplift at rates of ca. 0.10-0.20 mm/yr. Two units of backreef/reef limestone were deposited during ‘optimal’ (highest) highstands, tentatively correlated with MIS 7 and …

Tidal Flat Morphodynamics: A Synthesis, Carl T. Friedrichs

Presentations

Tidal flats commonly occur along coasts where the tidal range is large relative to typical wave height. They can be found where hydrodynamic energy is high or low, where sediments are sandy or muddy, and where shorelines are prograding, retreating, or stable. The study of the morphology and evolution of tidal flats is particularly well suited in the context of morphodynamics since characteristics such as profile shape, bed slope, and grain size clearly and systematically vary as a function of sediment supply and wave and tidal forcing, and the nature of wave- and tide-induced velocities across tidal flats is, in …

Methods For The Direct Simulation Of Nanoscale Film Breakup And Contact Angles, Kyle Mahady

Dissertations

This thesis investigates direct simulation of fluids with free surfaces and contact lines, with a focus on capturing nanoscale physics in a continuum based computational framework. Free surfaces and contact lines have long presented some of the most challenging problems in computational fluid dynamics. Extensive progress has been made in recent years, and a wide variety of different methods are currently employed for direct simulation in these contexts. The complexity of the full governing equations for such flows poses significant challenges in terms of analytical techniques, and leads to lengthy computational times for direct simulations. For these reasons, reduced models …

Thermochemistry And Kinetics: Hydrogen Atom Addition Reactions With Alkenes, Oxidation Of Cyclopentadienone, Trifluoroethene And Transport Properties, Suriyakit Yommee

Dissertations

Thermochemical and transport properties and reaction kinetic parameters are important to understand and to model atmospheric chemistry, combustion and other thermal systems. These processes are all important to the environment. Thermochemical properties kinetic parameters and models for several atmospheric and combustion related chemical systems are determined using computational chemistry coupled with fundamentals of thermodynamics and statistical mechanics. Transport properties of hydrocarbon and oxygenated hydrocarbons which are important to the calculation of fluid dynamics of gas phase flow reactions and mixing needed for evaluation in the combustion and thermal (flow) fluid dynamic modeling. Transport properties of radicals cannot be measured so …

Social Analytics For Health Integration, Intelligence, And Monitoring, Xiang Ji

Dissertations

Nowadays, patient-generated social health data are abundant and Healthcare is changing from the authoritative provider-centric model to collaborative and patient-oriented care. The aim of this dissertation is to provide a Social Health Analytics framework to utilize social data to solve the interdisciplinary research challenges of Big Data Science and Health Informatics. Specific research issues and objectives are described below.

The first objective is semantic integration of heterogeneous health data sources, which can vary from structured to unstructured and include patient-generated social data as well as authoritative data. An information seeker has to spend time selecting information from many websites and …

Investigation Of Infinite-Dimensional Dynamical System Models Applicable To Granular Flows, Hao Wu

Dissertations

Recently Blackmore, Samulyak and Rosato developed a class of infinite-dimensional dynamical systems in the form of integro-partial differential equations, which have been called the BSR models. The BSR models were originally derived to model granular flows, but they actually have many additional applications in a variety of fields. BSR models have already been proven to be completely integrable infinite-dimensional Hamiltonian dynamical systems for perfectly elastic interactions in the case of one space dimension, but the well-posedness question of these systems is at least partially answered for the first time here. In particular, dynamical systems of the BSR type are proven …

Southeast Florida Coral Reef Fishery-Independent Baseline Assessment, Kirk Kilfoyle, Brian K. Walker, Dana P. Fisco, Steven G. Smith, Richard E. Spieler

Marine & Environmental Sciences Faculty Reports

Reef fishes are important biologic, ecologic, and economic resources of the marine ecosystem which must be managed for sustainability. Until recently, there was no long-term monitoring program in place to assess the condition of reef fish resources of the northern Florida Reef Tract (FRT) (northern Miami-Dade, Broward, Palm Beach, and Martin counties). An assessment/monitoring plan for the northern portion of the Florida reef tract was designed through a joint cooperative effort by scientists at the University of Miami, Rosenstiel School of Marine and Atmospheric Science (RSMAS), National Oceanic and Atmospheric Administration (NOAA)-Southeast Fisheries Science Center (SEFSC) and Nova Southeastern University …

