Restoring the Shiawassee Flats: Estuarine Gateway to Saginaw Bay

In 2011, the U.S. Fish & Wildlife Service and Ducks Unlimited received a $1.5 million Sustain Our Great Lakes grant for the first phase of a wetland restoration project at the Shiawassee National Wildlife Refuge, outside Saginaw, Michigan. Phase I of the restoration seeks to reconnect 994 acres of former farmland to the natural, dynamic hydrology of the Shiawassee River, which flows through the Refuge. In 2012, staff at the Shiawassee National Wildlife Refuge contacted a team of master’s degree students at the University of Michigan School of Natural Resources and Environment and asked for an assessment of baseline conditions at the restoration site before the restoration project begins. The Refuge also asked for information about strategies used in other wetland restoration projects and about partners who might contribute to future restoration efforts at the Refuge. This report, organized into three sections, is the outcome of the team’s research. Part 1: Understanding the Past provides a brief history of the Flats and the Refuge, summarizing the key human and environmental factors which shaped their current conditions. • Saginaw County has experienced a 72% reduction in forests and a 96% reduction in wetlands since 1830. These losses were mirrored by dramatic increases in agricultural and urban land cover during this same time period. • The construction of drains, dikes, levees, and water control structures throughout the Flats has drastically altered the main channel position and sinuosity of the Shiawassee River and disrupted the natural flow regimes. The Flint and Bad Rivers also show extensive channel modifications near their confluence with the Shiawassee River. Part 2: Assessing the Present describes the current ecological conditions at the Refuge, including the restoration site, based on field data collected by the team in 2012. To collect these data, a fish community survey, an aquatic macroinvertebrate community survey, a vegetation survey, and water quality testing were conducted. • The fish community of the Shiawassee River is seasonally variable and distinct from the managed units surveyed in 2012, which exhibited a lack of migratory fishes and a predominance of sunfishes. Post-restoration fish monitoring during seasonal migrations and late summer would help evaluate improvements in richness of migratory and floodplain species within the Refuge. • The vegetation within the targeted restoration site and is primarily composed of weedy species. Annual vegetation monitoring by both ground sampling and remote sensing of community structure and composition could be used to assess changes in the plant community after restoration. • Aquatic macroinvertebrate species richness was greatest in the Grefe Pool, a currently restored and managed diked wetland. . All three macrohabitats sampled for macroinvertebrates indicated a macroinvertebrate community with high tolerance to nutrient loading and low dissolved oxygen. Post-restoration monitoring could compare v macroinvertebrate species richness in the restoration site to established wetland units like Grefe Pool. • Hydrologic analysis suggested that, during periods of low flow, significant discharge was released into the Saginaw River from storage in the wetlands of the Flats, exceeding or that measured from tributary river inputs. Further studies should be conducted to distinguish between low flow inputs from hydrologic storage in the Flats versus urban inputs from the city of Saginaw, directly downstream of the Flats. • Total reactive phosphorus loads were on average larger in the Saginaw River than the sum of phosphorus inputs from rivers entering the Saginaw. This indicates that the Flats themselves may be contributing available phosphorus to the Saginaw River, possibly due to release of phosphorus from sediments within the Flats. • Total inorganic nitrogen levels in the Saginaw River, however, were on average lower than the sum of the river inputs of nitrogen. This is indicative of an ability of the Flats to absorb soluble nitrogen, preventing it from entering the Saginaw River. Part 3: Planning for the Future presents case studies of wetland restoration on other National Wildlife Refuges and identifies potential partners and strategies for the Refuge’s future restoration activities. • Creating a post-restoration adaptive management plan could help the Refuge identify priorities for restoration and management, evaluate progress, and incorporate feedback from partners and monitoring, leading to long-term support from partners and ecologically sound outcomes. • Engaging many and varied partners in mutually informative and strategic planning in restoration of the Flats area could lead to increased support from both government officials and community groups, as well as funding and marketing opportunities. • Utilizing volunteers as part of Refuge activities could lead to community support, reduced project costs, stronger grant proposals, private partnerships, and unforeseen opportunities for funding.Master of ScienceMaster of Landscape ArchitectureNatural Resources and EnvironmentUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/97428/1/Shiawassee Master's Project Final Draft 2013.pd

Efficient mutation screening for cervical cancers from circulating tumor DNA in blood

Background Early diagnosis and continuous monitoring are necessary for an efficient management of cervical cancers (CC). Liquid biopsy, such as detecting circulating tumor DNA (ctDNA) from blood, is a simple, non-invasive method for testing and monitoring cancer markers. However, tumor-specific alterations in ctDNA have not been extensively investigated or compared to other circulating biomarkers in the diagnosis and monitoring of the CC. Therfore, Next-generation sequencing (NGS) analysis with blood samples can be a new approach for highly accurate diagnosis and monitoring of the CC. Method Using a bioinformatics approach, we designed a panel of 24 genes associated with CC to detect and characterize patterns of somatic single-nucleotide variations, indels, and copy number variations. Our NGS CC panel covers most of the genes in The Cancer Genome Atlas (TCGA) as well as additional cancer driver and tumor suppressor genes. We profiled the variants in ctDNA from 24 CC patients who were being treated with systemic chemotherapy and local radiotherapy at the Jeonbuk National University Hospital, Korea. Result Eighteen out of 24 genes in our NGS CC panel had mutations across the 24 CC patients, including somatic alterations of mutated genes (ZFHX3-83%,KMT2C-79%, KMT2D-79%, NSD1-67%,ATM-38% andRNF213-27%). We demonstrated that theRNF213mutation could be used potentially used as a monitoring marker for response to chemo- and radiotherapy. Conclusion We developed our NGS CC panel and demostrated that our NGS panel can be useful for the diagnosis and monitoring of the CC, since the panel detected the common somatic variations in CC patients and we observed how these genetic variations change according to the treatment pattern of the patient

A Meta-Analysis of the Existing Knowledge of Immunoreactivity against Hepatitis C Virus (HCV)

Approximately 3% of the world population is infected by HCV, which represents a major global health challenge. Almost 400 different scientific reports present immunological data related to T cell and antibody epitopes derived from HCV literature. Analysis of all HCV-related epitope hosted in the Immune Epitope Database (IEDB), a repository of freely accessible immune epitope data, revealed more than 1500 and 1900 distinct T cell and antibody epitopes, respectively. The inventory of all data revealed specific trends in terms of the host and the HCV genotypes from which sequences were derived. Upon further analysis we found that this large number of epitopes reflects overlapping structures, and homologous sequences derived from different HCV isolates. To access and visualize this information we developed a novel strategy that assembles large sets of epitope data, maps them onto reference genomes and displays the frequency of positive responses. Compilation of the HCV immune reactivity from hundreds of different studies, revealed a complex and thorough picture of HCV immune epitope data to date. The results pinpoint areas of more intense reactivity or research activities at the level of antibody, CD4 and CD8 responses for each of the individual HCV proteins. In general, the areas targeted by the different effector immune functions were distinct and antibody reactivity was positively correlated with hydrophilicity, while T cell reactivity correlated with hydrophobicity. At the sequence level, epitopes frequently recognized by both T cell and B cell correlated with low variability, and our analysis thus highlighted areas of potential interest for practical applications. The human reactivity was further analyzed to pinpoint differential patterns of reactivity associated with acute versus chronic infection, to reveal the apparent impact of glycosylation on T cell, but not antibody responses, and to highlight a paucity of studies involved antibody epitopes associated with virus neutralization

