cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15139/s3/s8zfdr
title: Mouse models for TB infection across the lifespan

description: Mycobacterium tuberculosis (Mtb) continues to cause significant morbidity and mortality worldwide. TB in the elderly can arise directly from a new infection, reflecting the documented general increase in susceptibility of the elderly to numerous infections including Mtb, or reactivate from a previously latent Mtb infection, and is frequently attributed to deficits in adaptive immune function. However, little experimental information exists to define the specific aspects of immune dysfunction that contribute to the increased susceptibility of the elderly to Mtb infection. There are numerous changes in central immune function (thymus production of T cells), peripheral T cell repertoire and functional parameters, and in the peripheral environment (e.g. increased inflammatory conditions) with aging, any or all of which could contribute to the increased risk for active Mtb infection in the elderly. However, each of these mechanisms would be best approached therapeutically in different ways. Thus, our long-term goal is to identify the specific contributions of these immune changes to increased rates of Mtb infection in the elderly and develop effective treatment strategies. In this proposal, we will use unique mouse genetic resources developed in the Manley lab to test two hypotheses: that this innate-like TEM subpopulation plays a critical role in controlling Mtb infection and establishing latency, and that time since thymic involution plays a significant role in enhanced rates of Mtb primary infections and latency reactivation in the elderly. In Aim 1 we will determine whether innate-like TEM peripheral T cells can enhance the immune response to primary Mtb infection, using the Foxn1�/� mouse model and in vitro and in vivo assays. In Aim 2 we will test whether enhanced disease progression and severity of active Mtb infection in the elderly is due to changes in the peripheral T cell pool caused by thymic involution, or by the physiological effects of aging using Foxn1Z/Z mice that undergo premature thymic involution. These studies may provide new insights into the T cell mechanisms regulating Mtb infection in the elderly, and define new mouse models that may be useful for the study of the immune response to Mtb infection.
DOI: 10.5281/zenodo.8284724
title: Abu Hureyra, Syria, Part 2: Additional evidence supporting the catastrophic destruction of this prehistoric village by a cosmic airburst ∼12,800 years ago, SUPPLEMENTARY DATA

description: This is the <strong>Supplementary Information</strong> (figures, text, and tables) for Moore et al. (2023) Abu Hureyra, Syria, Part 2: Additional evidence supporting the catastrophic destruction of this prehistoric village by a cosmic airburst ∼12,800 years ago. ScienceOpen 1.
DOI: 10.5281/zenodo.8284723
title: Abu Hureyra, Syria, Part 2: Additional evidence supporting the catastrophic destruction of this prehistoric village by a cosmic airburst ∼12,800 years ago, SUPPLEMENTARY DATA

description: This is the <strong>Supplementary Information</strong> (figures, text, and tables) for Moore et al. (2023) Abu Hureyra, Syria, Part 2: Additional evidence supporting the catastrophic destruction of this prehistoric village by a cosmic airburst ∼12,800 years ago. ScienceOpen 1.
DOI: 10.34683/sr1763
title: StoneRounds Case: SR1763
title: von Hippel Lindau

description: StoneRounds Case SR1763 was diagnosed with von Hippel Lindau likely caused by mutations in the gene: VHL.
DOI: 10.15139/s3/vi2z42
title: RNA modification and antibiotic resistance

description: The application of antibiotics to the treatment of bacterial infections revolutionized modern medical practice. In the decades since, a combination of improperly controlled usage and the remarkable ability of bacterial populations to develop resistance to these drugs has severely restricted the clinical usefulness of many antibiotics. We are now at a critical juncture where the majority of useful antibiotics have known and sometimes extensive resistance, and few novel replacements or strategies to combat the resistance problem are in active development. Many clinically useful antibiotics target the bacterial ribosome. One increasingly prevalent form of resistance to these drugs is alteration of the modification status of the ribosomal RNA (rRNA) via acquired or intrinsic methyltransferase enzymes. While enzymes responsible for incorporating these antibiotic resistance- associated rRNA modifications are known, we understand far less about their mechanisms of action (such as specific substrate recognition), which might offer viable new targets to counter the resistance. Further, we also currently have a poor understanding of the molecular basis for how rRNA methylation affects ribosome-antibiotic interactions. The experiments proposed in this application will directly address these critical gaps in our fundamental knowledge of rRNA methylation and bacterial antibiotic resistance. In the first two aims we will define the molecular mechanisms of ribosome subunit recognition by two different rRNA modification enzymes, the acquired aminoglycoside-resistance 16S rRNA (m7G1405) methyltransferases (Aim 1) and the intrinsic Mycobacterium tuberculosis methyltransferase TlyA (Aim 2). Next, we will develop a new computational and experimental framework for understanding antibiotic-methylated rRNA interactions (Aim 3). Our goal is to explain at the molecular level how rRNA modifications limit drug efficacy and how these effects can be evaded. Collectively, the results of these three independent but complementary aims will deepen our fundamental understanding of the molecular strategies used by rRNA modification enzymes and the impacts of rRNA methylation on antibiotic resistance in bacteria. Our results will support future innovative strategies to counter the resistance conferred by these enzymes, for example, by facilitating the development of inhibitors of m7G1405 methyltransferase activity or 30S substrate binding, and could also lead to the rational design of novel antimicrobials capable of fully evading the effects of rRNA modification.
DOI: 10.6075/j0pk0dgr
title: Why Are Bees Ecologically Important?. In Teaching Bee
DOI: 10.6075/j0v69gw4
title: Analysis of Stingless Bee Aggression. In Teaching Bee
DOI: 10.6075/j00000dt
title: Analysis of Honeybee Aggression. In Teaching Bee
DOI: 10.6075/j03r0r6r
title: Africanized Honeybees. In Teaching Bee
DOI: 10.6075/j0t72fsr
title: Predators and Pollinators: Smells of Danger. In Teaching Bee
DOI: 10.6075/j0z036g1
title: Pollinators in Peril. In Teaching Bee
DOI: 10.6075/j02r3q0g
title: Observing Natural Bee Behavior. In Teaching Bee
DOI: 10.6075/j06h4fr7
title: How a Social Insect Colony Works. In Teaching Bee
DOI: 10.6075/j0b856gz
title: Honeybee Flower Preference Modeling. In Teaching Bee
DOI: 10.6075/j0g15z69
title: Example of a Self Introduction. In Teaching Bee
DOI: 10.6075/j0ks6pwv
title: Build-A-Bee. In Teaching Bee
DOI: 10.6075/j0qf8r68
title: Bee Dissection. In Teaching Bee
DOI: 10.15139/s3/rum911
title: The role of antibodies in infant TB prevention

description: This proposal describes a 5-year training and research plan that will allow Lisa Cranmer, MD, MPH to build on her background in global pediatric TB/HIV and molecular epidemiology and gain critical skills in immunology and advanced biostatistics. In order to become an independent investigator focused on understanding immune mechanisms to prevent TB in children with a unique niche in maternal-infant immunology, Dr. Cranmer will develop additional skills in: 1) humoral and innate immunology methods, 2) advanced longitudinal data analysis, and 3) vaccinology. Dr. Cranmer will leverage her substantive field research experience in Kenya using ongoing cohorts of mother-infant pairs and will receive close mentorship from researchers with over 30 cumulative years of experience performing molecular epidemiology studies and vaccine trials in high TB/HIV burden settings. Using these resources, Dr. Cranmer will develop the expertise to lead future TB vaccine trials in mothers and infants. Research Plan In TB-endemic settings, HIV-exposed uninfected infants have &gt;20-fold higher risk of Mycobacterium tuberculosis (Mtb) infection compared to HIV-unexposed uninfected infants. Up to 40% of Mtb-infected infants develop TB disease with high morbidity and mortality. Current strategies to prevent Mtb infection in HEU infants, including BCG vaccination and primary isoniazid preventive therapy, have not been successful. In order to design new prevention strategies, Dr. Cranmer will evaluate the role of antibodies in protection of HEU infants from Mtb infection, and examine if maternal HIV exposure leads to changes in infant Mtb antibody-mediated innate immunity. Dr. Cranmer will evaluate if Mtb antibody levels or antibody-dependent cellular phagocytosis (ADCP)/antibody-dependent cellular cytotoxicity (ADCC) function in mother-infant pairs will confer protection against infant Mtb infection (Aim 1). She will then compare Mtb antibody-mediated immunity (e.g. antibody function and innate immune cytokine expression) to understand potential mechanisms of increased susceptibility to Mtb infection among Kenyan HEU infants (Aim 2). The proposed aims are designed to generate novel data that enhance our understanding of TB pathogenesis and inform development of innovative public health strategies to prevent infant Mtb infection, including new maternal and infant vaccines.
DOI: 10.15139/s3/vzyrah
title: Integrating data streams with multi-scale modeling to guide norovirus vaccine decision-making

description: Noroviruses cause over 20 million diarrhea cases annually in the United States, one-fifth of all diarrhea cases globally, and over 200,000 deaths worldwide. Norovirus vaccines are currently in development. Our goal is to develop a comprehensive detailed, user-friendly norovirus transmission and vaccination simulator that will help guide and inform norovirus vaccine design and implementation. To achieve this goal, a number of specific insights and parameter estimates are required, such as: At what rate does immunity to norovirus wane in individuals? How does prior infection (or vaccination) affect the course of illness and the duration/quantity of viral shedding? What is the degree of cross-protecting immunity at the genogroup, genotype and strain-level? With such results in hand, we can answer the following vaccine strategy questions: What frequency of re-vaccination is required for control? How often will a norovirus vaccine need to be updated to keep up with viral evolution? What are the population-level health impacts of age-targeted (or other) vaccination strategies? To answer these questions, we will integrate detailed data from multiple sources including volunteer infection studies, national surveillance, and viral sequence datasets. We will fit mathematical and statistical models to these datasets to answer the questions posed above. Our analyses will provide a thorough understanding of the epidemiological and evolutionary dynamics of the virus. This information will be used to develop and implement a detailed norovirus transmission and vaccination simulator. This simulator will be packaged as a user-friendly application for vaccine designers and policy implementers to analyze and forecast possible impacts of vaccine formulations and distribution strategies.
DOI: 10.15139/s3/hutfru
title: Comprehensive Profiling of Social Mixing Patterns in Resource Poor Countries

description: Dynamic transmission models of infectious diseases are increasingly influential for developing interventions and informing policy. Infectious disease transmissibility and hence, the effectiveness of control strategies, is strongly influenced by social interactions. Consequently, accurate data on social contact rates and mixing patterns are fundamental parameters in the calculation of the force of infection (i.e. the rate of susceptible individuals becoming infected). Despite the strong role social mixing patterns play in the accurate parameterization of mathematical models, these data remain limited, particularly in low and middle-income countries (LMICs). There are also limited data on the social interactions of young infants that are too young to be vaccinated or the diversity in patterns between rural and urban populations at the community level, which are important factors for understanding infectious disease transmission. We propose the first multi-site study with the overall goal to use standardized methods to collect social contact data from urban and rural populations in LMICs. Special focus will be given to study the social interactions of infants less than six months of age. Data will be rigorously collected from four different LMICs: Guatemala, Pakistan, India and Mozambique. We will use standardized social contact diaries to characterize the patterns of social contacts and mixing across the age range in urban and rural LMIC settings. We will also comprehensively profile the social contacts of infants with their household members in LMICs by analyzing high resolution measurements collected using wearable proximity-sensing devices. Moreover, through this project, we will create a database of social mixing data on LMIC populations. We will make this database publicly available using contemporary standards in Open Access data sharing and documentation. These data can be used by infectious disease modelers and other researchers in the biomedical and social science communities.
DOI: 10.15139/s3/bdlb9k
title: Estimating the Epidemiologic Impact of TB Vaccines using Mathematical Models

description: Tuberculosis (TB) is a major cause of ill health and was the leading infectious cause of death in 2019, a burden felt disproportionately in low- and middle-income countries. To accelerate progress towards the World Health Organization's ambitious goal to cut TB deaths by 95% and cases by 90% by 2035, new tools to prevent TB are essential. New and repurposed vaccines against TB hold promise to fill this gap: after decades of research, two TB vaccines have emerged from Phase II clinical trials with positive efficacy results. The existing BCG vaccine, currently given at birth, is being reconsidered for use ('revaccination') in adults after a Phase IIb trial showed 50% efficacy in preventing TB infection in adolescents. In a separate Phase IIb trial, subunit vaccine M72-AS01e was shown to be 50% efficacious in preventing TB disease in adults. The overarching objectives of this K01 are to (1) estimate the potential epidemiologic impact of new and repurposed TB vaccines; and (2) identify and assess potential vaccination strategies targeting high-risk groups. We will do this using data from the GlobalMix study, which will provide detailed country-specific social contact and mobility data from four countries - Mozambique, Guatemala, India, and Pakistan - with diverse TB epidemic profiles. Understanding potential differences in vaccine impact across countries can guide the design of further vaccine trials and inform strategies for introducing new and repurposed TB vaccines into immunization programs.
DOI: 10.6075/j0h41pbm
title: California Tobacco Survey (CTS)

description: The California Department of Public Health (Previously known as the California Department of Health Services until 2007) is required to conduct surveys of attitudes, behaviors, and media exposure regarding smoking and tobacco use as components of the smoking cessation evaluation effort required by California Assembly Bills AB75, AB99 and AB816. The objective of these surveys is to collect representative statewide data on cigarette smoking behavior, attitudes towards smoking, media exposure to smoking, and use of tobacco products other than cigarettes, from populations living in California. These surveys have been conducted approximately every three years through contracts with the University of California, San Diego (UCSD) to measure changes in attitudes and behaviors in the California population. The California Tobacco Survey (CTS) was conducted in 1990-1991, 1992, 1993, 1996, 1999, 2002, 2005, and 2008. Each survey year included adults 18 years and older but earlier years of the survey included other populations. The 1990-1991 survey included an adult pregnancy supplement. Survey years 1990-1991, 1993, 1996, 1999, 2002, and 2005 included surveys of adolescents between the ages of 12 and 17 years. Data for each survey year consists of a basic set of two surveys (household screener, and adult ages 18+). Household screener surveys interview the initial household respondent and are used to select adult and adolescent survey respondents. Demographic and regional geographic variables are included in the surveys. The 1996 CTS contains a short adult survey that is similar to the 1993 adult survey and a long adult survey that is similar to the 1992 adult survey. The 1999 and subsequent CTS surveys use an adult survey similar to the 1996 long adult survey. Users of these data should note that variables are deleted, changed or added over time. In addition to basic surveys, a Teen Longitudinal Survey was conducted from 1993 through 1999. The 1993 and 1996 CTS Teen surveys provided the baseline data, with follow-up surveys conducted in 1996 and 1999, respectively. Each survey data file contains data for only those individuals interviewed in the relevant waves.
DOI: 10.7278/s50d-4gxs-s4hj
title: Menstrual Cycles Length of Women in the USA and Canada, 1990-2013
DOI: 10.6075/j00v89rp
title: California Smokers Cohort (CSC) 2011. In California Smokers Cohort (CSC)

description: The 2011 California Smokers' Cohort (CSC) was ninth of a series of triennial surveys, called the California Tobacco Surveys (CTS) conducted since 1990. The previous CTS are a series of cross-sectional studies to collect information about tobacco use and behaviors among Californians. The 2011 survey design has been modified to survey only smokers, and moreover to perform longitudinal surveys to investigate factors associated with quitting behavior. It was sponsored by the State of California's Department of Public Health (CDPH, previous to 2007 it was known as the California Department of Health Services (DHS)) through a contract with the University of California at San Diego (UCSD), which subcontracted with Westat to conduct the data collection and support the sampling and weighting statistical tasks, and subcontracted with Princeton Survey Research Associates International (PSRAI). The CSC has two parts in 2011. One part is a follow up survey of smokers identified by the California Health Interview Survey (CHIS) and re-interviewed using the CTS smokers' questionnaire. This is titled as the CHIS Longitudinal Smokers Survey (CLSS). The second part is a convenient sample of smokers whose telephone contacts were purchased from data brokers and who were contacted to participate in a baseline interview and a follow up interview 12 months later. Data collection for CLSS began on July 8, 2011 and was completed on December 8, 2011. The objective of this survey was to collect statewide data on tobacco-related behaviors, knowledge of and attitudes towards smoking, and monitoring the effect of State-initiated programs on individual target populations. These data are used by the California CDPH to plan and assess the effectiveness of smoking cessation strategies. The currently posted data files are only for the PSRAI portion of CSC, i.e., the second part of the CSC 2011 survey, described above.
DOI: 10.15139/s3/pwr46o
title: System Biological Analyses of Innate and Adaptive Responses to Vaccination