Sikap Remaja Terhadap Keperawanan Dan Perilaku Seksual Dalam Berpacaran, Desi Rusmiati, Sutanto Priyo Hastono

Kesmas

Laporan Survei Demografi dan Kesehatan Indonesia (SDKI) tahun 2007 dan 2012 menunjukkan terjadinya penurunan jumlah remaja yang memiliki sikap positif terhadap pentingnya mempertahankan keperawanan bagi seorang perempuan. Dari laporan yang sama juga diketahui adanya peningkatan perilaku seksual remaja dalam hal berpegangan tangan, berciuman bibir, petting, dan melakukan hubungan seksual. Penelitian ini bertujuan untuk membuktikan adanya hubungan antara sikap remaja terhadap keperawanan dengan perilaku seksual dalam berpacaran dengan melibatkan usia, jenis kelamin, pendidikan, tempat tinggal, usia pertama kali pacaran, pengetahuan, dan pengaruh teman sebaya sebagai variabel perancu. Penelitian ini merupakan penelitian kuantitatif dengan rancangan potong lintang menggunakan model faktor risiko dari …

Analisis Sif Kerja, Masa Kerja, Dan Budaya K3 Dengan Fungsi Paru Pekerja Tambang Batu Bara, Qomariyatus Sholihah, Aprizal Satria Hanafi, Wanti Wanti, Ahmad Alim Bachri, Sutarto Hadi

Kesmas

Penambangan batu bara merupakan salah satu sumber pencemaran udara berupa partikel debu batu bara yang dapat mengganggu kesehatan pernapasan bila terhirup manusia. Risiko kerja yang sering terjadi dapat berasal dari faktor pekerjaan atau perilaku pekerja sendiri, di antaranya sif kerja dan masa kerja. Tujuan penelitian adalah untuk mengetahui hubungan sif kerja, masa kerja, dan budaya keselamatan dan kesehatan kerja (K3) dengan fungsi paru pekerja tambang batu bara. Penelitian ini merupakan desain kasus kontrol dengan jumlah masing-masing sampel untuk kasus dan kontrol sebesar 178 responden. Penelitian dilakukan pada bulan Oktober November 2014 di PT. X Kalimantan Selatan. Hasil penelitian berdasarkan uji …

Pendidikan Kesehatan Reproduksi Formal Dan Hubungan Seksual Pranikah Remaja Indonesia, Anggriyani Wahyu Pinandari, Siswanto Agus Wilopo, Djauhar Ismail

Kesmas

Transisi demografi kedua akan terjadi di Indonesia dan ditandai dengan revolusi seksual dan reproduksi. Masalah potensial di masa ini adalah peningkatan perilaku seksual pranikah, kehamilan yang tidak diinginkan, infeksi menular seksual dan penyalahgunaan obat. Penelitian ini bertujuan untuk menguji pengaruh pendidikan kesehatan reproduksi formal terhadap penundaan hubungan seksual pranikah pada remaja dan dewasa muda Indonesia. Penelitian potong lintang yang dianalisis sebagai kohort retrospektif menggunakan data Survei Kesehatan Reproduksi Remaja Indonesia tahun 2012 (10.980 laki-laki dan 8.902 perempuan). Efek pendidikan kesehatan reproduksi formal terhadap penundaan perilaku hubungan seksual dianalisis menggunakan kurva kaplan meier, uji log-rank, dan uji chi square, sedangkan analisis …

Assessment Of Nutrition Information System Using Health Metrics Network Framework, Mochamad Iqbal Nurmansyah, Catur Rosidati, Riastuti Kusuma Wardani, Badra Al-Aufa

