Imaging Electrical Properties Using MRI and In Vivo Applications

University of Minnesota Ph.D. dissertation. November 2015. Major: Biomedical Engineering. Advisor: Bin He. 1 computer file (PDF); viii, 137 pages.Electrical properties, namely conductivity and permittivity, describe the interaction of materials with the surrounding electromagnetic field. The electrical properties of biological tissue are associated with many fundamental aspects of tissue, such as cellular and molecular structure, ion concentration, cell membrane permeability, etc. Electrical properties of tissue in vivo can be used as biomarkers to characterize cancerous tissue or provide useful information in applications involving tissue and electromagnetic field. Among many related electrical-property imaging technologies, electrical properties tomography (EPT) is a promising one that noninvasively extracts the in vivo electrical properties with high spatial resolution based on measured B1 field using magnetic resonance imaging (MRI). In this thesis, advanced EPT methods have been developed to improve the imaging quality of conventional EPT. First of all, a multi-channel EPT framework was introduced to release its dependency on a B1 phase assumption and expand its application under high field strength. Secondly, a gradient-based EPT (gEPT) approach was proposed and implemented, showing enhanced robustness against effect of measurement noise and improved performance near tissue boundaries. Using gEPT, high resolution in vivo electrical-property images of healthy human brain were obtained, and an imaging system for rat tumor models was also developed. As a result of malignancy, increased conductivity was captured in tumors using the in vivo animal imaging system. Thirdly, based on EPT theory, quantitative water proton density imaging was proposed using measured B1 field information, provide a new way for estimating water content in tissue for diagnostic and research purpose

Improved test-retest reliability of R2∗\textit{R}_2^* and susceptibility quantification using multi-shot multi echo 3D EPI

This study aimed to evaluate the potential of 3D echo-planar imaging (EPI) for improving the reliability of $T_2^*$-weighted ($T_2^*w$) data and quantification of $\textit{R}_2^*$ decay rate and susceptibility ($\chi$) compared to conventional gradient echo (GRE)-based acquisition. Eight healthy subjects in a wide age range were recruited. Each subject received repeated scans for both GRE and EPI acquisitions with an isotropic 1 mm resolution at 3 T. Maps of $\textit{R}_2^*$ and $\chi$ were quantified and compared using their inter-scan difference to evaluate the test-retest reliability. Inter-protocol differences of $\textit{R}_2^*$ and $\chi$ between GRE and EPI were also measured voxel by voxel and in selected ROIs to test the consistency between the two acquisition methods. The quantifications of $\textit{R}_2^*$ and $\chi$ using EPI protocols showed increased test-retest reliability with higher EPI factors up to 5 as performed in the experiment and were consistent with those based on GRE. This result suggested multi-shot multi-echo 3D EPI can be a useful alternative acquisition method for $T_2^*w$ MRI and quantification of $\textit{R}_2^*$ and $\chi$ with reduced scan time, improved test-retest reliability and similar accuracy compared to commonly used 3D GRE.Comment: 18 pages, 8 figures and 1 tabl

Modeling Three-dimensional Invasive Solid Tumor Growth in Heterogeneous Microenvironment under Chemotherapy

A systematic understanding of the evolution and growth dynamics of invasive solid tumors in response to different chemotherapy strategies is crucial for the development of individually optimized oncotherapy. Here, we develop a hybrid three-dimensional (3D) computational model that integrates pharmacokinetic model, continuum diffusion-reaction model and discrete cell automaton model to investigate 3D invasive solid tumor growth in heterogeneous microenvironment under chemotherapy. Specifically, we consider the effects of heterogeneous environment on drug diffusion, tumor growth, invasion and the drug-tumor interaction on individual cell level. We employ the hybrid model to investigate the evolution and growth dynamics of avascular invasive solid tumors under different chemotherapy strategies. Our simulations reproduce the well-established observation that constant dosing is generally more effective in suppressing primary tumor growth than periodic dosing, due to the resulting continuous high drug concentration. In highly heterogeneous microenvironment, the malignancy of the tumor is significantly enhanced, leading to inefficiency of chemotherapies. The effects of geometrically-confined microenvironment and non-uniform drug dosing are also investigated. Our computational model, when supplemented with sufficient clinical data, could eventually lead to the development of efficient in silico tools for prognosis and treatment strategy optimization.Comment: 41 pages, 8 figure

Low expression of chloride channel accessory 1 predicts a poor prognosis in colorectal cancer

© 2014 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. Funded by Friends of ANCHOR NHS Grampian Endowment Fund. Grant Number: 12/50Peer reviewedPublisher PD

Exploring the Relationships Between Yield and Yield-Related Traits for Rice Varieties Released in China From 1978 to 2017

Despite evidence from previous case studies showing that agronomic traits partially determine the resulting yield of different rice (Oryza sativa L.) varieties, it remains unclear whether this is true at the ecotype level. Here, an extensive dataset of the traits of 7686 rice varieties, released in China from 1978 to 2017, was used to study the relationship between yield and other agronomic traits. We assessed the association between yield and other agronomic traits for four different rice ecotypes, i.e., indica inbred, indica hybrid, japonica inbred, and japonica hybrid. We found that associations between agronomic traits and yield were ecotype-dependent. For both the indica inbred and indica hybrid ecotypes, we found that greater values of certain traits, including the filled grain number per panicle, 1000-grain-weight, plant height, panicle length, grains per panicle, seed setting rate, long growth period, low panicle number per unit area, and low seed length/width ratio, have accounted for high grain yield. In the japonica inbred and japonica hybrid ecotypes, we found that only high panicle number per unit area and long growth period led to high grain yield. Indirectly, growth period consistently had a positive effect on yield in all ecotypes, and plant height had a positive effect on yield for the indicas and japonica inbred only. Plant height had a negative effect for the japonica hybrid. Altogether, our findings potentially have valuable implications for improving the breeds of rice ecotypes

Merging of Storm Time Midlatitude Traveling Ionospheric Disturbances and Equatorial Plasma Bubbles

Postsunset midlatitude traveling ionospheric disturbances (TIDs) and equatorial plasma bubbles (EPBs) were simultaneously observed over American sector during the geomagnetic storm on 8 September 2017. The characteristics of TIDs are analyzed by using a combination of the Millstone Hill incoherent scatter radar data and 2‐D detrended total electron content (TEC) from ground‐based Global Navigation Satellite System receivers. The main results associated with EPBs are as follows: (1) stream‐like structures of TEC depletion occurred simultaneously at geomagnetically conjugate points, (2) poleward extension of the TEC irregularities/depletions along the magnetic field lines, (3) severe equatorial and midlatitude electron density (Ne) bite outs observed by Defense Meteorological Satellite Program and Swarm satellites, and (4) enhancements of ionosphere F layer virtual height and vertical drifts observed by equatorial ionosondes near the EPBs initiation region. The stream‐like TEC depletions reached 46° magnetic latitudes that map to an apex altitude of 6,800 km over the magnetic equator using International Geomagnetic Reference Field. The formation of this extended density depletion structure is suggested to be due to the merging between the altitudinal/latitudinal extension of EPBs driven by strong prompt penetration electric field and midlatitude TIDs. Moreover, the poleward portion of the depletion/irregularity drifted westward and reached the equatorward boundary of the ionospheric main trough. This westward drift occurred at the same time as the sudden expansion of the convection pattern and could be attributed to the strong returning westward flow near the subauroral polarization stream region. Other possible mechanisms for the westward tilt are also discussed.Key PointsPostsunset EPBs driven by PPEF were observed to merge with midlatitude TIDs forming stream‐like depletion structures over American sectorDepletions reached 46 MLAT that map to 6,800 km over the equator and drifted westward reaching the equatorward boundary of the main troughStrong convection flow near SAPS region and disturbance thermospheric wind contributed to the westward drift of the midlatitude depletionsPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148412/1/swe20807.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148412/2/swe20807_am.pd

The causal association between smoking initiation, alcohol and coffee consumption, and women’s reproductive health: A two-sample Mendelian randomization analysis

Objective: A number of epidemiological studies have demonstrated that smoking initiation and alcohol and coffee consumption were closely related to women’s reproductive health. However, there was still insufficient evidence supporting their direct causality effect.Methods: We utilized two-sample Mendelian randomization (TSMR) analysis with summary datasets from genome-wide association study (GWAS) to investigate the causal relationship between smoking initiation, alcohol and coffee consumption, and women’s reproductive health-related traits. Exposure genetic instruments were used as variants significantly related to traits. The inverse-variance weighted (IVW) method was used as the main analysis approach, and we also performed MR-PRESSO, MR-Egger, weighted median, and weighted mode to supplement the sensitivity test. Then, the horizontal pleiotropy was detected by using MRE intercept and MR-PRESSO methods, and the heterogeneity was assessed using Cochran’s Q statistics.Results: We found evidence that smoking women showed a significant inverse causal association with the sex hormone-binding globulin (SHBG) levels (corrected β = −0.033, p = 9.05E-06) and age at menopause (corrected β = −0.477, p = 6.60E-09) and a potential positive correlation with the total testosterone (TT) levels (corrected β = 0.033, p = 1.01E-02). In addition, there was suggestive evidence for the alcohol drinking effect on the elevated TT levels (corrected β = 0.117, p = 5.93E-03) and earlier age at menopause (corrected β = −0.502, p = 4.14E-02) among women, while coffee consumption might decrease the female SHBG levels (corrected β = −0.034, p = 1.33E-03).Conclusion: Our findings suggested that smoking in women significantly decreased their SHBG concentration, promoted earlier menopause, and possibly reduced the TT levels. Alcohol drinking had a potential effect on female higher TT levels and earlier menopause, while coffee consumption might lead to lower female SHBG levels

Polyethylene microplastics alter soil microbial community assembly and ecosystem multifunctionality

Although pervasive microplastics (MPs) pollution in terrestrial ecosystems invites increasing global concern, impact of MPs on soil microbial community assembly and ecosystem multifunctionality received relatively little attention. Here, we manipulated a mesocosm experiment to investigate how polyethylene MPs (PE MPs; 0, 1%, and 5%, w/w) influence ecosystem functions including plant production, soil quality, microbial community diversity and assembly, enzyme activities in carbon (C), nitrogen (N) and phosphorus (P) cycling, and multifunctionality in the maize–soil continuum. Results showed that PE MPs exerted negligible effect on plant biomass (dry weight). The treatment of 5% PE MPs caused declines in the availability of soil water, C and P, whereas enhanced soil pH and C storage. The activity of C-cycling enzymes (α/β-1, 4-glucosidase and β-D-cellobiohydrolase) was promoted by 1% PE MPs, while that of β-1, 4-glucosidase was inhibited by 5% PE MPs. The 5% PE MPs reduced the activity of N-cycling enzymes (protease and urease), whereas increased that of the P-cycling enzyme (alkaline phosphatase). The 5% PE MPs shifted soil microbial community composition, and increased the number of specialist species, microbial community stability and networks resistance. Moreover, PE MPs altered microbial community assembly, with 5% treatment decreasing dispersal limitation proportion (from 13.66% to 9.96%). Overall, ecosystem multifunctionality was improved by 1% concentration, while reduced by 5% concentration of PE MPs. The activity of α/β-1, 4-glucosidase, urease and protease, and ammonium-N content were the most important predictors of ecosystem multifunctionality. These results underscore that PE MPs can alter soil microbial community assembly and ecosystem multifunctionality, and thus development and implementation of practicable solutions to control soil MPs pollution become increasingly imperative in sustainable agricultural production

Data Integration Analysis Indicates That Soil Texture and pH Greatly Influence the Acid Buffering Capacity of Global Surface Soils

Soil acidification is a global environmental issue that decreases soil functions, and it has been significantly accelerated by anthropogenic activities in recent decades. Soils can resist acidification upon receiving acid inputs due to the resistance or/and resilience capacity of soils, which is termed the acid buffering capacity of soils, and it is often indicated by the soil pH buffering capacity (pHBC). An increasing number of studies have been conducted to quantify soil pHBC at various sites, but to date, integration of global data is lacking; therefore, the variations in large-scale soil pHBC and the factors that influence these variations are still unclear. In this study, we collected previously published data on soil pHBC to analyze its variations on a large scale, as well as investigate the underlying factors influencing these variations. The results showed that soil pHBC varied substantially from site to site, with a mean of 51.07 ± 50.11 mmol kg−1 pH−1. Soil texture and pH, separately or collectively, explained a considerable proportion of the total variation of global soil pHBC. It is well-established that a series of processes contribute to the soil acid buffering capacity in different pH ranges, and the global data analyses showed that pH 5.5 could be a key threshold value; different buffering systems may be active at pH > 5.5 and pH < 5.5. Moreover, tropical soils were more acid-sensitive than temperate and subtropical soils, and forest soils had significantly lower soil pHBCs than grassland and cropland soils. This could be attributed in part to the different soil properties, such as soil texture or pH, among the different climatic zones and ecosystems