Digital Commons Network^™

Identifying Novel Transcription Factors Involved In The Inflammatory Response By Using Binding Site Motif Scanning In Genomic Regions Defined By Histone Acetylation., Peter S Askovich, Stephen A Ramsey, Alan H Diercks, Kathleen A Kennedy, Theo A Knijnenburg, Alan Aderem

Articles, Abstracts, and Reports

The innate immune response to pathogenic challenge is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of this response have been identified, the temporal complexity of gene expression changes in response to pathogen-associated molecular pattern receptor stimulation strongly suggest that additional layers of regulation remain to be uncovered. The evolved pathogen response program in mammalian innate immune cells is understood to reflect a compromise between the probability of clearing the infection and the extent of tissue damage and inflammatory sequelae it causes. Because of that, a key challenge to delineating the …

Development And Characterization Of Novel Anti-Bat Monoclonal Antibodies For Studying Bat Immunity, Cailyn Cowan

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Novel Approaches To Mitigating Bacterial Biofilm Formation And Intercellular Communication, Stephen Kasper

Legacy Theses & Dissertations (2009 - 2024)

Long thought of as solitary single-cell organisms, it is now widely accepted that bacteria can act and cooperate as social organisms. Phenomena such as biofilm formation and quorum sensing (QS) are two intimately intertwined cooperative behaviors that significantly contribute to the pathogenesis of many bacteria. Biofilms are surface associated communities of bacteria encased in a secreted extracellular matrix, which provides several advantages over an individualized lifestyle, such as increased protection from antimicrobial agents as well as enhanced opportunity for the exchange of genetic material. Bacterial QS is a system of population-based communication through the production, sensing, and response to chemical …

Study Of Biologically Important Macromolecules By Nuclear Magnetic Resonance, Christopher Michael Demott

Legacy Theses & Dissertations (2009 - 2024)

Intrinsically disordered proteins or unstructured segments within proteins play an important role in cellular physiology and pathology. A combination of peptide aptamers selected by using the yeast-two-hybrid scheme, and in-cell NMR identified high affinity binders to a transiently structured intrinsically disordered proteins (IDP). This method was validated using the prokaryotic ubiquitin-like protein, Pup, of the Mycobacterium proteasome. We discover two peptide aptamers that bind to opposite sites of a transient helix in Pup, an intrinsically disordered protein, that have vastly different effects on the survival of Mycobacterium bovis BCG.

The Association Of Comorbid Chronic Physical Conditions And Psychological Illness With Health Care Utilization In Middle-Aged And Older People, Allison Houston

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Impact Of Foreign Born East Asian Density On Liver Cancer Incidence Rate Among Neighborhoods In New York City During 2009-2013 : Multilevel Analysis, Sangwon Lee

Legacy Theses & Dissertations (2009 - 2024)

Objective: To investigate the impact of the density of foreign born Asian population on geographical incidence rate of liver cancer in New York City during 2009 – 2013 in order to find specific geographic areas in NYC where liver cancer intervention should be targeted.

Viral Suppression Among Older Persons Living With Diagnosed Hiv Infection (Plwdhi) With Multimorbidity : The Role Of Healthcare Setting, Health Literacy, And Health Knowledge (Mmp 2009-2014), Doris Ogechukwu Maduka

Legacy Theses & Dissertations (2009 - 2024)

For persons living with diagnosed HIV infection (PLWDHI) 50 years of age and older, in addition to living with diagnosed HIV infection, they are also at risk for age-related chronic conditions. Optimal management of these conditions in addition to HIV is needed if they hope to achieve positive health outcomes such as achieving durable viral suppression, which is the goal for persons receiving HIV treatment. For these patients, having adequate health related information, and the ability to access and navigate the healthcare system, would help them stay engaged and maintain adherence to HIV care. Factors that have been found to …

Detecting And Analyzing Trna Modification Systems And Homologs Using In Silico And Colorectal Cancer Models, Khadijah Onanuga

Legacy Theses & Dissertations (2009 - 2024)

tRNA modifications can be considered epitranscriptomic signaling components that regulate translation and play integral roles in stress response pathways. As such, tRNA modification enzymes have roles in cancer etiology and potential utility as biomarkers of pathological states. For my thesis project I have used computational and wet bench approaches to study tRNA modification systems. Chapter two of my thesis deals with tRNA modification detection, as current methods are costly, time consuming, and require RNA fragmentation. I present a single-molecule-based approach for RNA modification detection, which involves in slico studies using a 5-layered graphene nanopore. Our simulations using a 1.5 nm …

