Digital Commons Network^™

Dynamic Localization Of Endoplasmic Reticulum During Tetrahymena Conjugation, Guerrier Sabrice, Michael Patterson, Kaitlin Crofton, Michael Tucker, Shyhiem Walker

Faculty Publications

Changes in lipid composition at membrane fusion sites in mating Tetrahymena are thought to involve the endoplasmic reticulum (ER), but its localization to these sites has not been observed. Here we show ER distribution during Tetrahymena mating using TtRET1-GFP and GFP-KDEL. We find that both markers localize to perinuclear membranes and tubular structures that connect perinuclear membrane to plasma membrane at fusion sites. Interestingly, both markers disappear from parental macronuclei after emergence of zygotic macronuclei. These similarities in localization of established ER marker, GFP-KDEL, and TtRET1-GFP reveal TtRET1-GFP as a useful new live cell marker for the ER in Tetrahymena.

Accurate Crystal Structure Prediction Of New 2d Hybrid Organic–Inorganic Perovskites, Nima Karimitari, William J. Baldwin, Evan W. Muller, Zachary J.L. Bare, W. Joshua Kennedy, Gábor Csányi, Christopher Sutton

Faculty Publications

Low-dimensional hybrid organic–inorganic perovskites (HOIPs) are promising electronically active materials for light absorption and emission. The design space of HOIPs is extremely large, as a variety of organic cations can be combined with different inorganic frameworks. This not only allows for tunable electronic and mechanical properties but also necessitates the development of new tools for in silico high throughput analysis of candidate materials. In this work, we present an accurate, efficient, and widely applicable machine learning interatomic potential (MLIP) trained on 86 diverse experimentally reported HOIP materials. This MLIP was tested on 73 experimentally reported perovskite compositions and achieves a …

High-Fidelity Machine Learning Techniques For Driver Drowsiness Detection, Yasser Ismail, Ebenezer Essel, Abeer Abdelhamid, Mahmoud Darwich, Fahmi Khalifa, Fred Lacy

Faculty Publications

It is devastating that daily, there is an ample number of car crashes that cause damage to automobiles, onboard passengers get injured, and others tend to lose their lives. Road crashes are fast rising across the globe and have drawn many road safety commissions and concerned individuals to discuss ways to reduce this menacing situation drastically. With the introduction of artificial intelligence and technological advancement, the government and state commissions have beckoned on the various universities and research institutions to develop methods to curb the rise of automobile crashes. Some causes of these crashes include drunk driving and drowsiness, the …

Footprint Tools Tiptoeing Towards Nitrogen Sustainability, James N. Galloway, Elizabeth A. Castner, Elizabeth S M Dukes, Jessica Fox, Allison M. Leach

Faculty Publications

As we face multiple environmental crises (e.g. climate change, nutrient pollution, freshwater scarcity), there is often a disconnect between an entity’s activities and the pollution resulting from that activity. Footprint tools help address this disconnect. They are effective in educating people, institutions and communities on how their resource use results in environmental pollution and what we can do to moderate that pollution. These tools connect an entity’s activities with the associated pollution. Footprint tools are also constantly evolving. As we better understand how to best estimate emissions—especially from sources further removed like those from the supply chain—the guidance and methods …

Footprint Tools Tiptoeing Towards Nitrogen Sustainability, James N. Galloway, Elizabeth A. Castner, Elizabeth S M Dukes, Jessica Fox, Allison M. Leach

Faculty Publications

As we face multiple environmental crises (e.g. climate change, nutrient pollution, freshwater scarcity), there is often a disconnect between an entity’s activities and the pollution resulting from that activity. Footprint tools help address this disconnect. They are effective in educating people, institutions and communities on how their resource use results in environmental pollution and what we can do to moderate that pollution. These tools connect an entity’s activities with the associated pollution. Footprint tools are also constantly evolving. As we better understand how to best estimate emissions—especially from sources further removed like those from the supply chain—the guidance and methods …

Beyond Covid: Towards A Transdisciplinary Synthesis For Understanding Responses And Developing Pandemic Preparedness In Alaska, Taylor P. Van Doren, Ryan A. Brown, Guangqing Chi, Patricia Cochran, Katie Cueva, Laura Eichelberger, Ruby Fried, Stacey Fritz, Micah B. Hahn, Ron Heintz, Davin Holen, Andrey N. Petrov

