Geographic analysis of low birthweight and infant mortality in Michigan using automated zoning methodology

<p>Abstract</p> <p>Background</p> <p>Infant mortality is a major public health problem in the State of Michigan and the United States. The primary adverse reproductive outcome underlying infant mortality is low birthweight. Visualizing and exploring the spatial patterns of low birthweight and infant mortality rates and standardized incidence and mortality ratios is important for generating mechanistic hypotheses, targeting high-risk neighborhoods for monitoring and implementing maternal and child health intervention and prevention programs and evaluating the need for health care services. This study investigates the spatial patterns of low birthweight and infant mortality in the State of Michigan using automated zone matching (AZM) methodology and minimum case and population threshold recommendations provided by the National Center for Health Statistics and the US Census Bureau to calculate stable rates and standardized incidence and mortality ratios at the Zip Code (n = 896) level. The results from this analysis are validated using SaTScan. Vital statistics birth (n = 370,587) and linked infant death (n = 2,972) records obtained from the Michigan Department of Community Health and aggregated for the years 2004 to 2006 are utilized.</p> <p>Results</p> <p>For a majority of Zip Codes the relative standard errors (RSEs) of rates calculated prior to AZM were greater than 20%. Spurious results were the result of too few case and birth counts. Applying AZM with a target population of 25 cases and minimum threshold of 20 cases resulted in the reconstruction of zones with at least 50 births and RSEs of rates 20–22% and below respectively, demonstrating the stability reliability of these new estimates. Other AZM parameters included homogeneity constraints on maternal race and maximum shape compactness of zones to minimize potential confounding. AZM identified areas with elevated low birthweight and infant mortality rates and standardized incidence and mortality ratios. Most but not all of these areas were also detected by SaTScan.</p> <p>Conclusion</p> <p>Understanding the spatial patterns of low birthweight and infant deaths in Michigan was an important first step in conducting a geographic evaluation of the State's reported high infant mortality rates. AZM proved to be a useful tool for visualizing and exploring the spatial patterns of low birthweight and infant deaths for public health surveillance. Future research should also consider AZM as a tool for health services research.</p

For low income minority women in Detroit, traveling to meet their family's needs is a daily battle

In recent years, for many the city of Detroit has been a poster child for America's rust belt decline. And while the urban core of the city has been consolidating, it still presents many challenges for those who need to travel within it. Jieun Lee, Igor Vojnovic, and Sue C. Grady explore the class and racial elements of these challenges, finding that, compared to men and those in the suburbs, for low income mothers of color, living in inner-city Detroit means traveling more often and for longer distances to fulfil basic needs such as work, healthcare and food shopping

Population Vulnerability and Disability in Kenya's Tsetse Fly Habitats

The tsetse fly's influence on human health occurs through direct and indirect exposure pathways. Directly, the fly is a vector for the disease human African trypanosomiasis (HAT), which it spreads to nearly 18,000 new victims each year. Indirectly, the fly is a vector for African Animal Trypanosomaisis (AAT) also known as nagana, which restricts agricultural production, limiting the availability of food and contributing to impoverished conditions across rural sub-Saharan Africa. This historical study used 1999 census data to determine the prevalence of disability among residents and migrants living within Kenya's 7 tsetse fly belts. The results showed that the HAT transmission cycle may differ for residents and migrants with mechanisms leading to exposures that are environmentally driven for residents and economically driven for migrants. The combined burdens of HAT and AAT and the opportunity costs of agricultural production in AAT areas are potential contributors to disability within these tsetse-infested areas. Incorporating reports on disability from the national census appears to be an important surveillance tool that would enhance future HAT surveillance programs in sub-Saharan Africa

Gentrification and Air Quality in a Large Urban County in the United States

Introduction: Increases in industrialization and manufacturing have led to worsening pollution in some components of air quality. In addition, gentrification is occurring in large cities throughout the world. As these socioeconomic and demographic changes occur, there have been no studies examining the association of gentrification with air quality. To investigate this association, we studied the trends of gentrification, changes in racial distribution and changes in air quality in each zip code of a large urban county over a 40-year period. Methods: We conducted a retrospective longitudinal study over 40 years in Wayne County, Michigan using socioeconomic and demographic data from the National Historical Geographic Information System (NHGIS) and air quality data from the United States Environmental Protection Agency (EPA). To assess gentrification, longitudinal analyses were performed to examine median household income, percentage with a college education, median housing value, median gross rent and employment level. The racial distribution was evaluated in each zip code during the time period. Gentrification was studied in relation to air quality using nonparametric 2-sample Wilcon-Mann-Whitney tests and Binomial Generalized Linear Regression models. Results: Although air quality improved overall over the 40-year period, there was a lesser rate of improvement in gentrified areas. Furthermore, gentrification was strongly associated with racial distribution. The most substantial gentrification occurred from 2010 to 2020, in which a specific cluster of adjacent zip codes in downtown Detroit experienced intense gentrification and a drop in the percentage of African-American residents. Conclusions: Gentrified areas seem to have a less pronounced improvement in air quality over time. This reduction in air quality improvement is likely associated with demolitions and the construction of new buildings, such as sporting arenas and accompanying traffic density. Gentrification is also strongly associated with an increase in non-minority residents in an area. Although previous definitions of gentrification in the literature have not included racial distribution, we suggest that future definitions should include this metric given the strong association. Minority residents who are displaced as a result of gentrification do not experience the improvements in housing quality, accessibility to healthy foods and other associations of gentrification

A methodology for projecting hospital bed need: a Michigan case study

Michigan's Department of Community Health (MDCH) is responsible for managing hospitals through the utilization of a Certificate of Need (CON) Commission. Regulation is achieved by limiting the number of beds a hospital can use for inpatient services. MDCH assigns hospitals to service areas and sub areas by use patterns. Hospital beds are then assigned within these Hospital Service Areas and Facility Sub Areas. The determination of the number of hospital beds a facility subarea is authorized to hold, called bed need, is defined in the Michigan Hospital Standards and published by the CON Commission and MDCH. These standards vaguely define a methodology for calculating hospital bed need for a projection year, five years ahead of the base year (defined as the most recent year for which patient data have been published by the Michigan Hospital Association). MDCH approached the authors and requested a reformulation of the process. Here we present a comprehensive guide and associated code as interpreted from the hospital standards with results from the 2011 projection year. Additionally, we discuss methodologies for other states and compare them to Michigan's Bed Need methodology

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer

Colon tumors from four independent mouse models and 100 human colorectal cancers all exhibited striking recapitulation of embryonic colon gene expression from embryonic days 13.5-18.5

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant