Digital Commons Network^™

The Need For A Framework Addressing The Temporal Aspects Of Fish Sperm Motility Leading To Community-Level Standardization, Harvey Blackburn, Leticia Torres, Yue Liu, Terrence R. Tiersch

Faculty Publications

Motility is a widely available parameter that can be used to assess sperm quality of aquatic species. Sperm from fishes with external fertilization usually undergo a dynamic and short-lived period of motility after activation. The common practice of assigning a single value at an arbitrary peak of motility presents challenges for reproducibility, community-level standardization, and comparisons across studies. This study aimed to explore statistical approaches to standardize motility reporting, and to develop an initial framework for community-level standards. Sperm samples from 14 zebrafish (Danio rerio) with a total of 21,705 cells were analyzed by use of computer-assisted sperm analysis with …

Valley-Floor Snowfall In Taylor Valley, Antarctica, From 1995 To 2017: Spring, Summer And Autumn, Madeline E. Myers, Peter T. Doran, Krista F. Myers

Faculty Publications

We present an analysis of the 20 year snowfall dataset in Taylor Valley and the results of a new snow cover monitoring study. Snowfall has been measured at four sites in Taylor Valley from 1995 to 2017. We focus on valley-floor snowfall when wind does not exceed 5 m s-1, and we exclude winter from our analysis due to poor data quality. Snowfall averaged 11 mm water equivalent (w.e.) from 1995 to 2017 across all stations and ranged from 1 to 58 mm w.e. Standard deviations ranged from 3 to 17 mm w.e., highlighting the strong interannual variability of snowfall …

Weak Thermal State Quadrature-Noise Shadow Imaging, Pratik J. Barge, Ziqi Niu, Savannah L. Cuozzo, Eugeniy E. Mikhailov, Irina Novikova, Hwang Lee, Lior Cohen

Faculty Publications

In this work, we theoretically and experimentally demonstrate the possibility to create an image of an opaque object using a few-photon thermal optical field. We utilize the quadrature-noise shadow imaging (QSI) technique that detects the changes in the quadrature-noise statistics of the probe beam after its interaction with an object. We show that such a thermal QSI scheme has an advantage over the classical differential imaging when the effect of dark counts is considered. At the same time, the easy availability of thermal sources for any wavelength makes the method practical for broad range of applications, not accessible with, e.g., …

Alteration Of Biomolecular Conformation By Aluminum-Implications For Protein Misfolding Disease, Yuhai Zhao, Aileen I. Pogue, Peter N. Alexandrov, Leslie G. Butler, Wenhong Li, Vivian R. Jaber, Walter J. Lukiw

Faculty Publications

The natural element aluminum possesses a number of unique biochemical and biophysical properties that make this highly neurotoxic species deleterious towards the structural integrity, conformation, reactivity and stability of several important biomolecules. These include aluminum’s (i) small ionic size and highly electrophilic nature, having the highest charge density of any metallic cation with a Z²/r of 18 (ionic charge +3, radius 0.5 nm); (ii) inclination to form extremely stable electrostatic bonds with a tendency towards covalency; (iii) ability to interact irreversibly and/or significantly slow down the exchange-rates of complex aluminum–biomolecular interactions; (iv) extremely dense electropositive charge with one …

Invited Perspective: Existing Rules For Disinfection By-Products Are Good, But They Are Not Enough, Susan D. Richardson

Faculty Publications

No abstract provided.