description: The research proposed in years 6 and 7 of the Emory-HIPC will build on the considerable progress made during the first 5 years in using systems based approaches to understand the molecular networks driving innate and adaptive immune responses to vaccination. The major focus of the work planned in years 6 and 7 is to understand the immunological mechanisms by which the recently licensed subunit vaccine for herpes zoster (HZ, shingles) induces highly efficacious protection against shingles. HZ which is caused by the varicella zoster virus (VZV), affects several million people/year globally, and is a significant public health concern for the elderly. An important recent development is the development of a new subunit HZ vaccine, which contains the recombinant glycoprotein E subunit ("gE vaccine"), adjuvanted with AS01, a liposome-based adjuvant system containing the TLR4 agonist MPL, and the saponin, QS21 (1-4). The gE vaccine has recently been licensed for clinical use in subjects older than 50 years, under the trade name Shingrix®. Remarkably, the efficacy of Shingrix® is high (91%) even in 70 year old vaccinees (1-4). Although Shingrix® has revealed superior antibody responses and greater durability of CD4+ T cell responses to the gE vaccine, a comprehensive assessment of immune responses to the gE vaccine is lacking. This will be achieved in Aims 1 and 2, where we will analyze the innate and adaptive responses to Shingrix®. Importantly we will analyze these results in the context of data generated from our previous HIPC project on immune responses induced by the live attenuated zoster vaccine, Zostavax®. Aim 1: Systems analysis of innate responses elicited by Shingrix® in 50-60 year old and &gt;70 year old subjects. Aim 2: To analyze the adaptive immune response elicited by Shingrix® in 50-59 year old and &gt;70-85 years old subjects.
DOI: 10.6075/j0057cvk
title: California Tobacco Survey (CTS) 1996. In California Tobacco Survey (CTS)

description: The 1996 California Tobacco Survey (CTS) was the forth in a series of cross-sectional studies to collect information about tobacco use and behaviors among California adults and teenagers. It was sponsored by the State of California's Department of Health Services (DHS) under subcontract with the University of California at San Diego (UCSD). Westat Inc. was subcontracted to conduct this survey as well as the 1990-1991, 1992 and 1993 surveys. Four instruments were used in the 1996 CTS: Screener Interview, Extended Short Adult Interview, Extended Long Adult Interview, and Extended Youth Interview. Data collection for this CTS began on September 17, 1996 and ended on January 26, 1997. The objective of this survey was to collect representative statewide data on tobacco-related behaviors, knowledge and attitudes towards smoking, and monitoring the effect of programs on individual target populations. These data are used by the California DHS to plan and assess the effectiveness of smoking cessation strategies.
DOI: 10.6075/j0cc0xmw
title: California Tobacco Survey (CTS) 1990-1991. In California Tobacco Survey (CTS)

description: In the last quarter of 1989, the California Department of Health Services (DHS) put out a request for proposal to undertake “Initial baseline Survey of attitudes, behaviors and media exposure regarding smoking and tobacco use.” In January 1990, the contract was awarded to University of California, San Diego (UCSD). The 1990-1991 California Tobacco Survey (CTS) was the first in a series of cross-sectional studies to collect information about tobacco use and behaviors among California adults and teenagers. Westat Inc. was subcontracted to conduct this survey. Four instruments were used in this baseline CTS: Screener Interview, Extended Adult Interview, Extended Youth Interview, and Pregnancy Extended Interview. This baseline CTS was conducted between June 1990 and July 1991. The objective of this survey was to collect baseline representative statewide information on tobacco-related behaviors, knowledge and attitudes towards smoking. These data are used by the California DHS to plan and assess the effectiveness of smoking cessation strategies.