Kesmas

Sistem informasi gizi (Sigizi) dikembangkan oleh Direktorat Bina Gizi Kementerian Kesehatan sejak 2011. Data Sigizi mencakup data penimbangan balita di posyandu, kasus gizi buruk, cakupan pemberian tablet Fe pada ibu hamil, konsumsi garam beryodium, pemberian vitamin A, dan ASI eksklusif. Penelitian ini bertujuan untuk mengukur kinerja pengelolaan Sigizi di Dinas Kesehatan Kota Tangerang Selatan menggunakan kerangka Health Metrics Network yang dikeluarkan oleh WHO tahun 2008. Sigizi merupakan sistem informasi yang diaplikasikan pada tingkat nasional dengan mekanisme pelaporan berjenjang, dari 508 kabupaten/kota menuju 34 provinsi dan bermuara di tingkat nasional. Di Provinsi Banten, terdapat delapan kabupaten/kota yang menjalankan Sigizi. Informan penelitian …

Taxonomy Of The Bitentaculate Cirratulidae (Polychaeta), Stacy A. Tewari

Graduate Masters Theses

The bitentaculate cirratulid polychaetes are an important faunal element of both near shore and deep-sea benthic faunal communities. The true diversity of the family is currently unknown due to a large number of undescribed species and erroneously applied “cospmopolitan” names being applied to local species. Cirratulids have been misidentified even in the local waters near the University of Massachusetts Boston. The current study presents six new species from North America. Caulleriella venefica, Chaetozone anasimus, Chaetozone diodonta, and Chaetozone hystricosus are described from Boston Harbor and Massachusetts Bay where only two species had previously been reported. Aphelochaeta bullata …

An Investigation Into Transitions In Clay Mineral Chemistry On Mars, Seth Gainey

UNLV Theses, Dissertations, Professional Papers, and Capstones

This dissertation is comprised of three studies investigating clay mineralogy on, or near the martian surface, with an introductory chapter, introducing and linking the three studies. Chapter two is on the subject of clay mineral synthesis, including Fe/Mg clay minerals which have been detected at multiple locations across the southern highlands. These Fe/Mg clay minerals have been previously interpreted as forming in anoxic/reducing environments, conducive to the preservation of organic matter. The results of this study suggest that the previous interpretation of Fe/Mg-rich clay as requiring anoxic/reducing conditions may not be accurate, as the minor presence of Mg (below what …

Quantum Mechanics With A Quartic Dispersion Law, Joanna Ruhl

Graduate Masters Theses

Creation of three-dimensional matter waves, the three-dimensional analog of one-dimensional solitons, has been a goal of experimental physics for some time. A recent proposal has suggested that changing the dispersion law from quadratic to quartic for ultra cold atoms in a shaken lattice should allow for the creation of these objects. In this thesis, we develop the theoretical basis for quantum mechanics with a quartic dispersion law. The probability current functional is constructed from the corresponding time-dependent Schrödinger equation, and used to derive the junction conditions that connect the derivatives of the wavefunction on one side of a potential discontinuity …

Sociodemographic Factors To Dengue Hemmorrhagic Fever Case In Indonesia, Desy Nuryunarsih

Kesmas

Demam berdarah dengue (DBD) adalah penyebab utama rawat inap dan kematian pada anak-anak. Indonesia adalah salah satu negara yang oleh WHO dikategorikan hyperendemicity dengan empat serotipe virus tersebar di daerah perkotaan. Faktor sosiodemografi dianggap sebagai faktor pendukung terjadinya DBD di Indonesia. Studi ini menggunakan data sekunder yang diunduh dari Basis Data Kesehatan Provinsi tahun 2010 Kementerian Kesehatan Republik Indonesia untuk menentukan korelasi antara ketiga faktor sosiodemografi dengan insiden DBD. Penelitian ini menggunakan metode kuantitatif deskripsi korelasi. Hasil penelitian menunjukkan bahwa dua faktor sosiodemografi terpilih memiliki korelasi linier dengan insiden DBD. Analisa regresi multivariat menunjukkan kecilnya korelasi antara insiden DBD dengan …

Penerapan Sistem Remunerasi Dan Kinerja Pelayanan, Tri Wisesa Soetisna, Dumilah Ayuningtyas, Misnaniarti Misnaniarti

Kesmas

Remuneration can influence worker`s motivation, and improve their performance. Likewise in hospital as capital-intensive, human resources-intensive as well as knowledge and technology-intensive health care institution. This study aimed to analyze employee’s perception of remuneration system implementation and adult cardiac surgery services unit’s performance at hospital. This study used a mixed method approach (quantitative and qualitative). Quantitative study design was cross-sectional using questionnaire for self-assesment. Meanwhile, qualitative study design was descriptive conducted through focus group discussion and document review on data in forms of schedule book, registration book, nursing notes and medical records. Data collection was conducted in 2013 at one …