A Tale Of Two Regulators : Characterization Of The Novel Transcription Factor Abmr And The Small Non-Coding Rna Mcr11 In Mycobacterium Tuberculosis, Roxanne Candice Girardin

Legacy Theses & Dissertations (2009 - 2024)

Genes of unknown function make up nearly one third of Mtb’s genome (Cole,

Hepatitis C Status Awareness And Test Results Confirmation Among People Who Inject Drugs In Ukraine, Olena Iakunchykova

Legacy Theses & Dissertations (2009 - 2024)

Background. Hepatitis C virus (HCV) positivity is frequently found in people who inject drugs (PWID). The prevalence of HCV in this population in Ukraine is estimated at 71%. As treatment for HCV infection becomes more available, it is important to know what modifiable factors are related to testing, linkage to care and treatment.

Improving Hiv Outcomes In Pakistan : The Interaction Between Politics, Power And Implementation, Hina Khalid

Legacy Theses & Dissertations (2009 - 2024)

HIV contributes to the highest number of deaths from infectious diseases in low-income countries. In this three-paper dissertation, using the case of Pakistan, I focus on understanding how the exercise of power by actors at three different levels of the health system, individual, program and societal, influences policy implementation and shapes HIV program outcomes. The objective is to improve HIV service provision thereby achieving improved health policy outcomes. I adopt a mixed-methods approach and use quantitative (logit regression) and qualitative techniques (content analysis of newspapers and semi-structured interviews). One paper tests the role played by network operators in influencing condom …

Implementing Pharmacy-Based Travel Health Services: Insight And Guidance From Frontline Practitioners, Tania Gregorian, Albert Bach, Karl Hess, Keri Hurley, Edith Mirzaian, Jeff Goad

Pharmacy Faculty Articles and Research

PURPOSE In California, the passage of SB493 in July of 2013 was a milestone in advancing pharmacy practice. Among other things, the new legislation allows pharmacists to provide routine immunizations without a protocol and furnish medications for international travelers for conditions not requiring a diagnosis. When developing a pharmacist-run travel health service, consideration must be given to multiple important factors, including pharmacist training, physician partnership, logistics, from scheduling to documentation, and the resources necessary to provide a travel health service.5 This article sets out to provide guidance and insight to pharmacists seeking to implement a travel health service.

SUMMARY Travel …

Actionable Patient Safety Solution (Apss) #3a: Medication Errors, Ron Jordan, Jerika Lam, Anne Lyren, Nathaniel Sims, Coco Yang

Pharmacy Faculty Articles and Research

This report presents a plan of action for introducing a program to reduce medication errors, which are a major cause of patient morbidity and mortality.

Black Death Bodies, Sharon Dewitte, Maryanne Kowaleski

Faculty Publications

The fourteenth-century Black Death was one of the most important and devastating epidemics in human history. It caused or accelerated important demographic, economic, political, and social changes throughout the Old World and has therefore been the subject of scholarly research in a variety of fields, including history, anthropology, demography, and molecular biology. In this paper, we examine the Black Death (specifically, the first and second outbreaks of fourteenth-century plague, c. 1347–1351 and 1361–1362) from bioarchaeological and historical perspectives, focusing on attempts to reconstruct mortality patterns and addressing the questions: Who died in England during the Black Death? How did they …

An Ethnobotanical Survey In Selected Districts Of The Black Sea Region (Turkey), Emi̇ne Burcu Yeşi̇lyurt, Işil Şi̇mşek, Gali̇p Akaydin, Erdem Yeşi̇lada

Turkish Journal of Botany

The current study was carried out in selected districts of the Black Sea region of Turkey, in Trabzon (center), Çorum (İskilip town), Karabük (Yenice town), Amasya (Kapıkaya village), and Amasya (Belmebük village) in order to document the wild plants used by the local inhabitants, i.e. as a remedy or foodstuff or for other purposes. The data were collected from 352 individuals residing in these districts and volunteering to participate in the research through face-to-face interviewing. Depending on the data collected, the parts of the plants used, the purpose in using them, and the ways of preparation (simply cooking or decoction, …

Aftermath Of The Human Genome Project: An Era Of Struggle And Discovery, Zainab Hamdoun, Hashimul Ehsan