A Detailed Analysis of the Murine TAP Transporter Substrate Specificity

The transporter associated with antigen processing (TAP) supplies cytosolic peptides into the endoplasmic reticulum for binding to major histocompatibility complex (MHC) class I molecules. Its specificity therefore influences the repertoire of peptides presented by MHC molecules. Compared to human TAP, murine TAP's binding specificity has not been characterized as well, even though murine systems are widely used for basic studies of antigen processing and presentation.We performed a detailed experimental analysis of murine TAP binding specificity by measuring the binding affinities of 323 peptides. Based on this experimental data, a computational model of murine TAP specificity was constructed. The model was compared to previously generated data on human and murine TAP specificities. In addition, the murine TAP specificities for known epitopes and random peptides were predicted and compared to assess the impact of murine TAP selectivity on epitope selection.Comparisons to a previously constructed model of human TAP specificity confirms the well-established differences for peptide substrates with positively charged C-termini. In addition these comparisons show that several residues at the N-terminus of peptides which strongly influence binding to human TAP showed little effect on binding to murine TAP, and that the overall influence of the aminoterminal residues on peptide affinity for murine TAP is much lower than for the human transporter. Murine TAP also partly prefers different hydrophobic amino acids than human TAP in the carboxyterminal position. These species-dependent differences in specificity determined in vitro are shown to correlate with the epitope repertoire recognized in vivo. The quantitative model of binding specificity of murine TAP developed herein should be useful for interpreting epitope mapping and immunogenicity data obtained in humanized mouse models

Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare?

A wide variety of techniques have been developed to homogenize transport equations in multiscale and multiphase systems. This has yielded a rich and diverse field, but has also resulted in the emergence of isolated scientific communities and disconnected bodies of literature. Here, our goal is to bridge the gap between formal multiscale asymptotics and the volume averaging theory. We illustrate the methodologies via a simple example application describing a parabolic transport problem and, in so doing, compare their respective advantages/disadvantages from a practical point of view. This paper is also intended as a pedagogical guide and may be viewed as a tutorial for graduate students as we provide historical context, detail subtle points with great care, and reference many fundamental works

Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820 controls) to identify pleiotropic loci. Findings were replicated in independent association studies (55,789 cases, 330,490 controls). We identified a novel pleiotropic association at 1q22 involving breast and lung squamous cell carcinoma, with eQTL analysis showing an association with ADAM15/THBS3 gene expression in lung. We also identified a known breast cancer locus CASP8/ALS2CR12 associated with prostate cancer, a known cancer locus at CDKN2B-AS1 with different variants associated with lung adenocarcinoma and prostate cancer, and confirmed the associations of a breast BRCA2 locus with lung and serous ovarian cancer. This is the largest study to date examining pleiotropy across multiple cancer-associated loci, identifying common mechanisms of cancer development and progression. Cancer Res; 76(17); 5103-14. ©2016 AACR

Traffic impact assessment and mitigation strategies for disruptions

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] This dissertation research focuses on modeling traffic conditions affected by disruptive events such as work zones, incidents, and hurricanes. Using a combination of field data and simulation experiments, this research tried to address the relationship between disruptive events and their impact on traffic conditions and driver behavior. The first half of the dissertation assesses the impact of work zones. First, a data-driven assessment of the traffic impact of work zones using different data sources was conducted. A tool was developed for practitioners to estimate the delay and travel times of planned work zones. Second, traffic flow and speed prediction models were developed for work zones in order to assist with the better scheduling of work activity. Machine learning approaches were used to develop the prediction models. In addition to work zone effects, the effects of another special event, baseball gameday conditions, were also studied and traffic prediction models were developed. Third, using naturalistic driving study data, classification algorithms categorized work zone events into crashes, nearcrashes, and baseline conditions. In the second half of the dissertation, the focus shifts to the effect of emergency on evacuation. Two chapters in this section present the results of different traffic management strategies -- 1) contraflow crossover and ramp closure optimization and 2) reservation-based intersection control in connected and autonomous vehicle environment

Research Progress on Conducting Polymer-Based Biomedical Applications

Conducting polymers (CPs) have attracted significant attention in a variety of research fields, particularly in biomedical engineering, because of the ease in controlling their morphology, their high chemical and environmental stability, and their biocompatibility, as well as their unique optical and electrical properties. In particular, the electrical properties of CPs can be simply tuned over the full range from insulator to metal via a doping process, such as chemical, electrochemical, charge injection, and photo-doping. Over the past few decades, remarkable progress has been made in biomedical research including biosensors, tissue engineering, artificial muscles, and drug delivery, as CPs have been utilized as a key component in these fields. In this article, we review CPs from the perspective of biomedical engineering. Specifically, representative biomedical applications of CPs are briefly summarized: biosensors, tissue engineering, artificial muscles, and drug delivery. The motivation for use of and the main function of CPs in these fields above are discussed. Finally, we highlight the technical and scientific challenges regarding electrical conductivity, biodegradability, hydrophilicity, and the loading capacity of biomolecules that are faced by CPs for future work. This is followed by several strategies to overcome these drawbacks

Urinary bisphenol A versus serum bisphenol A concentration and ovarian reproductive outcomes among IVF patients: Which is a better biomarker of BPA exposure?

© 2017, The Korean Society of Toxicogenomics and Toxicoproteomics and Springer Science+Business Media B.V., part of Springer Nature. Bisphenol A (BPA) is an endocrine-disrupting compound (EDC) that is used widely in commercial products in the production of polycarbonate plastics for baby and water bottles, epoxy resins for lacquer lining of food and beverage cans and water pipes, dental sealants, dental composites and thermal receipts paper. There is inhibitory effect of BPA on nuclear estrogen (E2) production in granulosa cells of developing follicles that disrupt normal development to the antral follicles via suppression of E2 in granulosa cells of developing follicles during the menstrual cycle followed by reduction in the number of oocytes retrieved in in-vitro fertilization (IVF) patients. Several studies corroborate an inverse association between serum and/or urinary BPA concentration and the IVF outcome: Peak E2 levels and the number of oocytes retrieved. Upon oral ingestion, 99.5% of unconjugated parent BPA (free BPA) is metabolized to either BPA glucuronide (BPA-G) or BPA sulfate (BPA-S). The unconjugated BPA can bind to the estrogen receptors (ER) while conjugated BPA (biologically inactive BPA) do not bind the estrogen receptor (ER). The challenge is to assess the relationship between BPA exposure among infertile patients with respect to follicular response and health during IVF. The establishment of temporal sequence between BPA exposure and infertility would be the research question to answer: Which route is a better biomarker? The advantages of urine BPA collection would provide pragmatic advantages for clinicians in order to practice cost-effective medicine. However, unconjugated BPA measurement (compared to total BPA) introduces challenges in measurement accuracy since unconjugated BPA requires higher magnitude of limit of detection (LOD) with higher risk of contamination from the medical equipment. The difference in route of BPA assessment could introduce bias in the interpretation of results in terms of the association between BPA levels and the number of oocytes. Fujimoto et al. and Bloom et al. analyzed the relationship between serum BPA and IVF outcome in infertile women. It may sound hypothetically justified due to utilizing serum unconjugated BPA, this strategy is not successful in choosing a practical biomarker of BPA exposure due to toxicokinetic properties of BPA metabolism and excretion in humans

Identification of Optimal Fermentation Temperature for Dry-Fermented Sausage Using Strains Isolated from Korean Fermented Foods

This study aims at identifying the optimal fermentation temperature for dry-fermented sausage using strains isolated from Kimchi (GK1, Pediococcus pentosaceus-GK1; NK3, P. pentosaceus-NK3), Doenjang (D1, Debaryomyces hansenii-D1), and commercial fermented sausage (S6, spontaneously generated Penicillium nalgiovense-S6). The microbial population, pH, moisture content, color, thiobarbituric acid reactive substance (TBARS), volatile basic nitrogen (VBN), and electronic nose (E-nose) were analyzed to identify the optimal fermentation temperature. The dry-fermented sausages were inoculated with three types of starter cultures [CS (commercial starter culture), GD (GK1 + D1 + S6), and ND (NK3 + D1 + S6)]. The fermentation was performed for 3 days at 20 °C and 25 °C, and dried for 28 days. The Lactobacillus spp. plate count and TBARS showed significantly higher values in the 25 °C group than in the 20 °C group (p Staphylococcus spp. plate count of GD and ND were significantly higher than CS group at all temperatures. On day 31, the moisture content and VBN values of all groups were less than 35 % and 20 mg%, respectively. According to E-nose, the highest amount of acetoin was detected at the GD group fermented at 25 °C. Thus, the optimal fermentation temperature is expected at 25 °C after using GD in the manufacturing of dry-fermented sausages