A Machine Learning Framework For Detecting Covid-19 Infection Using Surface-Enhanced Raman Scattering, Eloghosa Ikponmwoba, Okezzi Ukorigho, Parikshit Moitra, Dipanjan Pan, Manas Ranjan Gartia, Opeoluwa Owoyele

Faculty Publications

In this study, we explored machine learning approaches for predictive diagnosis using surface-enhanced Raman scattering (SERS), applied to the detection of COVID-19 infection in biological samples. To do this, we utilized SERS data collected from 20 patients at the University of Maryland Baltimore School of Medicine. As a preprocessing step, the positive-negative labels are obtained using Polymerase Chain Reaction (PCR) testing. First, we compared the performance of linear and nonlinear dimensionality techniques for projecting the high-dimensional Raman spectra to a low-dimensional space where a smaller number of variables defines each sample. The appropriate number of reduced features used was obtained …

Bio-Inspired Geotechnical Engineering: Principles, Current Work, Opportunities And Challenges, Alejandro Martinez, Jason Dejong, Idil Akin, Ali Aleali, Chloe Arson, Jared Atkinson, Paola Bandini, Tugce Baser, Rodrigo Borela, Ross Boulanger, Matthew Burrall, Yuyan Chen, Clint Collins, Douglas Cortes, Sheng Dai, Theodore Dejong, Emanuela Del Dottore, Kelly Dorgan, Richard Fragaszy, J. David Frost, Robert Full, Majid Ghayoomi, Daniel I. Goldman, Nicholas Gravish, Ivan L. Guzman, James Hambleton, Elliot Hawkes, Michael Helms, David Hu, Lin Huang, Sichuan Huang, Christopher Hunt, Duncan Irschick

Faculty Publications

A broad diversity of biological organisms and systems interact with soil in ways that facilitate their growth and survival. These interactions are made possible by strategies that enable organisms to accomplish functions that can be analogous to those required in geotechnical engineering systems. Examples include anchorage in soft and weak ground, penetration into hard and stiff subsurface materials and movement in loose sand. Since the biological strategies have been 'vetted' by the process of natural selection, and the functions they accomplish are governed by the same physical laws in both the natural and engineered environments, they represent a unique source …

Systematic Overexpression Of Genes Encoded By Mycobacteriophage Waterfoul Reveals Novel Inhibitors Of Mycobacterial Growth, Danielle Heller, Isabel Amaya, Aleem Mohamed, Ilzat Ali, Dmitri Mavrodi, Padraig Deighan, Viknesh Sivanathan

Faculty Publications

Bacteriophages represent an enormous reservoir of novel genes, many of which are unrelated to existing entries in public databases and cannot be assigned a predicted function. Characterization of these genes can provide important insights into the intricacies of phage–host interactions and may offer new strategies to manipulate bacterial growth and behavior. Overexpression is a useful tool in the study of gene-mediated effects, and we describe here the construction of a plasmid-based overexpression library of a complete set of genes for Waterfoul, a mycobacteriophage closely related to those infecting clinically important strains of Mycobacterium tuberculosis and/or Mycobacterium abscessus. The arrayed …

Optimising Predictive Models To Prioritise Viral Discovery In Zoonotic Reservoirs, Daniel J. Becker, Gregory F. Albery, Anna R. Sjodin, Timothée Poisot, Laura M. Bergner, Binqi Chen, Lily E. Cohen, Tad Dallas, Evan A. Eskew, Anna C. Fagre, Maxwell J. Farrell, Sarah Guth, Barbara A. Han, Nancy B. Simmons, Michiel Stock, Emma C. Teeling, Colin J. Carlson

Faculty Publications

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use the bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of probable reservoir hosts. In early 2020, we generated an ensemble of eight statistical models that predicted host–virus associations and …

Invigorating Seventh-Day Adventist Science Education With Chemical Knowledge Of God's Creation, Ryan T. Hayes, D. David Nowack

Faculty Publications

No abstract provided.

Sorption Of Cellulases In Biofilm Enhances Cellulose Degradation By Bacillus Subtilis, Yijie Deng, Shiao Y. Wang

Faculty Publications

Biofilm commonly forms on the surfaces of cellulosic biomass but its roles in cellulose degradation remain largely unexplored. We used Bacillus subtilis to study possible mechanisms and the contributions of two major biofilm components, extracellular polysaccharides (EPS) and TasA protein, to submerged biofilm formation on cellulose and its degradation. We found that biofilm produced by B. subtilis is able to absorb exogenous cellulase added to the culture medium and also retain self-produced cellulase within the biofilm matrix. The bacteria that produced more biofilm degraded more cellulose compared to strains that produced less biofilm. Knockout strains that lacked both EPS and …

Does Sea Spray Aerosol Contribute Significantly To Aerosol Trace Element Loading? A Case Study From The U.S. Geotraces Pacific Meridional Transect (Gp15), Chris M. Marsay, William M. Landing, Devon Umstead, Claire P. Till, Robert Freiberger, Jessica N. Fitzsimmons, Nathan T. Lanning, Alan Shiller, Mariko Hatta, Rebecca Chmiel, Mak Saito, Clifton S. Buck

Faculty Publications

Atmospheric deposition represents a major input for micronutrient trace elements (TEs) to the surface ocean and is often quantified indirectly through measurements of aerosol TE concentrations. Sea spray aerosol (SSA) dominates aerosol mass concentration over much of the global ocean, but few studies have assessed its contribution to aerosol TE loading, which could result in overestimates of “new” TE inputs. Low-mineral aerosol concentrations measured during the U.S. GEOTRACES Pacific Meridional Transect (GP15; 152°W, 56°N to 20°S), along with concurrent towfish sampling of surface seawater, provided an opportunity to investigate this aspect of TE biogeochemical cycling. Central Pacific Ocean surface seawater …

How The “Blueprint” For Agriculture In Adventist Education Can Be Relevant In The 21st Century, Katherine Koudele

Faculty Publications

No abstract provided.

Strengthening Causal Inference From Randomised Controlled Trials Of Complex Interventions, Jef L. Leroy, Edward A. Frongillo Jr. Ph.D., Bezawit E. Kase, Silvia Alonso, Mario Chen, Ian Dohoo, Lieven Huybregts, Suneetha Kadiyala, Naomi M. Saville

Faculty Publications

Researchers conducting randomised controlled trials (RCTs) of complex interventions face design and analytical challenges that are not fully addressed in existing guidelines. Further guidance is needed to help ensure that these trials of complex interventions are conducted to the highest scientific standards while maximising the evidence that can be extracted from each trial. The key challenge is how to manage the multiplicity of outcomes required for the trial while minimising false positive and false negative findings. To address this challenge, we formulate three principles to conduct RCTs: (1) outcomes chosen should be driven by the intent and programme theory of …

Hair Zidovudine Concentrations Predict Virologic Outcomes Among People Living With Hiv/Aids In China, Yan Wu, Shuaifeng Liu, Liuxi Chu, Quan Zhang, Jin Yang, Shan Qiao, Xiaoming Li Ph.D., Yuejiao Zhou, Huihua Deng, Zhiyong Shen

Faculty Publications

Background: Hair antiretroviral concentrations are an objective and non-invasive measure of adherence to long-term antiretroviral therapy (ART) and can further predict virologic outcomes among people living with HIV/AIDS (PLWH). Zidovudine, one of the mainstream antiretrovirals in China, has been verified to have high reliability in adherence assessment, especially for its hair concentrations. However, data are limited in its predicting virologic outcomes. Therefore, this study aimed to characterize whether hair zidovudine concentrations can predict virologic suppression among Chinese PLWH compared with hair lamivudine concentrations and two self-reported measures, the overall frequency of adherence behaviors and percentage adherence. Methods: This cross-sectional study …

Effect Of Ultraviolet Light Treatment On Microbiological Safety And Quality Of Fresh Produce: An Overview, Veerachandra Yemmireddy, Achyut Adhikari, Juan Moreira

Faculty Publications

Fresh and fresh-cut fruits and vegetables have been associated in several foodborne illness outbreaks. Although investigations from those outbreaks reported that the contamination with pathogenic microorganisms may occur at any point in the farm to fork continuum, effective control strategies are still being widely investigated. In that direction, the concept of hurdle technology involving a sequence of different interventions have been widely explored. Among those interventions, ultraviolet (UV) light alone or in combination with other treatments such as use of organic acids or sanitizer solutions, has found to be a promising approach to maintain the microbiological safety and quality of …