Turkish Journal of Biology

The collaboration between the Human Genome Project and the Sanger Institute, spurred on by their contemporary- Celera Genomics, in the race to sequence the human genome, opened the door to a generation of research concerned with the study of the nucleic manual. Following this monumental achievement, the genomic era was born, heralding the development of gene therapy, personalized medicine, pharmacogenomics, and CRISPR/Cas9 gene-editing systems. These 'omic' disciplines offer a wide range of applications in the treatment of disease and the betterment of the quality of human life. Their notability, however, manifests in the unique mix of sociological and scientific discourse …

Pooled Analysis Of 899 Nosocomial Meningitis Episodes From Turkey, Oğuz Reşat Si̇pahi̇, Arzu Nazli Zeka, Meltem Taşbakan, Hüsnü Pullukçu, Bi̇lgi̇n Arda, Tansu Yamazhan, Hi̇lal Si̇pahi̇, Sercan Ulusoy

Turkish Journal of Medical Sciences

Background/aim: Healthcare-associated meningitis (HCAM) is a relatively rare entity with significant morbidity and mortality. The aim of this study was to systematically review the Turkish medical literature for acute nosocomial meningitis. Materials and methods: One national (ULAKBİM) and two international (www.scopus.com and www.pubmed.com) databases were searched. In addition, abstracts of four national congresses held between 2004 and 2013 were searched for reports for HCAM meningitis. Results: Data for 899 HCAM meningitis episodes were obtained from 24 reports. In terms of clinical findings, 177 of 216 (81.9%) had fever (>38 °C), 55 of 64 (85.9%) had high CRP levels, 105 …

Prevalence And Associated Factors Of Thrombocytopenia Among Human Immunodeficiency Virus-Infected Patients At A Tertiary Care Hospital In İzmir, Turkey, Can Hüseyi̇n Heki̇moğlu, Fi̇gen Kaptan, İlknur Vardar, Serap Ural, Nesri̇n Türker, Bahar Örmen, Nurbanu Sezak, Si̇bel El

Turkish Journal of Medical Sciences

Background/aim: The aim of this study was to determine the prevalence and associated factors of thrombocytopenia in human immunodeficiency virus (HIV)-infected patients. Materials and methods: A cross-sectional study was conducted in a tertiary care hospital in İzmir, Turkey. All HIV-infected patients admitted to the Department of Infectious Diseases and Clinical Microbiology between 2006 and 2011 were recruited. Patients with thrombocytopenia at any time point were defined as the case group and the remaining patients were defined as the control group. Results: The frequency of thrombocytopenia was 35.8%. Thrombocytopenia was more frequent in patients with acquired immune deficiency syndrome (AIDS) than …

Nitric Oxide In Cerebrospinal Fluid Of Central Nervous System Tuberculosis: Correlations With Culture, Antibody Response, And Cell Count, Kavitha Kumar, Prashant Giribhattanavar, Shripad Patil

Turkish Journal of Medical Sciences

Background/aim: The role of nitric oxide (NO) has been established in infection over the years. NO functions by inhibiting the growth of intracellular pathogens. The present study was undertaken to ascertain the role of NO in central nervous system (CNS) infection by Mycobacterium tuberculosis. Materials and methods: A total of 781 chronic meningitis cerebrospinal fluid (CSF) samples suspected of CNS tuberculosis (TB) were categorized based on M. tuberculosis culture positivity, anti-TB antibody response, and CSF cell count and were analyzed for NO. Results: We found that NO levels were positive in 10.88% of the CSF samples. Positivity for NO was …

Epidemiology Of Under-Five Mortality In İstanbul: Changes From 1988 To 2011, Fahri̇ye Aysun Buzcu, Ayli̇n Yeti̇m Şahi̇n, Esra Karapinar, Özge Erol, Emi̇ne Gülbi̇n Gökçay

Turkish Journal of Medical Sciences

Background/aim: Understanding the causes of under-five deaths is key to realizing sustainable developmental goals. The aim of this descriptive study was to investigate the causes of under-five mortality in İstanbul during 2011 and compare the findings to those of 1988 and 2000. Materials and methods: All burial records of İstanbul were evaluated, and cemetery records of 1494 children, who died at under five years of age and were buried in İstanbul Metropolitan Municipality Cemeteries between 1 January and 31 December 2011, were analyzed. Several sociodemographic characteristics and causes of death were compared with the results of studies carried out in …

Analysis Of Epidemiology And Risk Factors For Mortality In Ventilator-Associated Pneumonia Attacks In Intensive Care Unit Patients, Ayşe But, Meltem Arzu Yetki̇n, Di̇lek Kanyilmaz, Hali̇de Aslaner, Ali̇ye Baştuğ, Adalet Aypak, Pinar Öngürü, Esragül Akinci, Nevzat Mehmet Mutlu, Hurrem Bodur

Turkish Journal of Medical Sciences

Background/aim: The aim of this study was to investigate the epidemiologic characteristics, the causative microorganisms and their antimicrobial susceptibility patterns, and the prognostic risk factors for mortality in critically ill patients with ventilator-associated pneumonia (VAP). Materials and methods: In this retrospective observational study, all the critically ill patients with VAP hospitalized in a medical/surgical intensive care unit (ICU) between January 2010 and June 2015 were evaluated. Patients' demographic features and microbiological data were reviewed. Results: A total of 417 patients were clinically diagnosed with VAP; 51.1% of them were male and the average age was found as 69.9 ± 15.9 …

Social Support And Quality Of Life In A Group Of Cancer Patients (Ankara, Turkey), Mustafa Soner Yilmaz, Bi̇rgül Pi̇yal, Recep Akdur

Turkish Journal of Medical Sciences

Background/aim: Cancer has become an important public health challenge all around the world. Though the demographic and clinical features of cancer patients are well documented in Turkey, the establishment of social support networks has been somewhat neglected. The aim of the study was to assess cancer patients' perceived social support and quality of life characteristics. Materials and methods: The Multidimensional Perceived Social Support Scale, European Organization of Research and Treatment of Cancer Quality of Life Questionnaire, and Turkish version of the EUROHIS measurements were obtained from the study group. Associations between the scores and sociodemographic variables of the patients were …

Screening Of Immunocompromised Patients At Risk Of Strongyloidiasis In Western Turkey Using Elisa And Real-Time Pcr, Esra Erdem Kivrak, Esra Atalay Şahar, Hüseyi̇n Can, Mert Döşkaya, Mümtaz Yilmaz, Hüsnü Pullukçu, Ayşe Caner, Hüseyi̇n Töz, Adnan Yüksel Gürüz, Meltem Işikgöz Taşbakan

Turkish Journal of Medical Sciences

Background/aim: Strongyloides stercoralis causes life-threatening hyperinfection or disseminated strongyloidiasis in immunocompromised patients such as HIV-positive, organ transplantation, and cancer patients. This study investigated the presence of strongyloidiasis in immunocompromised patients for the first time in Turkey. Materials and methods: Serum and stool samples were collected from 108 patients (25.9% of them were chronic renal failure and 74.1% were renal transplantation patients) who were admitted to Ege University Medical School in İzmir, located in western Turkey. Serum samples were analyzed by ELISA (DRG, Germany) and the presence of 18S rRNA gene of S. stercoralis was detected in stool samples by real-time …

Isolation Rates And Antibiotic Susceptibilities Of Different Enterobacteriaceae Species As Urinary Tract Infection Agents In Turkey: A Systematic Review, Caner Yürüyen, Yeşi̇m Gürol, Sabi̇re Ferda Kaleağasioğlu, Eli̇f Çi̇ğdem Kaspar, Gülden Yilmaz

Turkish Journal of Medical Sciences

Background/aim: In Turkey, few systematic reviews have analyzed the results of studies on the isolation rates of urinary tract infection agents and their antibiotic susceptibilities. This review was done to fill this gap and enable the correct application of guideline-based medical therapy by determining the isolation rates and antibiotic susceptibilities of different Enterobacteriaceae species in Turkey. Materials and methods: Relevant studies found from various databases with the help of previously specified search strategies were examined and eliminated according to eligibility criteria. The remaining 22 studies were included in this systematic review. Results: Escherichia coli was the most frequently isolated species …

What Is The Rectal Colonization Rate Of Carbapenem-Resistant Enterobacteriaceae (Cre)-Infected Patients? What Is The Decolonization Rate Of Cre-Colonized Patients In The Hospital?, Fatma Feri̇ha Çi̇lli̇, Bi̇lgi̇n Arda, Ayşe Uyan, Münevver Kayin, Demet Di̇ki̇ş, Ni̇lay Korkmaz, Ni̇lgün Deni̇z Küçükler, Nurhayat Kepeli̇, Behi̇ye Ulusoy, Şükran Akşi̇t Barik, Mehmet Ali̇ Özi̇nel, Sercan Ulusoy, Oğuz Reşat Si̇pahi̇

Turkish Journal of Medical Sciences

No abstract provided.

