281 research outputs found

    Someone Is Waiting At Home, Sweet Home

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    https://digitalcommons.library.umaine.edu/mmb-vp/2486/thumbnail.jp

    Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus

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    BACKGROUND: The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed by virtue of their effect on antigenicity, enabling the virus to evade immune surveillance. RESULTS: We performed phylogenetic analyses of the recently obtained large and relatively unbiased samples of the HA sequences from 1995–2005 isolates of the H3N2 and H1N1 subtypes of influenza A virus. Unexpectedly, it was found that the evolution of H3N2 HA includes long intervals of generally neutral sequence evolution without apparent substantial antigenic change ("stasis" periods) that are characterized by an excess of synonymous over nonsynonymous substitutions per site, lack of association of amino acid replacements with epitope regions, and slow extinction of coexisting virus lineages. These long periods of stasis are punctuated by shorter intervals of rapid evolution under positive selection during which new dominant lineages quickly displace previously coexisting ones. The preponderance of positive selection during intervals of rapid evolution is supported by the dramatic excess of amino acid replacements in the epitope regions of HA compared to replacements in the rest of the HA molecule. In contrast, the stasis intervals showed a much more uniform distribution of replacements over the HA molecule, with a statistically significant difference in the rate of synonymous over nonsynonymous substitution in the epitope regions between the two modes of evolution. A number of parallel amino acid replacements – the same amino acid substitution occurring independently in different lineages – were also detected in H3N2 HA. These parallel mutations were, largely, associated with periods of rapid fitness change, indicating that there are major limitations on evolutionary pathways during antigenic change. The finding that stasis is the prevailing modality of H3N2 evolution suggests that antigenic changes that lead to an increase in fitness typically result from epistatic interactions between several amino acid substitutions in the HA and, perhaps, other viral proteins. The strains that become dominant due to increased fitness emerge from low frequency strains thanks to the last amino acid replacement that completes the set of replacements required to produce a significant antigenic change; no subset of substitutions results in a biologically significant antigenic change and corresponding fitness increase. In contrast to H3N2, no clear intervals of evolution under positive selection were detected for the H1N1 HA during the same time span. Thus, the ascendancy of H1N1 in some seasons is, most likely, caused by the drop in the relative fitness of the previously prevailing H3N2 lineages as the fraction of susceptible hosts decreases during the stasis intervals. CONCLUSION: We show that the common view of the evolution of influenza virus as a rapid, positive selection-driven process is, at best, incomplete. Rather, the interpandemic evolution of influenza appears to consist of extended intervals of stasis, which are characterized by neutral sequence evolution, punctuated by shorter intervals of rapid fitness increase when evolutionary change is driven by positive selection. These observations have implications for influenza surveillance and vaccine formulation; in particular, the possibility exists that parallel amino acid replacements could serve as a predictor of new dominant strains. REVIEWERS: Ron Fouchier (nominated by Andrey Rzhetsky), David Krakauer, Christopher Le

    Early age at first childbirth and skilled birth attendance during delivery among young women in sub-Saharan Africa

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    Background: Despite the numerous policy interventions targeted at preventing early age at first childbirth globally, the prevalence of adolescent childbirth remains high. Meanwhile, skilled birth attendance is considered essential in preventing childbirth-related complications and deaths among adolescent mothers. Therefore, we estimated the prevalence of early age at first childbirth and skilled birth attendance among young women in sub-Saharan Africa and investigated the association between them. Methods: Demographic and Health Survey data of 29 sub-Saharan African countries was utilized. Skilled birth attendance and age at first birth were the outcome and the key explanatory variables in this study respectively. Overall, a total of 52,875 young women aged 20-24 years were included in our study. A multilevel binary logistic regression analysis was performed and the results presented as crude and adjusted odds ratios at 95% confidence interval. Results: Approximately 73% of young women had their first birth when they were less than 20 years with Chad having the highest proportion (85.7%) and Rwanda recording the lowest (43.3%). The average proportion of those who had skilled assistance during delivery in the 29 sub-Saharan African countries was 75.3% and this ranged from 38.4% in Chad to 93.7% in Rwanda. Young women who had their first birth at the age of 20-24 were more likely to have skilled birth attendance during delivery (aOR = 2.4, CI = 2.24-2.53) than those who had their first birth before 20 years. Conclusion: Early age at first childbirth has been found to be associated with low skilled assistance during delivery. These findings re-emphasize the need for sub-Saharan African countries to implement programs that will sensitize and encourage the patronage of skilled birth attendance among young women in order to reduce complications and maternal mortalities. The lower likelihood of skilled birth attendance among young women who had their first birth when they were adolescents could mean that this cohort of young women face some barriers in accessing maternal healthcare services

    Tracing the Mixing and Movement of Groundwater into Florida Bay with Four Naturally Occurring Radium Isotopes