Tradisi Dan Lingkungan Sosial Memengaruhi Dukungan Menyusui Pada Bayi Berat Badan Lahir Rendah Di Kota Malang, Muladefi Choiriyah, Elsi Dwi Hapsari, Wiwin Lismidiati

Kesmas

Berat badan lahir rendah (BBLR) merupakan salah satu penyebab utama kematian bayi di dunia. World Health Organization tahun 2003 telah merekomendasikan menyusui sebagai salah satu penanganan BBLR. Namun, ibu yang memiliki bayi BBLR mengalami kesulitan di awal persalinan. Selain itu, menyusui di Indonesia juga dipengaruhi oleh sosial dan budaya yang dipercayai sehingga memengaruhi keputusan ibu untuk memilih tetap menyusui atau tidak sama sekali di periode awal postpartum. Tujuan penelitian ini untuk mengeksplorasi makna pengalaman ibu untuk tetap menyusui bayi dengan BBLR. Penelitian kualitatif ini dengan pendekatan fenomenologi. Tujuh orang partisipan adalah ibu yang pernah menyusui bayi BBLR. Pengumpulan data dilakukan …

Functional –Esime3 Containing Reagents: From Organo-Polychalcogenolates To Nhc Ligated M-E-Sime3, Mahmood Azizpoor Fard

Electronic Thesis and Dissertation Repository

The reaction of M[ESiMe₃] (M = Li/Na; E = S, Se) with polyorganobromides, has afforded polychalcogenotrimethylsilane complexes Ar(CH₂ESiMe₃)_n: 1,4-(Me₃SiECH₂)₂(C₆Me₄) (E = S, 1; E = Se, 2), 1,3,5-(Me₃SiECH₂)₃(C₆Me₃) (E = S, 3; E = Se, 4) and 1,2,4,5-(Me₃SiECH₂)₄(C₆H₂)(E = S, 5; E = Se, 6). The powerful potential of these complexes as precursor to combine with …

A Study Of Pseudo-Periodic And Pseudo-Bordered Words For Functions Beyond Identity And Involution, Manasi Kulkarni

Electronic Thesis and Dissertation Repository

Periodicity, primitivity and borderedness are some of the fundamental notions in combinatorics on words. Motivated by the Watson-Crick complementarity of DNA strands wherein a word (strand) over the DNA alphabet \{A, G, C, T\} and its Watson-Crick complement are informationally ``identical", these notions have been extended to consider pseudo-periodicity and pseudo-borderedness obtained by replacing the ``identity" function with ``pseudo-identity" functions (antimorphic involution in case of Watson-Crick complementarity). For a given alphabet $\Sigma$, an antimorphic involution $\theta$ is an antimorphism, i.e., $\theta(uv)=\theta(v) \theta(u)$ for all $u,v \in \Sigma^{*}$ and an involution, i.e., $\theta(\theta(u))=u$ for all $u \in \Sigma^{*}$. In this thesis, …

Small Phytoplankton Drive High Summertime Carbonand Nutrient Export In The Gulf Of California And Eastern Tropical North Pacific, Viena Puigcorbé, Claudia R. Benitez-Nelson, Pere Masqué, Elisabet Verdeny, Angelicque E. White, Brian N. Popp, Fredrick G. Prahl, Phoebe J. Lam

Faculty Publications

Summertime carbon, nitrogen, and biogenic silica export was examined using 234Th:238U disequilibria combined with free floating sediment traps and fine scale water column sampling with in situ pumps (ISP) within the Eastern Tropical North Pacific and the Gulf of California. Fine scale ISP sampling provides evidence that in this system, particulate carbon (PC) and particulate nitrogen (PN) concentrations were more rapidly attenuated relative to 234Th activities in small particles compared to large particles, converging to 1–5 µmol dpm−1 by 100 m. Comparison of elemental particle composition, coupled with particle size distribution analysis, suggests that small particles are major contributors to …