The Knowledge And High Seroprevalence Of Hepatitis A In A High-Risk Group(Agricultural Reproductive-Aged Women) In The Southeastern Region Of Turkey, Nebi̇ye Yentür Doni̇, Zeynep Şi̇mşek, Gülcan Gürses, Fadi̇le Yildiz Zeyrek, Muhsi̇n Akbaba

Turkish Journal of Medical Sciences

Background/aim: The aim of this study was to determine the seroprevalence of antihepatitis A virus (HAV), risk factors, and the knowledge of female farm workers living in the Southeastern Anatolia Region (SAR) of Turkey. Materials and methods: This representative cross-sectional survey was conducted between January and April of 2013 in the SAR. A total of 705 reproductive-aged women were randomly selected by clustering method using Epi Info software. The sera were analyzed for anti-HAV antibodies using ELISA. Sociodemographic information and the knowledge of female farm workers regarding hepatitis A were collected using a questionnaire. Results: Of the female farm workers, …

Neuroendocrine Disorder In Chronic Fatigue Syndrome, Slavica Tomic, Snezana Brkic, Dajana Lendak, Daniela Maric, Milica Medic-Stojanoska, Aleksandra Novakov-Mikic

Turkish Journal of Medical Sciences

Background/aim: Neuroendocrine disorders are considered a possible pathogenetic mechanism in chronic fatigue syndrome (CFS). The aim of our study was to determine the function of the hypothalamic-pituitary-adrenal axis (HPA) and thyroid function in women of reproductive age suffering from CFS. Materials and methods: The study included 40 women suffering from CFS and 40 healthy women (15-45 years old). Serum levels of cortisol (0800 and 1800 hours), ACTH, total T4, total T3, and TSH were measured in all subjects. The Fibro Fatigue Scale was used for determination of fatigue level. Results: Cortisol serum levels were normal in both groups. The distinctively …

Risk Factors For Recurrent Central Line-Associated Bloodstream Infections In Apediatric Intensive Care Unit, Rana İşgüder, İlker Devri̇m, Gökhan Ceylan, Ahu Kara, Gamze Gülfi̇dan, Hasan Ağin

Turkish Journal of Medical Sciences

Background/aim: It is recommended that a central venous catheter (CVC) be removed if central line-associated bloodstream infection (CLABSI) has been diagnosed. The objective of this retrospective study was to evaluate the risk factors for recurrent CLABSI in reinserted catheters in a pediatric intensive care unit. Materials and methods: Patients with recurrent and nonrecurrent CLABSI were compared in terms of the catheter exchange interval, the interval between negative blood culture and reinsertion of the CVC, and the pre-/reinsertion treatment duration. Results: Thirty-one patients with initial CLABSI had reinserted CVCs, and 12 (38.7%) of these patients were diagnosed with recurrent CLABSI. In …

A Study Of The Chikungunya Virus In Humans In Turkey, Tuğba Atalay, Sedat Kaygusuz, Ahmet Kürşat Azkur

Turkish Journal of Medical Sciences

Background/aim: The chikungunya virus (CHIKV) is a mosquito-borne disease and has recently been causing explosive outbreaks. The CHIKV has spread throughout all continents. Although the first chikungunya case imported from India to Turkey was reported in 2012, there is no detailed epidemiologic study in Turkey yet. The aim of this study was to investigate the seroprevalence of the CHIKV in Turkey. Materials and methods: ELISA was used to screen 500 random serum samples of healthy people collected from Kırıkkale, which is located in central Anatolia in Turkey. The results were verified by indirect immunofluorescence test (IIFT). Results: The results showed …

Risk Factors For Colistin-Associated Nephrotoxicity And Mortality In Critically Ill Patients, Hüseyi̇n Özkarakaş, Işil Köse, Çi̇ler Zi̇nci̇rci̇oğlu, Si̇bel Ersan, Gürsel Ersan, Ni̇met Şenoğlu, Şükran Köse, Riza Hakan Erbay

Turkish Journal of Medical Sciences

Background/aim: Colistin is gaining popularity against multidrug-resistant bacteria. The primary concern with colistin is its nephrotoxicity (NT). The aim of this study was to evaluate the incidence and risk factors for NT and to evaluate the risk factors for mortality in the toxicity group. Materials and methods: NT was defined according to the RIFLE criteria. Data of patients who did or did not develop NT were compared. Positive and negative predictive values, risk ratio, and correlation coefficients were calculated. Results: NT was seen in 39 patients (70%). Hypoalbuminemia, old age, and the use of vasopressors (VPs) were associated with NT. …