Mir-489 Confines Uncontrolled Estrogen Signaling Through A Negative Feedback Mechanism And Regulates Tamoxifen Resistance In Breast Cancer, Mithil Soni, Ozge Saatci, Gourab Gupta, Yogin Patel, Manikanda Raja Keerthi Raja, Jie Li, Xinfeng Liu, Peisheng Xu Ph.D., Hongjun Wang, Daping Fan, Ozgur Sahin, Hexin Chen

Faculty Publications

Approximately 75% of diagnosed breast cancer tumors are estrogen-receptor-positive tumors and are associated with a better prognosis due to response to hormonal therapies. However, around 40% of patients relapse after hormonal therapies. Genomic analysis of gene expression profiles in primary breast cancers and tamoxifen-resistant cell lines suggested the potential role of miR-489 in the regulation of estrogen signaling and development of tamoxifen resistance. Our in vitro analysis showed that loss of miR-489 expression promoted tamoxifen resistance, while overexpression of miR-489 in tamoxifen-resistant cells restored tamoxifen sensitivity. Mechanistically, we found that miR-489 is an estrogen-regulated miRNA that negatively regulates estrogen receptor …

Completing Single-Cell Dna Methylome Profiles Via Transfer Learning Together With Kl-Divergence, Sanjeeva Dodlapati, Zongliang Jiang, Jiangwen Sun

Faculty Publications

The high level of sparsity in methylome profiles obtained using whole-genome bisulfite sequencing in the case of low biological material amount limits its value in the study of systems in which large samples are difficult to assemble, such as mammalian preimplantation embryonic development. The recently developed computational methods for addressing the sparsity by imputing missing have their limits when the required minimum data coverage or profiles of the same tissue in other modalities are not available. In this study, we explored the use of transfer learning together with Kullback-Leibler (KL) divergence to train predictive models for completing methylome profiles with …

Author Correction: In Situ Recording Of Mars Soundscape (Nature, (2022), 605, 7911, (653-658), 10.1038/S41586-022-04679-0), S. Maurice, B. Chide, N. Murdoch, R. D. Lorenz, D. Mimoun, R. C. Wiens, A. Stott, X. Jacob, T. Bertrand, F. Montmessin, N. L. Lanza, C. Alvarez-Llamas, S. M. Angel Ph.D., M. Aung, J. Balaram, O. Beyssac, A. Cousin, G. Delory, O. Forni, T. Fouchet, O. Gasnault, H. Grip, M. Hecht, J. Hoffman, J. Laserna, J. Lasue, J. Maki, J. Mcclean, P. Y. Meslin, S. Le Mouélic, S. Le Mouélic, A. Munguira

Faculty Publications

In the version of this article initially published, the Acknowledgements statement was missing the text “Part of this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004),” which has now been inserted in the HTML and PDF versions of the article.

Sexual Stature Difference Fluctuations In Pre- And Post-Black Death London As An Indicator Of Living Standards, Emily J. Brennan, Sharon Dewitte

Faculty Publications

Objectives: The degree of sexual stature difference (SSD), the ratio of male to female height, is argued to be an indicator of living standards based on evidence that physical growth for males is more sensitive to environmental fluctuations. In a resource-poor environment, the degree of SSD is expected to be relatively low. The aim of this study is to comparatively assess SSD in medieval London in the context of repeated famine events and other environmental stressors before the Black Death (BD) and the improved living conditions that characterized the post-Black Death period.

