Merging Multiple Existing Geotechnical Databases

This report discusses a project undertaken by Kentucky Transportation Center (KTC) researchers to create a comprehensive geotechnical database for highway planning, design, maintenance, and repair. The project consolidated multiple geotechnical data sources into a unified database accessible to Kentucky Transportation Cabinet (KYTC) staff, enabling informed decision making and improving project outcomes. Databases were merged with great attention to detail, ensuring data integrity and coherence. A geotechnical data collector app developed as part of the project supports convenient and efficient data collection in the field, even when phones or tablets lack network connectivity. A rockfall rating app and landslide hazard rating system streamline the collection and assessment of rockfall and landslide data. The report highlights tools used to complete the project, including the ArcGIS suite (i.e., ArcMap, ArcGIS Pro, ArcGIS Online, Collector, Field Maps, Survey123), Microsoft Visual Studio, and Microsoft SQL Server. These tools facilitate geodatabase management, field data collection, and data analysis. Detailed instructions and user manuals are provided for each application. Overall, project deliverables strengthen the Cabinet’s geotechnical data management as well as its geotechnical investigations, risk assessments, and mitigation strategies. It empowers staff by giving them access to valuable tools for data collection, analysis, and visualization, which in turn positively influence the safety and performance of Kentucky\u27s highways

The Developmental Origins of Health and Disease in Women from the Michigan Bone Health and Metabolism Study: An Examination with Longitudinal and Intergenerational Data.

Fetal and early life experiences may be associated with development of adult chronic disease and effects may extend across generations. Epidemiologists have adapted these concepts to identify risk factors for chronic disease, but studies with longitudinal or intergenerational data are limited. Using data from a cohort study of Caucasian women, aged 24-50 years in 1992 and followed annually for over 15 years, we evaluated whether low and high birth weight women had different adult body composition, carbohydrate metabolism, or lipid trajectories compared to normal birth weight women. We assessed whether longitudinal risk profiles for diabetes or metabolic clustering differed by birth weight. To better understand intergenerational continuity of risk, we evaluated whether pregnancy characteristics across two generations influenced the birth weight of these women’s offspring. High birth weight women had higher adult body composition measures compared to normal birth weight women; however, slopes did not differ, suggesting the higher body composition measures observed among high birth weight women were constant over time. High birth weight women had steeper rates of change in glucose levels, but no differences were observed in lipid, insulin, or insulin resistance levels or in their trajectories over time compared to normal birth weight women. Body composition, carbohydrate metabolism, and lipid trajectories did not differ between low and normal birth weight women and the risk for developing type-2 diabetes or metabolic clustering did not differ by birth weight groups. When we examined the intergenerational effects, we found that women with in utero cigarette smoking exposure had offspring who were an average of 136 grams heavier than women without in utero smoking exposure (p=0.02). Similarly, women born to older mothers had heavier offspring than women born to younger mothers. This dissertation expands our understanding of the relationship between birth weight and trajectories in adult body composition, carbohydrate metabolism, and lipids – known risk factors for many chronic diseases - and provides further support of an intergenerational effect on birth weight. Understanding these relationships contributes to knowledge about chronic disease etiology and can motivate research and interventions aimed at improving reproductive and women’s health and preventing chronic disease.Ph.D.Epidemiological ScienceUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/77888/1/erillama_1.pd

Dual Function of CD81 in Influenza Virus Uncoating and Budding

As an obligatory pathogen, influenza virus co-opts host cell machinery to harbor infection and to produce progeny viruses. In order to characterize the virus-host cell interactions, several genome-wide siRNA screens and proteomic analyses have been performed recently to identify host factors involved in influenza virus infection. CD81 has emerged as one of the top candidates in two siRNA screens and one proteomic study. The exact role played by CD81 in influenza infection, however, has not been elucidated thus far. In this work, we examined the effect of CD81 depletion on the major steps of the influenza infection. We found that CD81 primarily affected virus infection at two stages: viral uncoating during entry and virus budding. CD81 marked a specific endosomal population and about half of the fused influenza virus particles underwent fusion within the CD81-positive endosomes. Depletion of CD81 resulted in a substantial defect in viral fusion and infection. During virus assembly, CD81 was recruited to virus budding site on the plasma membrane, and in particular, to specific sub-viral locations. For spherical and slightly elongated influenza virus, CD81 was localized at both the growing tip and the budding neck of the progeny viruses. CD81 knockdown led to a budding defect and resulted in elongated budding virions with a higher propensity to remain attached to the plasma membrane. Progeny virus production was markedly reduced in CD81-knockdown cells even when the uncoating defect was compensated. In filamentous virus, CD81 was distributed at multiple sites along the viral filament. Taken together, these results demonstrate important roles of CD81 in both entry and budding stages of the influenza infection cycle