Faculty Publications

Pandemics are regularly occurring events, and there are foundational principles of pandemic preparation upon which communities, regions, states, and nations may draw upon for elevated preparedness against an inevitable future infectious disease threat. Many disciplines within the social sciences can provide crucial insight and transdisciplinary thinking for the development of preparedness measures. In 2023, the National Science Foundation funded a conference of circumpolar researchers and Indigenous partners to reflect on COVID-19-related research. In this article, we synthesise our diverse social science perspectives to: (1) identify potential areas of future pandemic-related research in Alaska, and (2) pose new research questions that …

Neurosymbolic Cognitive Methods For Enhancing Foundation Model-Based Reasoning, Kaushik Roy, Siyu Wu, Alessandro Oltramari

Faculty Publications

Foundation models have emerged as powerful tools, exhibiting extraordinary performance across various tasks, such as language processing, visual recognition, code generation, and human-centered engagement. However, recent studies have highlighted their limitations when grounded, abstract, and generalized reasoning capabilities are required. Complex tasks often involve multiple hierarchical reasoning steps, which are typical features of human thinking processes. In fact, in this chapter we claim that cognitively-inspired computational models, such as the so-called Common Model of Cognition, are key to enable complex reasoning within foundation model-based artificial intelligence (AI) systems. We investigate neurosymbolic approaches for mapping AI system components to those of …

Engineered Transcription Activator-Like Effector Dimer Proteins Confer Dna Loop-Dependent Gene Repression Comparable To Lac Repressor, Nicole A. Becker, Justin P. Peters, Elizabeth Lewis, Camden L. Daby, Karl Clark, L. James Maher

Faculty Publications

Natural prokaryotic gene repression systems often exploit DNA looping to increase the local concentration of gene repressor proteins at a regulated promoter via contributions from repressor proteins bound at distant sites. Using principles from the Escherichia coli lac operon we design analogous repression systems based on target sequence-programmable Transcription Activator-Like Effector dimer (TALED) proteins. Such engineered switches may be valuable for synthetic biology and therapeutic applications. Previous TALEDs with inducible non-covalent dimerization showed detectable, but limited, DNA loop-based repression due to the repressor protein dimerization equilibrium. Here, we show robust DNA loop-dependent bacterial promoter repression by covalent TALEDs and verify …

Association Between Bullying Victimization And Health Risk Behavior In Adolescents, Ana Beatriz Pacífico, Eliane Denise Araújo Bacil, Mariana Ardengue, Thiago Silva Piola, Michael Pereira Da Silva, Fabio Fontana, Ademar Avelar, Wagner De Campos

Faculty Publications

Objective: The aim of this study was to examine the association between bullying victimization and health risk behaviors in adolescents. Methods: A representative sample of 1020 adolescents participated in the study. The variables such as bullying, health risk behaviors (tobacco, drugs, alcohol, sedentary behavior, smartphone use, level of physical activity, and sleep), and economic status were assessed using self-reported questionnaires. Odds ratios with 95% confidence intervals (95%CI) were obtained using binary logistic regression and ordinal, gross, and adjusted logistic regression (p< 0.05). Results: Victims of bullying were more likely to smoke (OR 1.75; 95%CI 1.28–2.40), consume alcohol (OR1.43; 95%CI 1.05–1.94), have worse sleep quality (OR 1.94; 95%CI 1.28–2.91), and more sedentary behavior (OR 1.43; 95%CI 1.08–1.89) than those who were not bullied. However, victims were more likely to have high levels of physical activity than their non-bullied peers (OR 1.66; 95%CI 1.22–2.27). Conclusions: Bullying victimization was associated with an increased predisposition for the adoption of health risk behaviors. Interestingly, victims were also more prone to participate in physical activity.

Early Preclinical Studies Of Ergosterol Peroxide And Biological Evaluation Of Its Derivatives, Taotao Ling, Luz V. Arroyo-Cruz, William R. Smither, Emily K. Seighman, Michelle M. Martínez-Montemayor, Fatima Rivas

Faculty Publications

Ganoderma lucidum is a medicinal mushroom that produces various pharmacological compounds, including triterpenoids. A major bioactive component of G. lucidum is ergosterol peroxide (EP), which is attributed to its anticancer effects. The current study focuses on the in vitro ADME (absorption, distribution, metabolism, and elimination), in vivo efficacy and toxicity of EP, and the synthesis of new EP derivatives to improve aqueous solubility. It was found that EP is metabolically stable in liver microsomes and plasma. In vivo studies showed that EP inhibits tumor growth in murine cancer models, and it is well tolerated by mice. The maximum tolerated dose …