Methods: To test the hypothesis that a poor …

Parochial Altruism And Political Ideology, Marilynn B. Brewer, Nancy R. Buchan, Orgul D. Ozturk, Gianluca Grimalda

Faculty Publications

Parochial altruism refers to the propensity to direct prosocial behavior toward members of one's own ingroup to a greater extent than toward those outside one's group. Both theory and empirical research suggest that parochialism may be linked to political ideology, with conservatives more likely than liberals to exhibit ingroup bias in altruistic behavior. The present study, conducted in the United States and Italy, tested this relationship in the context of the COVID-19 pandemic, assessing willingness to contribute money to charities at different levels of inclusiveness—local versus national versus international. Results indicated that conservatives contributed less money overall and were more …

Structure-Property Investigations In Urea Tethered Iodinated Triphenylamines, Muhammad Saddam Hossain, Fiaz Ahmed, Stavros G. Karakalos, Mark D. Smith, Namrata Pant, Sophya V. Garashchuk, Andrew B, Greytak, Pablo Docampo, Linda S. Shimizu

Faculty Publications

Herein, we report structural, computational, and conductivity studies on urea-directed self-assembled iodinated triphenylamine (TPA) derivatives. Despite numerous reports of conductive TPAs, the challenges of correlating their solid-state assembly with charge transport properties hinder the efficient design of new materials. In this work, we compare the assembled structures of a methylene urea bridged dimer of di-iodo TPA (1) and the corresponding methylene urea di-iodo TPA monomer (2) with a di-iodo mono aldehyde (3) control. These modifications lead to needle shaped crystals for 1 and 2 that are organized by urea hydrogen bonding, π⋯π stacking, I⋯I, and I⋯π interactions as determined by …

Post-Embryonic Phase Transitions Mediated By Polycomb Repressive Complexes In Plants, Valerie Hinsch, Samuel Adkins, Darren Manuela, Mingli Xu

Faculty Publications

Correct timing of developmental phase transitions is critical for the survival and fitness of plants. Developmental phase transitions in plants are partially promoted by controlling relevant genes into active or repressive status. Polycomb Repressive Complex1 (PRC1) and PRC2, originally identified in Drosophila, are essential in initiating and/or maintaining genes in repressive status to mediate developmental phase transitions. Our review summarizes mechanisms in which the embryo-to-seedling transition, the juvenile-to-adult transition, and vegetative-to-reproductive transition in plants are mediated by PRC1 and PRC2, and suggests that PRC1 could act either before or after PRC2, or that they could function independently of each other. …

Optimised Adjoint Sensitivity Analysis Using Adjoint Guided Mesh Adaptivity Applied To Neutron Detector Response Calculations, Andrew G. Buchan, Dan Gabriel Cacuci, Steven Dargaville, Christopher C. Pain

Faculty Publications

This article presents a new approach for the efficient calculation of sensitivities in radiation dose estimates, subject to imprecisely known nuclear material cross-section data. The method is a combined application of adjoint-based models to perform, simultaneously, both the sensitivity calculation together with optimal adaptive mesh refinement. Adjoint-based sensitivity methods are known for their efficiency since they enable sensitivities of all parameters to be formed through only two solutions to the problem. However, the efficient solutions can also be obtained by their computation on optimal meshes, here guided by goal-based adjoint approaches. It is shown that both mesh adaptivity and sensitivity …

An Acoustofluidic Scanning Nanoscope Using Enhanced Image Stacking And Processing, Geonsoo Jin, Joseph Rich, Jianping Xia, Albert J. He, Chenglong Zhao, Tony Jun Huang

Faculty Publications

Nanoscale optical resolution with a large field of view is a critical feature for many research and industry areas, such as semiconductor fabrication, biomedical imaging, and nanoscale material identification. Several scanning microscopes have been developed to resolve the inverse relationship between the resolution and field of view; however, those scanning microscopes still rely upon fluorescence labeling and complex optical systems. To overcome these limitations, we developed a dual-camera acoustofluidic nanoscope with a seamless image merging algorithm (alpha-blending process). This design allows us to precisely image both the sample and the microspheres simultaneously and accurately track the particle path and location. …

Too Much Of A Good Thing? A Governing Knowledge Commons Review Of Abundance In Context, Brett M. Frischmann, Michael J. Madison, Madelyn R. Sanfilippo, Katherine J. Strandburg

Faculty Publications

The economics of abundance, along with the sociology of abundance, the law of abundance, and so forth, should be re-framed, linked, and situated in a common context for empirical rather than conceptual research. Abundance may seem to be a new, big thing, between anxiety over information overload, Big Data, and related technological disruptions. But scholars know that abundance is an ancient phenomenon, which only seemed to disappear as twentieth century social science focused on scarcity instead. Restoring the study of abundance, and figuring out how to solve the problems that abundance might create, means shedding disciplinary blinders and going back …

Future Orientation Among Children Affected By Parental Hiv In China: An Exploratory Analysis Of Complex Interactions, Heather L. Mcdaniel, Sayward Harrison, Amanda Fairchild, Xiaoming Li

Faculty Publications

We utilized an exploratory analytic approach to examine predictors of children's future beliefs, an internal asset associated with resilience among children affected by HIV, with emphasis on complex interactions among multisystem factors. Children (N = 1221) affected by parental HIV in China reported on psychosocial functioning, as well as internal, familial, and community resilience assets. Exploratory data analysis was conducted using a binary segmentation program. Six binary splits on predictors accounted for 22.78% of the variance in future expectation, suggesting interactions between children's perceived control of their future, loneliness, caregiver trust, and social support. Four binary splits accounted for …

Khsrp Loss Increases Neuronal Growth And Synaptic Transmission And Alters Memory Consolidation Through Rna Stabilization, Sarah L. Olguin, Priyanka Patel, Courtney N. Buchanan, Michela Dell'orco, Amy S. Gardiner, Robert Cole, Lauren S. Vaughn, Anitha Sundararajan, Joann Mudge, Andrea M. Allen, Pavel Ortinski, Jonathan L. Brigman, Jeffery L. Twiss, Nora L. Perrone-Bizzozero

Faculty Publications

KH-type splicing regulatory protein (KHSRP) regulates levels of several neuronal mRNAs linked to nervous system development and function.

The KH-type splicing regulatory protein (KHSRP) is an RNA-binding protein linked to decay of mRNAs with AU-rich elements. KHSRP was previously shown to destabilize Gap43 mRNA and decrease neurite growth in cultured embryonic neurons. Here, we have tested functions of KHSRP in vivo. We find upregulation of 1460 mRNAs in neocortex of adult Khsrp(-/-) mice, of which 527 bind to KHSRP with high specificity. These KHSRP targets are involved in pathways for neuronal morphology, axon guidance, neurotransmission and long-term memory. Khsrp(-/-) mice …

Circadiomics: Circadian Omic Web Portal, Muntaha Samad, Forest Agostinelli, Tomoki Sato, Kohei Shimaji, Pierre Baldi

Faculty Publications

Circadian rhythms are a foundational aspect of biology. These rhythms are found at the molecular level in every cell of every living organism and they play a fundamental role in homeostasis and a variety of physiological processes. As a result, biomedical research of circadian rhythms continues to expand at a rapid pace. To support this research, CircadiOmics (http://circadiomics.igb.uci.edu/) is the largest annotated repository and analytic web server for high-throughput omic (e.g. transcriptomic, metabolomic, proteomic) circadian time series experimental data. CircadiOmics contains over 290 experiments and over 100 million individual measurements, across >20 unique tissues/organs, and 11 different species. Users are …

Leaf Development In Medicago Truncatula, Liren Du, Samuel Winright Adkins, Mingli Xu

Faculty Publications

Forage yield is largely dependent on leaf development, during which the number of leaves, leaflets, leaf size, and shape are determined. In this mini-review, we briefly summarize recent studies of leaf development in Medicago truncatula, a model plant for legumes, with a focus on factors that could affect biomass of leaves. These include: floral development and related genes, lateral organ boundary genes, auxin biosynthesis, transportation and signaling genes, and WOX related genes.