Melt processing and properties of linear low density polyethylene-graphene nanoplatelet composites

Composites of Linear Low Density Polyethylene (LLDPE) and Graphene Nanoplatelets (GNPs) were processed using a twin screw extruder under different extrusion conditions. The effects of screw speed, feeder speed and GNP content on the electrical, thermal and mechanical properties of composites were investigated. The inclusion of GNPs in the matrix improved the thermal stability and conductivity by 2.7% and 43%, respectively. The electrical conductivity improved from 10-11 to 10-5 S/m at 150 rpm due to the high thermal stability of the GNPs and the formation of phonon and charge carrier networks in the polymer matrix. Higher extruder speeds result in a better distribution of the GNPs in the matrix and a significant increase in thermal stability and thermal conductivity. However, this effect is not significant for the electrical conductivity and tensile strength. The addition of GNPs increased the viscosity of the polymer, which will lead to higher processing power requirements. Increasing the extruder speed led to a reduction in viscosity, which is due to thermal degradation and/or chain scission. Thus, while high speeds result in better dispersions, the speed needs to be optimized to prevent detrimental impacts on the properties.</p

Delineating the biosynthesis of gentamicin x2, the common precursor of the gentamicin C antibiotic complex.

Gentamicin C complex is a mixture of aminoglycoside antibiotics used worldwide to treat severe Gram-negative bacterial infections. Despite its clinical importance, the enzymology of its biosynthetic pathway has remained obscure. We report here insights into the four enzyme-catalyzed steps that lead from the first-formed pseudotrisaccharide gentamicin A2 to gentamicin X2, the last common intermediate for all components of the C complex. We have used both targeted mutations of individual genes and reconstitution of portions of the pathway in vitro to show that the secondary alcohol function at C-3″ of A2 is first converted to an amine, catalyzed by the tandem operation of oxidoreductase GenD2 and transaminase GenS2. The amine is then specifically methylated by the S-adenosyl-l-methionine (SAM)-dependent N-methyltransferase GenN to form gentamicin A. Finally, C-methylation at C-4″ to form gentamicin X2 is catalyzed by the radical SAM-dependent and cobalamin-dependent enzyme GenD1.This work was supported by a project grant from the Medical Research Council, UK (G1001687) to P.F.L.; and by the 973 and 863 programs from the Ministry of Science and Technology of China, National Science Foundation of China, and the Translational Medical Research Fund of Wuhan University School of Medicine to Y.S.; E.M. thanks the Gates Cambridge Trust for a scholarship. We also gratefully acknowledge Dr. Xinzhou Yang, SouthCentral University for Nationalities, for his assistance in separation of gentamicin A2. We thank Dr. Andrew Truman (John Innes Institute) for helpful discussions.This is the final published version. It was originally published in Chemistry and Biology, Volume 22, Issue 2, 19 February 2015, Pages 251–261, doi:10.1016/j.chembiol.2014.12.01

Can Community Gardens with Workshops Increase Gardening Behavior? A Navajo Wellness Collaboration

This paper seeks to evaluate the potential efficacy of a community gardening intervention on the Navajo Nation to increase gardening and healthy eating behaviors, which are potentially important in preventing obesity and related health conditions. Rates of obesity are high among American Indians, including those living on Navajo Nation land. Eating fresh fruits and vegetables is part of healthy eating. However, availability and access to fresh fruits and vegetables are severely limited on the Navajo Nation, due to distance and cost. One way to increase both availability and consumption of fresh fruits and vegetables is through community gardening, yet many on the Navajo Nation have limited knowledge and capacity to garden. Methods: We used a quasi-experimental pre-post study design to estimate the effect of a community gardening intervention. Primary outcomes of interest were gardening frequency and fruit and vegetable consumption. Community gardens were constructed and planted in two communities on the Navajo Nation. In addition, a series of gardening workshops were held in each community. Community members were recruited to complete surveys at time points before and after the workshops. The time between baseline and follow-up was approximately one year. Results: We surveyed 169 participants at one time point at least, across both communities, and 25 of these participated in the gardening workshops. Within the 169, there was a cohort of 32 participants completing both baseline and follow-up surveys. For this cohort, interest in gardening increased from 78% to 97% (p=0.014), but none of the changes in gardening self-efficacy, knowledge or gardening frequency reached statistical significance. There were no measurable changes in reported fruit and vegetable consumption, self-efficacy or knowledge. Overall, the reported financial barriers to gardening increased from baseline to follow-up from 4.6 to 5.5 (p=0.035). Altogether 52 participants completed follow-up. In this group, those who attended at least one workshop gardened more frequently at follow-up than those who did not attend any workshops (21 times per month compared to 10 times per month (p=0.07). Conclusion: Despite enthusiasm for the community garden in both the communities studied and the increased interest in gardening, workshop attendance and participant retention in the study were low. These factors limited our ability to evaluate the potential efficacy of the intervention on gardening and healthy eating behaviors. Nonetheless, we found some evidence that participating in gardening workshops may lead to increased gardening frequency. Future studies should augment the intervention to include explicit efforts to reduce barriers to long term engagement and extend intervention reach

