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  • Authors: Pharoah, PDP;

    Genotype data and related phenotype data for Ovarian Cancer Association Consortium project investigating common variantion in GTPAse genes and ovarian cancer risk

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  • A Data Guide for this study is available as a web page and for download. The National Longitudinal Study of Adolescent to Adult Health (Add Health), 1994-2008 [Public Use] is a longitudinal study of a nationally representative sample of U.S. adolescents in grades 7 through 12 during the 1994-1995 school year. The Add Health cohort was followed into young adulthood with four in-home interviews, the most recent conducted in 2008 when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents' social, economic, psychological, and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships. Add Health Wave I data collection took place between September 1994 and December 1995, and included both an in-school questionnaire and in-home interview. The in-school questionnaire was administered to more than 90,000 students in grades 7 through 12, and gathered information on social and demographic characteristics of adolescent respondents, education and occupation of parents, household structure, expectations for the future, self-esteem, health status, risk behaviors, friendships, and school-year extracurricular activities. All students listed on a sample school's roster were eligible for selection into the core in-home interview sample. In-home interviews included topics such as health status, health-facility utilization, nutrition, peer networks, decision-making processes, family composition and dynamics, educational aspirations and expectations, employment experience, romantic and sexual partnerships, substance use, and criminal activities. A parent, preferably the resident mother, of each adolescent respondent interviewed in Wave I was also asked to complete an interviewer-assisted questionnaire covering topics such as inheritable health conditions, marriages and marriage-like relationships, neighborhood characteristics, involvement in volunteer, civic, and school activities, health-affecting behaviors, education and employment, household income and economic assistance, parent-adolescent communication and interaction, parent's familiarity with the adolescent's friends and friends' parents. Add Health data collection recommenced for Wave II from April to August 1996, and included almost 15,000 follow-up in-home interviews with adolescents from Wave I. Interview questions were generally similar to Wave I, but also included questions about sun exposure and more detailed nutrition questions. Respondents were asked to report their height and weight during the course of the interview, and were also weighed and measured by the interviewer. From August 2001 to April 2002, Wave III data were collected through in-home interviews with 15,170 Wave I respondents (now 18 to 26 years old), as well as interviews with their partners. Respondents were administered survey questions designed to obtain information about family, relationships, sexual experiences, childbearing, and educational histories, labor force involvement, civic participation, religion and spirituality, mental health, health insurance, illness, delinquency and violence, gambling, substance abuse, and involvement with the criminal justice system. High School Transcript Release Forms were also collected at Wave III, and these data comprise the Education Data component of the Add Health study. Wave IV in-home interviews were conducted in 2008 and 2009 when the original Wave I respondents were 24 to 32 years old. Longitudinal survey data were collected on the social, economic, psychological, and health circumstances of respondents, as well as longitudinal geographic data. Survey questions were expanded on educational transitions, economic status and financial resources and strains, sleep patterns and sleep quality, eating habits and nutrition, illnesses and medications, physical activities, emotional content and quality of current or most recent romantic/cohabiting/marriage relationships, and maltreatment during childhood by caregivers. Dates and circumstances of key life events occurring in young adulthood were also recorded, including a complete marriage and cohabitation history, full pregnancy and fertility histories from both men and women, an educational history of dates of degrees and school attendance, contact with the criminal justice system, military service, and various employment events, including the date of first and current jobs, with respective information on occupation, industry, wages, hours, and benefits. Finally, physical measurements and biospecimens were also collected at Wave IV, and included anthropometric measures of weight, height and waist circumference, cardiovascular measures such as systolic blood pressure, diastolic blood pressure, and pulse, metabolic measures from dried blood spots assayed for lipids, glucose, and glycosylated hemoglobin (HbA1c), measures of inflammation and immune function, including High sensitivity C-reactive protein (hsCRP) and Epstein-Barr virus (EBV). Datasets: DS0: Study-Level Files DS1: Wave I: In-Home Questionnaire, Public Use Sample DS2: Wave I: Public Use Contextual Database DS3: Wave I: Network Variables DS4: Wave I: Public Use Grand Sample Weights DS5: Wave II: In-Home Questionnaire, Public Use Sample DS6: Wave II: Public Use Contextual Database DS7: Wave II: Public Use Grand Sample Weights DS8: Wave III: In-Home Questionnaire, Public Use Sample DS9: Wave III: In-Home Questionnaire, Public Use Sample (Section 17: Relationships) DS10: Wave III: In-Home Questionnaire, Public Use Sample (Section 18: Pregnancies) DS11: Wave III: In-Home Questionnaire, Public Use Sample (Section 19: Relationships in Detail) DS12: Wave III: In-Home Questionnaire, Public Use Sample (Section 22: Completed Pregnancies) DS13: Wave III: In-Home Questionnaire, Public Use Sample (Section 23: Current Pregnancies) DS14: Wave III: In-Home Questionnaire, Public Use Sample (Section 24: Live Births) DS15: Wave III: In-Home Questionnaire, Public Use Sample (Section 25: Children and Parenting) DS16: Wave III: Public Use Education Data DS17: Wave III: Public Use Graduation Data DS18: Wave III: Public Use Education Data Weights DS19: Wave III: Add Health School Weights DS20: Wave III: Peabody Picture Vocabulary Test (PVT), Public Use DS21: Wave III: Public In-Home Weights DS22: Wave IV: In-Home Questionnaire, Public Use Sample DS23: Wave IV: In-Home Questionnaire, Public Use Sample (Section 16B: Relationships) DS24: Wave IV: In-Home Questionnaire, Public Use Sample (Section 16C: Relationships) DS25: Wave IV: In-Home Questionnaire, Public Use Sample (Section 18: Pregnancy Table) DS26: Wave IV: In-Home Questionnaire, Public Use Sample (Section 19: Live Births) DS27: Wave IV: In-Home Questionnaire, Public Use Sample (Section 20A: Children and Parenting) DS28: Wave IV: Biomarkers, Measures of Inflammation and Immune Function DS29: Wave IV: Biomarkers, Measures of Glucose Homeostasis DS30: Wave IV: Biomarkers, Lipids DS31: Wave IV: Public Use Weights Wave I: The Stage 1 in-school sample was a stratified, random sample of all high schools in the United States. A school was eligible for the sample if it included an 11th grade and had a minimum enrollment of 30 students. A feeder school -- a school that sent graduates to the high school and that included a 7th grade -- was also recruited from the community. The in-school questionnaire was administered to more than 90,000 students in grades 7 through 12. The Stage 2 in-home sample of 27,000 adolescents consisted of a core sample from each community, plus selected special over samples. Eligibility for over samples was determined by an adolescent's responses on the in-school questionnaire. Adolescents could qualify for more than one sample.; Wave II: The Wave II in-home interview surveyed almost 15,000 of the same students one year after Wave I.; Wave III: The in-home Wave III sample consists of over 15,000 Wave I respondents who could be located and re-interviewed six years later.; Wave IV: All original Wave I in-home respondents were eligible for in-home interviews at Wave IV. At Wave IV, the Add Health sample was dispersed across the nation with respondents living in all 50 states. Administrators were able to locate 92.5% of the Wave IV sample and interviewed 80.3% of eligible sample members. ; For additional information on sampling, including detailed information on special oversamples, please see the Add Health Study Design page. Add Health was developed in response to a mandate from the U.S. Congress to fund a study of adolescent health. Waves I and II focused on the forces that may influence adolescents' health and risk behaviors, including personal traits, families, friendships, romantic relationships, peer groups, schools, neighborhoods, and communities. As participants aged into adulthood, the scientific goals of the study expanded and evolved. Wave III explored adolescent experiences and behaviors related to decisions, behavior, and health outcomes in the transition to adulthood. Wave IV expanded to examine developmental and health trajectories across the life course of adolescence into young adulthood, using an integrative study design which combined social, behavioral, and biomedical measures data collection. Response Rates: Response rates for each wave were as follows: Wave I: 79 percent; Wave II: 88.6 percent; Wave III: 77.4 percent; Wave IV: 80.3 percent; Adolescents in grades 7 through 12 during the 1994-1995 school year. Respondents were geographically located in the United States. audio computer-assisted self interview (ACASI) computer-assisted personal interview (CAPI) computer-assisted self interview (CASI) paper and pencil interview (PAPI) face-to-face interview

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    Authors: Gupta, Richa; Dongen, Jenny; Fu, Yu; Abdellaoui, Abdel; +7 Authors

    Table S3. Cis acting methylation quantitative trait loci in the 40 genes highlighted in the EWAS. (XLS 31 kb)

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    Authors: Gupta, Richa; Dongen, Jenny; Fu, Yu; Abdellaoui, Abdel; +7 Authors

    Table S7. CpG sites showing significant (FDR pâ

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  • These data are being released in BETA version to facilitate early access to the study for research purposes. This collection has not been fully processed by NACDA or ICPSR at this time; the original materials provided by the principal investigator were minimally processed and converted to other file types for ease of use. As the study is further processed and given enhanced features by ICPSR, users will be able to access the updated versions of the study. Please report any data errors or problems to user support and we will work with you to resolve any data related issues.The Biomarker study is Project 4 of the MIDUS longitudinal study, a national survey of more than 7,000 Americans (aged 25 to 74) begun in 1994. The purpose of the larger study was to investigate the role of behavioral, psychological, and social factors in understanding age-related differences in physical and mental health. With support from the National Institute on Aging, a longitudinal follow-up of the original MIDUS samples [core sample (N = 3,487), metropolitan over-samples (N = 757), twins (N = 957 pairs), and siblings (N = 950)] was conducted in 2004-2006. Guiding hypotheses, at the most general level, were that behavioral and psychosocial factors are consequential for health (physical and mental). A description of the study and findings from it are available on the MIDUS Web site. The Biomarker Project (Project 4) of MIDUS II contains data from 1,255 respondents. These respondents include two distinct subsamples, all of whom completed the Project 1 Survey: (1) longitudinal survey sample (n = 1,054) and (2) Milwaukee sample (n = 201). The Milwaukee group contained individuals who participated in the baseline MIDUS Milwaukee study, initiated in 2005. The purpose of the Biomarker Project (Project 4) was to add comprehensive biological assessments on a subsample of MIDUS respondents, thus facilitating analyses that integrate behavioral and psychosocial factors with biology. The broad aim is to identify biopsychosocial pathways that contribute to diverse health outcomes. A further theme is to investigate protective roles that behavioral and psychosocial factors have in delaying morbidity and mortality, or in fostering resilience and recovery from health challenges once they occur. The research was not disease-specific, given that psychosocial factors have relevance across multiple health endpoints. Biomarker data collection was carried out at three General Clinical Research Centers (at UCLA, University of Wisconsin, and Georgetown University). The biomarkers reflect functioning of the hypothalamic-pituitary-adrenal axis, the autonomic nervous system, the immune system, cardiovascular system, musculoskeletal system, antioxidants, and metabolic processes. Our specimens (fasting blood draw, 12-hour urine, saliva) allow for assessment of multiple indicators within these major systems. The protocol also included assessments by clinicians or trained staff, including vital signs, morphology, functional capacities, bone densitometry, medication usage, and a physical exam. Project staff obtained indicators of heart-rate variability, beat to beat blood pressure, respiration, and salivary cortisol assessments during an experimental protocol that included both a cognitive and orthostatic challenge. Finally, to augment the self-reported data collected in Project 1, participants completed a medical history, self-administered questionnaire, and self-reported sleep assessments. For respondents at one site (UW-Madison), objective sleep assessments were also obtained with an Actiwatch(R) activity monitor. The MIDUS and MIDJA Biomarker Clinic Visits include collection of comprehensive information about medications of all types, as well as basic information about allergic reactions to any type of medication. Respondents were instructed to bring all their medications, or information about their medications, to the clinic visit to ensure the information about those medications was recorded accurately. Information regarding Prescription Medications (FDA approved medications prescribed by someone authorized/licensed under the Western medical tradition, or medications prescribed by individuals authorized under Japanese law to prescribe Western and/or Eastern/Chinese traditional medicine), Quasi Medications (including Over the Counter Medications i.e. vitamins, minerals, non-prescription pain relief, antacids, etc. that can be purchased without a prescription) and Alternative Medications (i.e. herbs, herbal blends (excluding herbal teas), homeopathic remedies, and other alternative remedies that may be purchased over the counter or "prescribed" by a health care practitioner trained in a non-western tradition)was collected at this time.The following information was collected for each medication type Medication name, dosage, and route of administration; How often the medication is taken(frequency); How long the participant has been taking a given medication; Why they think they are taking the medication; After basic cleaning protocols were completed, standardized protocols were applied to both MIDUS and MIDJA medication data to link medications first to Generic Names and associated DrugIDs and then to therapeutic and pharmacologic class information from the Lexicomp Lexi-Data database, and also to code text data describing why participants think they are taking a given medication. The scope of this collected medication data lends itself to within person analysis of medication use, thus the medication data are also released in a standalone stacked format. The stacked file only contains data about medications used where each case represents an individual medication, thus it does not include any data about medication allergies. ICPSR data undergo a confidentiality review and are altered when necessary to limit the risk of disclosure. ICPSR also routinely creates ready-to-go data files along with setups in the major statistical software formats as well as standard codebooks to accompany the data. In addition to these procedures, ICPSR performed the following processing steps for this data collection: Created variable labels and/or value labels.; Created online analysis version with question text.; Checked for undocumented or out-of-range codes.. All respondents participating in MIDUS II (ICPSR 4652) or the Milwaukee study (ICPSR 22840) who completed Project 1 were eligible to participate in the Biomarker assessments. Presence of Common Scales: Data users interested in the scales used for this study should refer to the scaling documentation provided on both the ICPSR and NACDA Web site. Adult non-institutionalized population of the United States. Smallest Geographic Unit: No geographic information is included other than for the Milwaukee cases. Response Rates: The response rate was 39.3 percent for each of the 2 samples (longitudinal survey sample, and Milwaukee). Datasets: DS0: Study-Level Files DS1: Aggregated Data DS2: Stacked Medication Data Midlife in the United States (MIDUS) Series face-to-face interview on-site questionnaire mixed mode

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    Authors: Gupta, Richa; Dongen, Jenny; Fu, Yu; Abdellaoui, Abdel; +7 Authors

    Table S5. Mediation analysis omnibus P values for the 19 meQTLs associated with serum cotinine levels. (XLS 33 kb)

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    Authors: Bianconi, Irene; Jeukens, Julie; Freschi, Luca; AlcalĂĄ-Franco, Beatriz; +7 Authors

    Non-synonymous SNPs between prototype strain PA14 and strains RP73, RP45 and RP1. (XLS 2195Â kb)

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    Authors: Gupta, Richa; Dongen, Jenny; Fu, Yu; Abdellaoui, Abdel; +7 Authors

    Table S9. Literature search results for smoking EWAS. (XLS 9 kb)

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  • Authors: Dvořák, Zdeněk; Kopp, Felix; Costello, Cait M.; Kemp, Jazmin S.; +38 Authors

    Related Article: Zdeněk Dvořák, Felix Kopp, Cait M. Costello, Jazmin S. Kemp, Hao Li, Aneta Vrzalová, Martina Štěpánková, Iveta Bartoňková, Eva Jiskrová, Karolína Poulíková, Barbora Vyhlídalová, Lars U. Nordstroem, Chamini V. Karunaratne, Harmit S. Ranhotra, Kyu Shik Mun, Anjaparavanda P. Naren, Iain A. Murray, Gary H. Perdew, Julius Brtko, Lucia Toporova, Arne Schön, William G. Wallace, William G. Walton, Matthew R. Redinbo, Katherine Sun, Amanda Beck, Sandhya Kortagere, Michelle C. Neary, Aneesh Chandran, Saraswathi Vishveshwara, Maria M. Cavalluzzi, Giovanni Lentini, Julia Yue Cui, Haiwei Gu, John C. March, Shirshendu Chatterjee, Adam Matson, Dennis Wright, Kyle L. Flannigan, Simon A. Hirota, Ryan Balfour Sartor, Sridhar Mani|2020|EMBO Mol. Med.|12||doi:10.15252/emmm.201911621 An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

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    Authors: Mohammed Taha, Hiba; Aalizadeh, Reza; Alygizakis, Nikiforos; Antignac, Jean-Philippe; +93 Authors

    Additional file 3: Summary of Zenodo view and download statistics, plus citations (CSV format) as of 28 April 2022 [235].

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Universiteit van Ams...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Universiteit van Ams...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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