scholarly journals Investigating the Use of Nurse Paradata in Understanding Nonresponse to Biological Data Collection

2020 ◽  
pp. 221-234
Author(s):  
Fiona Pashazadeh ◽  
Alexandru Cernat ◽  
Joseph W. Sakshaug
Keyword(s):  
Data Collection ◽  
Biological Data

scholarly journals Health Disparities in Staphylococcus aureus Transmission and Carriage in a Border Region of the United States Based on Cultural Differences in Social Relationships: Protocol for a Survey Study (Preprint)

2019 ◽  
Author(s):  
Talima Pearson ◽  
Steven D Barger ◽  
Monica Lininger ◽  
Heidi Wayment ◽  
Crystal Hepp ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Social Network ◽  
Data Collection ◽  
Social Determinants Of Health ◽  
Social Relationships ◽  
Social Determinants ◽  
Social Groups ◽  
Biological Data ◽  
Determinants Of Health ◽  
Sampling Procedures

BACKGROUND Health care–associated <italic>Staphylococcus aureus</italic> infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cultural-biological evidence of carriage and transmission to inform intervention strategies that reduce <italic>S aureus</italic> transmission in the community. Broad differences in social interactions because of cultural affiliation, travel, and residency patterns may impact <italic>S aureus</italic> carriage and transmission, either as risk or as protective factors. OBJECTIVE This study aims to (1) characterize <italic>S aureus</italic> carriage rates and compare circulating pathogen genotypes with those associated with disease isolated from local clinical specimens across resident groups and across Hispanic and non-Hispanic white ethnic groups and (2) evaluate social network relationships and social determinants of health-based risk factors for their impact on carriage and transmission of <italic>S aureus</italic>. METHODS We combine sociocultural survey approaches to population health sampling with <italic>S aureus</italic> carriage and pathogen genomic analysis to infer transmission patterns. Whole genome sequences of <italic>S aureus</italic> from community and clinical sampling will be phylogenetically compared to determine if strains that cause disease (clinical samples) are representative of community genotypes. Phylogenetic comparisons of strains collected from participants within social groups can indicate possible transmission within the group. We can therefore combine transmission data with social determinants of health variables (socioeconomic status, health history, etc) and social network variables (both egocentric and relational) to determine the extent to which social relationships are associated with <italic>S aureus</italic> transmission. RESULTS We conducted a first year pilot test and feasibility test of survey and biological data collection and analytic procedures based on the original funded design for this project (#NIH U54MD012388). That design resulted in survey data collection from 336 groups and 1337 individuals. The protocol, described below, is a revision based on data assessment, new findings for statistical power analyses, and refined data monitoring procedures. CONCLUSIONS This study is designed to evaluate ethnic-specific prevalence of <italic>S aureus</italic> carriage in a US border community. The study will also examine the extent to which kin and nonkin social relationships are concordant with carriage prevalence in social groups. Genetic analysis of <italic>S aureus</italic> strains will further distinguish putative transmission pathways across social relationship contexts and inform our understanding of the correspondence of <italic>S aureus</italic> reservoirs across clinical and community settings. Basic community-engaged nonprobabilistic sampling procedures provide a rigorous framework for completion of this 5-year study of the social and cultural parameters of <italic>S aureus</italic> carriage and transmission.

Ethics of Working with Incarcerated Populations: A View From the IRB

2019 ◽  
Vol 41 (4) ◽  
pp. 17-20
Author(s):  
Tinna Traustadóttir ◽  
Mary Hanabury ◽  
Marie Peoples
Keyword(s):  
Data Collection ◽  
Best Practice ◽  
Biological Data ◽  
Detention Center ◽  
Institutional Review ◽  
Policies And Procedures ◽  
Incarcerated Populations ◽  
Collection Data ◽  
Conducting Research ◽  
Privacy And Confidentiality

This article will present our perspective, as Institutional Review Board (IRB) members, on the experiences and issues that emerge when conducting research with incarcerated populations. The goal is to provide information to other IRBs and researchers to ease the review process of research protocols involving prisoners and to mitigate potential problems before they arise. We focus in this article on one project we reviewed that involved prisoners. Vulnerable populations such as prisoners require special conditions and protections for recruitment, consent, compensation, data collection, data protection, and analysis. Special considerations also include compliance with detention center policies and procedures, especially when the research project includes analyzing data containing Private Identifiable information (PII), Protected Health Information (PHI), and biological data collection. The four main issues we will address are in regard to (1) the informed consent process, (2) the balance between privacy and confidentiality of the subjects and researchers' safety within the facility, (3) payment to subjects, and (4) the ability of subjects to communicate with researchers and with the IRB. We will conclude with some recommendations for “best practice.”

scholarly journals Health Disparities in Staphylococcus aureus Transmission and Carriage in a Border Region of the United States Based on Cultural Differences in Social Relationships: Protocol for a Survey Study

10.2196/14853 ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. e14853
Author(s):  
Talima Pearson ◽  
Steven D Barger ◽  
Monica Lininger ◽  
Heidi Wayment ◽  
Crystal Hepp ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Social Network ◽  
Data Collection ◽  
Social Determinants Of Health ◽  
Social Relationships ◽  
Social Determinants ◽  
Social Groups ◽  
Biological Data ◽  
Determinants Of Health ◽  
Sampling Procedures

Background Health care–associated Staphylococcus aureus infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cultural-biological evidence of carriage and transmission to inform intervention strategies that reduce S aureus transmission in the community. Broad differences in social interactions because of cultural affiliation, travel, and residency patterns may impact S aureus carriage and transmission, either as risk or as protective factors. Objective This study aims to (1) characterize S aureus carriage rates and compare circulating pathogen genotypes with those associated with disease isolated from local clinical specimens across resident groups and across Hispanic and non-Hispanic white ethnic groups and (2) evaluate social network relationships and social determinants of health-based risk factors for their impact on carriage and transmission of S aureus. Methods We combine sociocultural survey approaches to population health sampling with S aureus carriage and pathogen genomic analysis to infer transmission patterns. Whole genome sequences of S aureus from community and clinical sampling will be phylogenetically compared to determine if strains that cause disease (clinical samples) are representative of community genotypes. Phylogenetic comparisons of strains collected from participants within social groups can indicate possible transmission within the group. We can therefore combine transmission data with social determinants of health variables (socioeconomic status, health history, etc) and social network variables (both egocentric and relational) to determine the extent to which social relationships are associated with S aureus transmission. Results We conducted a first year pilot test and feasibility test of survey and biological data collection and analytic procedures based on the original funded design for this project (#NIH U54MD012388). That design resulted in survey data collection from 336 groups and 1337 individuals. The protocol, described below, is a revision based on data assessment, new findings for statistical power analyses, and refined data monitoring procedures. Conclusions This study is designed to evaluate ethnic-specific prevalence of S aureus carriage in a US border community. The study will also examine the extent to which kin and nonkin social relationships are concordant with carriage prevalence in social groups. Genetic analysis of S aureus strains will further distinguish putative transmission pathways across social relationship contexts and inform our understanding of the correspondence of S aureus reservoirs across clinical and community settings. Basic community-engaged nonprobabilistic sampling procedures provide a rigorous framework for completion of this 5-year study of the social and cultural parameters of S aureus carriage and transmission.

scholarly journals baRcodeR with PyTrackDat: Open-source labelling and tracking of biological samples for repeatable science

2018 ◽  
Author(s):  
Yihan Wu ◽  
David R. Lougheed ◽  
Stephen C. Lougheed ◽  
Kristy Moniz ◽  
Virginia K. Walker ◽  
...  
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Biological Samples ◽  
Low Cost ◽  
R Package ◽  
Biological Data ◽  
Human Errors ◽  
Field Samples ◽  
Sample Management ◽  
Globally Distributed

AbstractRepeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult to achieve in practice. Several flexible, open-source tools developed for the R and Python coding environments aid the reproducibility of data wrangling and analysis in scientific research. In contrast, analogous tools are generally lacking for earlier stages, such as systematic labelling and processing of field samples with hierarchical structure (e.g. time points of individuals from multiple lines or populations) or curating heterogenous data collected by different researchers over several years. Such tools are critical for modern research given trends toward globally distributed collaborators using higher-throughput technologies. As a step toward improving repeatability of methods for the collection of biological samples, and curation of biological data, we introduce the R package baRcodeR and the PyTrackDat pipeline in Python. The baRcodeR package provides tools for generating biologically informative, hierarchical labels with digitally encoded 2D barcodes that can be printed and scanned using low-cost commercial hardware. The PyTrackDat pipeline integrates with baRcodeR output to build a web interface for sample management and tracking along with data collection and curation. We briefly describe the application of principles from baRcodeR and PyTrackDat in three large research projects, which demonstrate their value to (i) help document sampling methods, (ii) facilitate collaboration and (iii) reduce opportunities for human errors and omissions that could otherwise propagate through downstream data analysis to compromise biological inference.

scholarly journals The second generation of The Avon Longitudinal Study of Parents and Children (ALSPAC-G2): a cohort profile

2019 ◽  
Vol 4 ◽  
pp. 36 ◽  
Author(s):  
Deborah A. Lawlor ◽  
Melanie Lewcock ◽  
Louise Rena-Jones ◽  
Claire Rollings ◽  
Vikki Yip ◽  
...  
Keyword(s):  
Longitudinal Study ◽  
Data Collection ◽  
Glucose Monitoring ◽  
Placental Tissue ◽  
Late Pregnancy ◽  
Biological Data ◽  
Parents And Children ◽  
Wide Range ◽  
Set Up ◽  
Avon Longitudinal Study

Background: The Avon Longitudinal Study of Parents and Children-Generation 2 (ALSPAC-G2) was set up to provide a unique multi-generational cohort. It builds on the existing ALSPAC resource, which recruited 14,541 pregnancies to women resident in the South West of England who were expected to deliver between 01/04/1991 and 31/12/1992. Those women and their partners (Generation 0; ALSPAC-G0) and their offspring (ALSPAC-G1) have been followed for the last 27 years. This profile describes recruitment and data collection on the next generation (ALSPAC-G2)—the grandchildren of ALSPAC-G0 and children of ALSPAC-G1. Recruitment: Recruitment began on the 6 th of June 2012 and we present details of recruitment and participants up to 30 th June 2018 (~6 years). We knew at the start of recruitment that some ALSPAC-G1 participants had already become parents and ALSPAC-G2 is an open cohort; we recruit at any age. We hope to continue recruiting until all ALSPAC-G1 participants have completed their families. Up to 30 th June 2018 we recruited 810 ALSPAC-G2 participants from 548 families. Of these 810, 389 (48%) were recruited during their mother’s pregnancy, 287 (35%) before age 3 years, 104 (13%) between 3-6 years and 30 (4%) after 6 years. Over 70% of those invited to early pregnancy, late pregnancy, second week of life, 6-, 12- and 24-month assessments (whether for their recruitment, or a follow-up, visit) have attended, with attendance being over 60% for subsequent visits up to 7 years (too few are eligible for the 9- and 11-year assessments to analyse). Data collection: We collect a wide-range of socioeconomic, lifestyle, clinical, anthropometric and biological data on all family members repeatedly. Biological samples include blood (including cord-blood), urine, meconium and faeces, and placental tissue. In subgroups detailed data collection, such as continuous glucose monitoring and videos of parent-child interactions, are being collected.

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