The Alliance for Cellular Signaling Plasmid Collection: A Flexible Resource for Protein Localization Studies and Signaling Pathway Analysis

Cellular responses to inputs that vary both temporally and spatially are determined by complex relationships between the components of cell signaling networks. Analysis of these relationships requires access to a wide range of experimental reagents and techniques, including the ability to express the protein components of the model cells in a variety of contexts. As part of the Alliance for Cellular Signaling, we developed a robust method for cloning large numbers of signaling ORFs into Gateway® entry vectors, and we created a wide range of compatible expression platforms for proteomics applications. To date, we have generated over 3000 plasmids that are available to the scientific community via the American Type Culture Collection. We have established a website at www.signaling-gateway.org/data/plasmid/ that allows users to browse, search, and blast Alliance for Cellular Signaling plasmids. The collection primarily contains murine signaling ORFs with an emphasis on kinases and G protein signaling genes. Here we describe the cloning, databasing, and application of this proteomics resource for large scale subcellular localization screens in mammalian cell lines

Development and application of an automated algorithm to identify a window of consecutive days of accelerometer wear for large-scale studies

Abstract Background Some accelerometer studies ask participants to document in a daily log when the device was worn. These logs are used to inform the window of consecutive days to extract from the accelerometer for analysis. Logs can be missing or inaccurate, which can introduce bias in the data. To mitigate this bias, we developed a simple computer algorithm that used data within the accelerometer to identify the window of consecutive wear days. To evaluate the algorithm’s performance, we compared how well it agreed to the window of days identified by visual inspection and participant logs. Findings Participants were older women (mean age 79 years) in a cohort study that aimed to examine the relationship of objective physical activity on cardiovascular health. The study protocol requested that participants wear an accelerometer 24 h per day over nine calendar days (to capture seven consecutive wear days) and to complete daily logs. A stratified sample with (n = 75) and without (n = 100) participant logs were selected. The Objective Physical Activity and Cardiovascular Health (OPACH) algorithm was applied to the accelerometer data to identify a window of up to seven consecutive wear days. Participant logs documented dates the device was first put on, worn, and removed. Using pre-established guidelines, two independent raters visually reviewed the accelerometer data and characterized the dates representing up to seven consecutive days of 24-h wear. Average agreement level between the two raters was 90%. The percent agreement was compared between the three methods. The OPACH algorithm and visual inspection had 83% agreement in identifying a window with the same total number of days, if one or more shifts in calendar dates were allowed. For visual inspection vs. logs and algorithm vs. logs, this agreement was 81 and 74%, respectively. Conclusion The OPACH algorithm can be efficiently and readily applied in large-scale accelerometer studies for the identification of a window of consecutive days of accelerometer wear. This algorithm was comparable to visual inspection and participant logs and might provide a quicker and more cost-effective alternative to selecting which data to extract from the accelerometer for analysis. Trial Registration: clinicaltrials.gov identifier: NCT0000061

Merging Multiple Existing Geotechnical Databases

SPR 20-588This report discusses a project undertaken by Kentucky Transportation Center (KTC) researchers to create a comprehensive geotechnical database for highway planning, design, maintenance, and repair. The project consolidated multiple geotechnical data sources into a unified database accessible to Kentucky Transportation Cabinet (KYTC) staff, enabling informed decision making and improving project outcomes. Databases were merged with great attention to detail, ensuring data integrity and coherence. A geotechnical data collector app developed as part of the project supports convenient and efficient data collection in the field, even when phones or tablets lack network connectivity. A rockfall rating app and landslide hazard rating system streamline the collection and assessment of rockfall and landslide data. The report highlights tools used to complete the project, including the ArcGIS suite (i.e., ArcMap, ArcGIS Pro, ArcGIS Online, Collector, Field Maps, Survey123), Microsoft Visual Studio, and Microsoft SQL Server. These tools facilitate geodatabase management, field data collection, and data analysis. Detailed instructions and user manuals are provided for each application. Overall, project deliverables strengthen the Cabinet\u2019s geotechnical data management as well as its geotechnical investigations, risk assessments, and mitigation strategies. It empowers staff by giving them access to valuable tools for data collection, analysis, and visualization, which in turn positively influence the safety and performance of Kentucky's highways

Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1

Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinus strain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales