Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression.

The systematic identification of genetic events driving cellular transformation and tumor progression in the absence of a highly recurrent oncogenic driver mutation is a challenge in cutaneous oncology. In cutaneous squamous cell carcinoma (cuSCC), the high UV-induced mutational burden poses a hurdle to achieve a complete molecular landscape of this disease. Here, we utilized the Sleeping Beauty transposon mutagenesis system to statistically define drivers of keratinocyte transformation and cuSCC progression in vivo in the absence of UV-IR, and identified both known tumor suppressor genes and novel oncogenic drivers of cuSCC.

Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq.

A central challenge in oncology is how to kill tumors containing heterogeneous cell populations defined by different combinations of mutated genes. Identifying these mutated genes and understanding how they cooperate requires single-cell analysis, but current single-cell analytic methods, such as PCR-based strategies or whole-exome sequencing, are biased, lack sequencing depth or are cost prohibitive. Transposon-based mutagenesis allows the identification of early cancer drivers, but current sequencing methods have limitations that prevent single-cell analysis.

Epidemiology of undiagnosed trichomoniasis in a probability sample of urban young adults.

T. vaginalis infection (trichomoniasis) is the most common curable sexually transmitted infection (STI) in the U.S.

Gender-based screening for chlamydial infection and divergent infection trends in men and women.

Objectives: To assess the potential impact of chlamydial screening policy that recommends routine screening of women but not men.

Methods: Population surveys of probability samples of Baltimore adults aged 18 to 35 years in 1997-1998 and 2006-2009 collected biospecimens to estimate trends in undiagnosed chlamydial infection. Survey estimates are compared to surveillance data on diagnosed chlamydial infections reported to the Health Department.

Ensuring good quality RNA for quantitative real-time PCR isolated from renal proximal tubular cells using laser capture microdissection.

Background: In order to provide gene expression profiles of different cell types, the primary step is to isolate the specific cells of interest via laser capture microdissection (LCM), followed by extraction of good quality total RNA sufficient for quantitative real-time polymerase chain reaction (qPCR) analysis. This LCM-qPCR strategy has allowed numerous gene expression studies on specific cell populations, providing valuable insights into specific cellular changes in diseases. However, such strategy imposed challenges as cells of interests are often available in limited quantities and quality of RNA may be compromised during long periods of time spent on collection of cells and extraction of total RNA; therefore, it is crucial that protocols for sample preparation should be optimised according to different cell populations.

'What's in the NIDDK CDR?'--public query tools for the NIDDK central data repository.

The National Institute of Diabetes and Digestive Disease (NIDDK) Central Data Repository (CDR) is a web-enabled resource available to researchers and the general public. The CDR warehouses clinical data and study documentation from NIDDK funded research, including such landmark studies as The Diabetes Control and Complications Trial (DCCT, 1983-93) and the Epidemiology of Diabetes Interventions and Complications (EDIC, 1994-present) follow-up study which has been ongoing for more than 20 years. The CDR also houses data from over 7 million biospecimens representing 2 million subjects.

Incarceration, high-risk sexual partnerships and sexually transmitted infections in an urban population.

Objectives: The authors examined the associations between personal and partner incarceration, high-risk sexual partnerships and biologically confirmed sexually transmitted infection (STI) in a US urban population.

Methods: Data from a probability survey of young adults 15-35 years of age in Baltimore, Maryland, USA, were analysed to assess the prevalence of personal and partner incarceration and its association with several measures of high-risk sexual partnerships including multiple partners, partner concurrency and current STI.

Results: A history of incarceration was common (24.

The NIDDK Central Repository at 8 years--ambition, revision, use and impact.

The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Central Repository makes data and biospecimens from NIDDK-funded research available to the broader scientific community. It thereby facilitates: the testing of new hypotheses without new data or biospecimen collection; pooling data across several studies to increase statistical power; and informative genetic analyses using the Repository's well-curated phenotypic data. This article describes the initial database plan for the Repository and its revision using a simpler model.

Chlamydia trachomatis infection among 15- to 35-year-olds in Baltimore, MD.

Background: Chlamydia trachomatis (Ct) is the most frequently reported infectious disease in the United States. This article reports population and subpopulation prevalence estimates of Ct and correlates of infection among 15- to 35-year-olds in Baltimore, MD.

Methods: The Monitoring STIs Survey Program (MSSP) monitored sexually transmitted infection (STI) prevalence among probability samples of residents of Baltimore, a city with high STI rates.

The available pool of sex partners and risk for a current bacterial sexually transmitted infection.

Purpose: Sexually transmitted infection (STI) transmission models propose that incident STIs are related to exposure to infected sex partners. The objective of this study was to determine whether the prevalence of STIs among the available pool of sex partners in a neighborhood, measured indirectly, is an independent determinant of a current incident STI.

Methods: The target population comprised 58,299 English-speaking, sexually active 15- to 24-year-olds in 486 census block groups (CBGs) in Baltimore, MD.

Impact of T-ACASI on Survey Measurements of Subjective Phenomena.

Numerous studies have shown that audio-computer-assisted self-interviewing (audio-CASI) and telephone audio-CASI (T-ACASI) technologies yield increased reporting of sensitive and stigmatized objective phenomena such as sexual and drug use behaviors. Little attention has been given, however, to the impact of these technologies on the measurement of subjective phenomena (attitudes, opinions, feelings, etc.).

Improving epidemiological surveys of sexual behaviour conducted by telephone.

Background: This study assesses the impact of Telephone Audio Computer-Assisted Self-Interviewing (T-ACASI) on the reporting of sensitive (mainly heterosexual) behaviours.

Methods: A randomized experiment was embedded in a telephone survey that drew probability samples of the populations of the USA (N = 1543) and Baltimore city (N = 744). Respondents were randomly assigned to have questions asked either by a T-ACASI computer or by a human telephone interviewer.

T-ACASI reduces bias in STD measurements: the National STD and Behavior Measurement Experiment.

Background: Although telephone surveys provide an economical method for assessing patterns of diagnosed sexually transmitted diseases (STDs) and STD-related behaviors in populations, the requirement that respondents report such information to human telephone interviewers introduces an opportunity for substantial reporting bias. Telephone computer-assisted self-interviewing (T-ACASI) surveys substitute a computer for human interviewers when asking sensitive questions.

Methods: A randomized experiment was embedded in a telephone survey that drew probability samples of the populations of the United States (N = 1543) and Baltimore city (N = 744).

Health care access and follow-up of chlamydial and gonococcal infections identified in an emergency department.

Background: We examined 2 potentially important factors influencing successful treatment of Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (GC) infections identified in an emergency department (ED), health care coverage and reporting the ED as a primary source for health care.

Methods: Adult patients aged 18 to 35 years attending an urban ED were screened for Ct and GC. Patients testing positive were contacted by Disease Intervention Specialists and notified of their infection status.

Evaluation of risk score algorithms for detection of chlamydial and gonococcal infections in an emergency department setting.

Objectives: To develop and evaluate screening algorithms to predict current chlamydial and gonococcal infections in emergency department (ED) settings and assess their performance.

Methods: Between 2002 and 2005, adult patients aged 18 to 35 years attending an urban ED were screened for Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (GC) and completed a brief demographic and behavioral questionnaire. Using multiple unconditional logistic regressions, the authors developed four separate predictive models and applicable clinical risk scores to screen for infection.

SAME-GENDER SEX IN THE UNITED STATES IMPACT OF T-ACASI ON PREVALENCE ESTIMATES.

Well-conducted telephone surveys provide an economical means of estimating the prevalence of sexual and reproductive behaviors in a population. There is, however, a nontrivial potential for bias since respondents must report sensitive information to a human interviewer. The National STD and Behavior Measurement Experiment (NSBME) evaluates a new survey technology-telephone audio computer-assisted self-interviewing (T-ACASI)-that eliminates this requirement.

SAME-GENDER SEX AMONG U.S. ADULTS: TRENDS ACROSS THE TWENTIETH CENTURY AND DURING THE 1990s.

Trends in reporting of same-gender sex are assessed using data from the 1988-2002 General Social Surveys (Ns = 9,487 males and 12,336 females). Analyses indicate that the reported prevalence of female-female sexual contact increased substantially and monotonically across twentieth-century birth cohorts, rising from 1.6 percent (Standard error [SE] = 0.

Reducing bias in telephone survey estimates of the prevalence of drug use: a randomized trial of telephone audio-CASI.

Aim: To assess the impact of telephone audio computer-assisted self-interviewing (T-ACASI) on reporting of alcohol use, alcohol problems and illicit drug use in telephone surveys of the general population. Prior research suggests that illicit drug use is underreported in traditional, interviewer-administered, telephone surveys.

Design: Randomized experiment embedded in telephone survey of probability samples of populations of USA and Baltimore, MD.

Polymerase chain reaction detection of Y chromosome sequences in vaginal fluid: preliminary studies of a potential biomarker for sexual behavior.

Background: Self-reported measures of sexual behavior are subject to nontrivial reporting biases.

Objective: The objective of this study was to develop a behavioral biomarker of recent sexual activity among females that is inexpensive, easily administered, and can be used in low sexually transmitted disease prevalence populations.

Methods: We developed a polymerase chain reaction (PCR) assay to detect Y chromosome (Yc) fragments.

NAAT-identified and self-reported gonorrhea and chlamydial infections: different at-risk population subgroups?

Background: Information on the characteristics and behaviors of persons at high risk for gonorrhea and chlamydial infection has typically been derived from studies of sexually transmitted disease (STD) clinic populations. The Baltimore STD and Behavior Survey (BSBS) used urine-based nucleic acid amplification testing (NAAT) to assess the prevalence and behavioral correlates of gonorrhea and chlamydial infection in a population-based cross-sectional survey of adults in Baltimore, Maryland.

Goal: The goal of this study was to examine the demographic characteristics and behavioral markers of gonorrhea and chlamydial infection as reported by adults with a self-reported history of gonorrhea and chlamydial infection and to compare these to the characteristics and behaviors of individuals with current NAAT-identified gonorrhea and/or chlamydial infection.

Untreated gonococcal and chlamydial infection in a probability sample of adults.

Context: The prevalence and distribution of gonococcal and chlamydial infections in the general population are poorly understood. Development of nucleic acid amplification tests, such as the ligase chain reaction assay, provides new opportunities to estimate the prevalence of untreated infections in the population.

Objective: To estimate the overall prevalence of untreated gonococcal and chlamydial infections and to describe patterns of infection within specific demographic subgroups of the young adult population in Baltimore, Md.

Using Touch Screen Audio-CASI to Obtain Data on Sensitive Topics.

This paper describes a new interview data collection system that uses a laptop personal computer equipped with a touch-sensitive video monitor. The touch-screen-based audio computer-assisted self-interviewing system, or touch screen audio-CASI, enhances the ease of use of conventional audio CASI systems while simultaneously providing the privacy of self-administered questionnaires. We describe touch screen audio-CASI design features and operational characteristics.

Interview Mode and Measurement of Sexual Behaviors: Methodological Issues.

Studies of sexual and other sensitive behaviors are often fraught with a variety of reporting biases. When IAQs are used to collect data, respondents may underreport certain sensitive behaviors and overreport normative behaviors. SAQs can also pose problems: requiring that respondents be literate and able to follow skip patterns.