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    Proceedings of the 1999 Georgia Water Resources Conference, March 30 and 31, Athens, Georgia.Four naturally occurring isotopes of radium (²²³, ²²⁴, ²²⁶, ²²⁸Ra) have a range in half-life that extends from a few days to over 1,600 years. Unique geochemical attributes make these radium isotopes ideal to examine sediment/water interface exchange processes in coastal waters. Here we present initial radium isotopic data of Florida Bay, a heavily impacted coastal system in south Florida. Florida Bay is a shallow, brackish, semi-enclosed water body that receives most of its limited freshwater supply from the Everglades, principally by surficial water runoff through Trout Creek/Taylor River. Because the entire region is underlain by highly porous Key Largo limestone and due to other hydrologic constraints, there is the possibility that ground water exchange may be significant in Florida Bay. To evaluate the extent of such a subsurface contribution, radium isotopes are being determined in shallow wells, seepage meter sites, and a series of water column samples across the Everglades National Park-Florida Bay boundary. All four radium isotopes were at least an order of magnitude greater in the two shallow well samples than in the water column samples. For example, ²²⁶Ra ranged from about 0.50 dpm L⁻¹ at a salinity of 5 to over 13 dpm L⁻¹ in Well B (salinity = 47.2). Isotopic radium ratios reveal that the well waters (i.e., marine ground water) are geochemically distinct from surficial waters and are regenerated on a time-scale of several days (i.e., ²²⁴Ra/²²³Ra). Results indicate that this radium quartet can be used effectively in Florida Bay to examine the exchange of surficial water and ground water.Sponsored and Organized by: U.S. Geological Survey, Georgia Department of Natural Resources, The University of Georgia, Georgia State University, Georgia Institute of TechnologyThis book was published by the Institute of Ecology, The University of Georgia, Athens, Georgia 30602-2202 with partial funding provided by the U.S. Department of Interior, geological Survey, through the Georgia Water Research Insttitute as authorized by the Water Research Institutes Authorization Act of 1990 (P.L. 101-397). The views and statements advanced in this publication are solely those of the authors and do not represent official views or policies of the University of Georgia or the U.S. Geological Survey or the conference sponsors

    Sex inequality in early initiation of breastfeeding in 24 sub-Saharan African countries: A multi-country analysis of Demographic and Health Surveys

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    Background: The Sustainable Development Goal (SDG) 3 aims at reducing neonatal and under-5 mortality to below 12 per 1000 and 25 per 1000 live births, respectively, globally by 2030. Studies have found that initiation of breastfeeding within one hour of birth and continuous breastfeeding for over 12 months can positively impact neonatal and infant health. However, there is evidence that the sex of a child may influence the breastfeeding practices of a mother. Thus, we examined sex inequality in early breastfeeding initiation in sub-Saharan Africa. Materials and methods: Data from Demographic and Health Surveys conducted in 24 sub-Saharan African countries between January 2010 and December 2019 were pooled and analysed. A total of 137,677 women of reproductive age (15-49 years) were considered in this study. Bivariate and multivariable regression analyses were performed, and the results were presented using crude odds ratio (cOR) and adjusted odds ratio (aOR) with statistical significance at a p-value less than 0.05. Results: The highest inequality in early initiation of breastfeeding was reported in Togo with a difference of 5.21% between the female and male children, while the lowest inequality was reported in Guinea with 0.48% difference between the female and male children. A higher odds of breastfeeding within 1 hour was observed among female children [cOR = 1.05; 95% (CI = 1.02-1.09)] compared to male children, and this persisted after controlling for the confounders included in this study [aOR = 1.05; 95%(CI = 1.02-1.08)]. Conclusion: We found higher odds for early breastfeeding initiation of female children compared to male children in sub-Saharan Africa. To reduce breastfeeding initiation inequalities, programmes that educate and encourage early initiation of breastfeeding irrespective of the child sex should be promoted among mothers

    A Mutational Hotspot in the 2B Domain of Human Hair Basic Keratin 6 (hHb6) in Monilethrix Patients

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    Monilethrix is an inherited hair dystrophy in which affected, fragile, hairs have an unique beaded morphology. Ultrastructural studies suggest a defect in filament structure in the cortex of the hair, and the hard keratins of hair and nail are thus candidate genes. In several families with autosomal dominant monilethrix, the disorder has been linked to the type II keratin gene cluster at chromosome 12q13. Recently, causative mutations in the critical helix termination motif in the 2B domain of the human hair basic keratin 6 (hHb6) have been identified. We now report the results of sequencing this domain in 13 unrelated families or cases with monilethrix. Five of the 13 had the same mutation as previously found, a G to A transversion leading to a lysine for glutamic acid substitution (E413K) in the 2B domain (residue 117 of the 2B helix) of hHb6. The mutation was confirmed by a restriction fragment length polymorphism assay developed for this purpose, and, as this mutation is evidently a common cause of the syndrome, for use in screening other cases. In eight families or cases, however, including three in whom linkage data are consistent with a defect at the type II keratin locus, no mutation was found in this domain of hHb6

    The Pan-STARRS Moving Object Processing System

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    We describe the Pan-STARRS Moving Object Processing System (MOPS), a modern software package that produces automatic asteroid discoveries and identifications from catalogs of transient detections from next-generation astronomical survey telescopes. MOPS achieves > 99.5% efficiency in producing orbits from a synthetic but realistic population of asteroids whose measurements were simulated for a Pan-STARRS4-class telescope. Additionally, using a non-physical grid population, we demonstrate that MOPS can detect populations of currently unknown objects such as interstellar asteroids. MOPS has been adapted successfully to the prototype Pan-STARRS1 telescope despite differences in expected false detection rates, fill-factor loss and relatively sparse observing cadence compared to a hypothetical Pan-STARRS4 telescope and survey. MOPS remains >99.5% efficient at detecting objects on a single night but drops to 80% efficiency at producing orbits for objects detected on multiple nights. This loss is primarily due to configurable MOPS processing limits that are not yet tuned for the Pan-STARRS1 mission. The core MOPS software package is the product of more than 15 person-years of software development and incorporates countless additional years of effort in third-party software to perform lower-level functions such as spatial searching or orbit determination. We describe the high-level design of MOPS and essential subcomponents, the suitability of MOPS for other survey programs, and suggest a road map for future MOPS development.Comment: 57 Pages, 26 Figures, 13 Table
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