The Past And Future Of The Fisheries And Marine Ecosystem Model Intercomparison Project, Camilla Novaglio, Andrea Bryndum-Buchholz, Derek P. Tittensor, Tyler D. Eddy, Heike K. Lotze, Cheryl S. Harrison, Ryan F. Heneghan, Olivier Maury, Kelly Ortega-Cisneros, Colleen M. Petrik, Kelsey E. Roberts, Julia L. Blanchard

Faculty Publications

Climate change is increasingly affecting the world's ocean ecosystems, necessitating urgent guidance on adaptation strategies to limit or prevent catastrophic impacts. The Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) is a network and framework that provides standardised ensemble projections of the impacts of climate change and fisheries on ocean life and the benefits that it provides to people. Since its official launch in 2013 as a small, self-organized project within the larger Inter-Sectoral Impact Model Intercomparison Project, the FishMIP community has grown substantially and contributed to key international policy processes, such as the Intergovernmental Panel on Climate Change Assessment …

Too Sensitive Or Not Sensitive Enough? Sensitivity To Context And Justice-Involved Youths' Response To Violence Exposure, Colleen Sbeglia, Curtis Donovyn Smith, Paul J. Frick, Laurence Steinberg, Elizabeth Cauffman

Faculty Publications

With high rates of violence exposure among justice-involved youth, it is critical to identify factors that might impact the likelihood of youth engaging in violence themselves. One such factor is sensitivity to context, which describes how sensitive youth are to experiences in their environment. Using an ethnically diverse sample of justice-involved male adolescents (47% Latino, 38% Black/African American, 15% White) aged 13-17 at the time of their first arrest, the results of this study indicate that exposure to violence was related to increased violent behavior six months later, and this effect was strongest among youth who were low in sensitivity …

Far From Their Origins: A Transcriptomic Investigation On How 2,4-Di-Tert-Butyl-6-(5-Chloro-2h-Benzotriazol-2-Yl) Phenol Affects Rainbow Trout Alevins, Andreas N.M. Eriksson, Justin Dubiel, Alper James Alcaraz, Jon A. Doering, Steve Wiseman

Faculty Publications

Benzotriazole ultraviolet stabilizers (BUVSs) are a group of widely used chemicals added to a variety of consumer (e.g., plastics) and industrial (e.g., metal coating) goods. Although detected globally as an environmentally persistent pollutant, BUVSs have received relatively little toxicological attention and only recently have been acknowledged to affect development and the endocrine system in vivo. In our previous study, altered behavior, indicative of potential neurotoxicity, was observed among rainbow trout alevins (day 14 posthatching) that were microinjected as embryos with a single environmentally relevant dose of 2,4-di-tert-butyl–6-(5-chloro-2H-benzotriazol-2-yl) phenol (UV-327). In the present follow-up study, we performed whole-transcriptome profiling (RNA sequencing) …

Discarded Vehicle Tires And Their Association With Mosquito Vector Abundance Across Socioenvironmental Gradients In New Orleans, La, Rebeca De Jesús Crespo, Alexandros Pavlakis, Jennifer Breaux, Claudia Riegel

Faculty Publications

Discarded vehicle tires serve as habitat for mosquito vectors. In New Orleans, Louisiana, discarded tires are an increasingly important public concern, especially considering that the city is home to many medically important mosquito species. Discarded tires are known to be associated with mosquito abundance, but how their presence interacts with other socioenvironmental gradients to influence mosquito ecology is poorly understood. Here, we ask whether discarded tire distribution could be explained by social factors, particularly median income, home vacancy and human population density, and whether these factors interact with urban heat islands (UHI) to drive mosquito vector assemblages. We surveyed tire …

The Structure Of The Sufs–Sufe Complex Reveals Interactions Driving Protected Persulfide Transfer In Iron-Sulfur Cluster Biogenesis, Rajleen K. Gogar, Nidhi Chhikara, Minh Vo, Nathaniel C. Gilbert, Jack A. Dunkle, Patrick A. Frantom

Faculty Publications

Fe-S clusters are critical cofactors for redox chemistry in all organisms. The cysteine desulfurase, SufS, provides sulfur in the SUF Fe-S cluster bioassembly pathway. SufS is a dimeric, pyridoxal 5'-phosphate-dependent enzyme that uses cysteine as a substrate to generate alanine and a covalent persulfide on an active site cysteine residue. SufS enzymes are activated by an accessory transpersulfurase protein, either SufE or SufU depending on the organism, which accepts the persulfide product and delivers it to downstream partners for Fe-S assembly. Here, using Escherichia coli proteins, we present the first X-ray crystal structure of a SufS/SufE complex. There is a …

Reconstructive Evolutionary Morphology: Tracing The Historical Process Of Modifications Of Complex Systems Driven By Natural Selection Through Changing Ecological Conditions, Dominique G. Homberger

Faculty Publications

There is general consensus among evolutionary biologists that natural selection drives phenotypic modifications within populations over generational time. How to reconstruct this historical process, however, has been discussed mostly in theoretical terms, and recommendations and explanations on how to translate such theoretical insights into practice are needed. The present study aims at providing a theory-supported practical guide on how to reconstruct historical evolutionary processes by applying a morphology-centered approach through a series of interdependent steps of descriptive morphology, functional analysis, ecological observation, integration of paleoecological data, and evolutionary synthesis. Special attention is given to the development of tests regarding the …

Toward A Comparative Framework For Studies Of Altitudinal Migration, David Vander Pluym, Nicholas A. Mason

Faculty Publications

The study and importance of altitudinal migration has attracted increasing interest among zoologists. Altitudinal migrants are taxonomically widespread and move across altitudinal gradients as partial or complete migrants, subjecting them to a wide array of environments and ecological interactions. Here, we present a brief synthesis of recent developments in the field and suggest future directions toward a more taxonomically inclusive comparative framework for the study of altitudinal migration. Our framework centers on a working definition of altitudinal migration that hinges on its biological relevance, which is scale-dependent and related to fitness outcomes. We discuss linguistic nuances of altitudinal movements and …

Insights From Augmented Data Integration And Strong Regularization In Drug Synergy Prediction With Synergnet, Mengmeng Liu, Gopal Srivastava, J. Ramanujam, Michal Brylinski

Faculty Publications

SynerGNet is a novel approach to predicting drug synergy against cancer cell lines. In this study, we discuss in detail the construction process of SynerGNet, emphasizing its comprehensive design tailored to handle complex data patterns. Additionally, we investigate a counterintuitive phenomenon when integrating more augmented data into the training set results in an increase in testing loss alongside improved predictive accuracy. This sheds light on the nuanced dynamics of model learning. Further, we demonstrate the effectiveness of strong regularization techniques in mitigating overfitting, ensuring the robustness and generalization ability of SynerGNet. Finally, the continuous performance enhancements achieved through the integration …

Shifting Baselines: Visualizing Climate Change In America’S National Parks, Lee Lines

Faculty Publications

No abstract provided.

Predicting Poor Mental Health Among Older Syrian Refugees In Lebanon During The Covid-19 Pandemic: A Nested Cross-Sectional Study, Berthe Abi Zeid, Leen Farouki, Tanya El Khoury, Abla M. Sibai, Carlos Mendes F. De Leon, Marwan F. Alawieh, Zeinab Ramadan, Sawsan Abdulrahim, Hala Ghattas Ph.D., Stephen J. Mccall

Faculty Publications

Background: Post-term pregnancy, defined as reaching or exceeding 42 + 0 weeks of gestation, is known to be associated with unfavourable birth outcomes. High-income countries have responded to this risk by widely adopting labour induction protocols in late-term, but many low- and middle-income countries have not. However, understanding underlying mechanisms linking post-term births to adverse newborn and infant outcomes remains limited.

Objective:To investigate the (a) prevalence of post-term, (b) the risk factors associated with post-term (c) the association between post-term births and the risk of smallfor-gestational-age (SGA) neonates and of infant mortality in middle-income settings.

Methods:We used existing …

Neuronal Injury Model Divulges Differences In Dendrite And Axonal Function And Regeneration In Adults, Lauren S. Vaughn, Jinyoung Lee

Faculty Publications

No abstract provided.

Utilisation Of The Site Assessment Energy Indices For Aquaculture In Exposed Waters: Biology, Technology, Operations And Maintenance, Kevin G. Heasman, Tyler Sclodnick, Nils Goseberg, Nicholas Scott, Michael Chambers, Tobias Dewhurst, Samuel Rickerich, Heidi Moe Føre, Bela H. Buck

Faculty Publications

When moving from a very sheltered aquaculture site to a very exposed oceanic aquaculture site, the energy increases proportionally in a continuum. Lojek et al. (in review) considered the primary influential parameters (water current, wave height, wave period, wavelength and water depth) which influence the species, structure, technology, methods, and operational aspects of any aquaculture endeavour and investigated six possible indices which cover these variables. Added to advanced computer modelling, assisted by detailed and constant environmental monitoring, it may be possible to refine site selection, structure selection and design, species selection, equipment and logistic requirements and health and safety requirements. …

Improvement Of Single-Crystal Structures Of Very Heavy Element Compounds By Refining Anomalous Dispersion Parameters, Florian Meurer, Gregory Morrison, Birgit Hischa, Hans Conrad Zur Loye, Christoph Hennig, Michael Bodensteiner

Faculty Publications

Refining the anomalous dispersion parameters of the four uranium compounds NaUF5, NaU2F9, Cs2(UO2)TiO4, and Cs2(UO2)Ti2O6 gave insights into the crystallographic model improvement of very heavy atoms. We found that the values for the dispersive and absorptive parts, f′ and f″, closely followed the X-ray absorption spectra on their L3, L2, and L1 edges. The obtained values are sensitive to the chemical environment at each crystallographically independent position. An incorrect treatment of the anomalous dispersion correction can lead to a wrong crystallographic model. The above-mentioned, already published structures were improved by this process. General guidelines were given for the crystal structure …

Photoactivated Cyclic Polyphthalaldehyde Microcapsules For Payload Delivery, Youngsu Shin, Jared M. Schwartz, Anthony C. Engler, Brad Jones, Oleg Davydovich, Paul A. Kohl

Faculty Publications

Microcapsules with a cyclic polyphthalaldehyde (cPPA) shell and oil core were fabricated by an emulsification process. The low ceiling temperature cPPA shell was made phototriggerable by incorporating a photoacid generator (PAG). Photoactivation of the PAG created a strong acid which catalyzed cPPA depolymerization, resulting in the release of the core payload, as quantified by 1H NMR. The high molecular weight cPPA (197 kDa) yielded uniform spherical microcapsules. The core diameter was 24.8 times greater than the cPPA shell thickness (2.4 to 21.6 μm). Nonionic bis(cyclohexylsulfonyl)diazomethane (BCSD) and N-hydroxynaphthalimide triflate (HNT) PAGs were used as the PAG in the microcapsule shells. …

A Tribute To Gregory A. Voth, Jaehyeok Jin, William G. Noid, Jianing Li, Revati Kumar, Jianshu Cao, Seogjoo Jang, Francesco Paesani, David Reichman

Faculty Publications

No abstract provided.

Building A Simplistic Automatic Extruder: Instrument Development Opportunities For The Laboratory, Stefanie Klisch, Dylan Gilbert, Emma Breaux, Aliyah Dalier, Sudipta Gupta, Bruno Jakobi, Gerald J. Schneider

Faculty Publications

This work presents an automatic extruder as a research experience for undergraduate students. The system offers a user-friendly approach to preparing vesicles, such as liposomes or polymersomes, with a defined size and polydispersity─properties crucial for research in biology and macromolecules. It comprises two syringe pumps connected by a membrane filter. The setup is controlled by software. Compared to manual extrusion, this automated system provides advantages, such as precisely controlled variables. The project describes a tool to enhance undergraduate learning in science and engineering laboratories. Building an automatic extruder serves as a simplified model of a complex industrial process. It offers …

Partial In-Vitro Dispersal Of S. Mutans Ua159 Biofilms By Silver-(I)Cyanoximate Compounds, Brendaliz Santiago Narvaez, Sarah Hameer, Jamie L. Perry, Tiffany Rojas, Laurel G. Habgood

Faculty Publications

Silver(I) cyanoximate compounds have antibacterial activity against the oral pathogen Streptococcus mutans, a resident of oral plaque biofilm. As oral biofilm strategies focus on the inhibition of attachment or physical removal of the existing microbes, we were interested in exploring the ability of six different silver(I) cyanoximate compounds to target and disperse a pre-existing biofilm. Here we report that these compounds were only able to partially disperse S. mutans biofilms as the compounds were more effective at inhibiting biofilm formation. None of the six compounds were able to outperform silver nitrate, a commonly used antibacterial in dentistry.

Dominant Role Of Grazing And Snow Cover Variability On Vegetation Shifts In The Drylands Of Kazakhstan, Venkatesh Kolluru, Ranjeet John, Jiquan Chen, Preethi Konkathi, Srinivas Kolluru, Sakshi Saraf, Geoffrey M. Henebry, Jingfeng Xiao, Khushboo Jain, Maira Kussainova

Faculty Publications

Decomposing the responses of ecosystem structure and function in drylands to changes in human-environmental forcing is a pressing challenge. Though trend detection studies are extensive, these studies often fail to attribute them to potential spatiotemporal drivers. Most attribution studies use a single empirical model or a causal graph that cannot be generalized or extrapolated to larger scales or account for spatial changes and multiple independent processes. Here, we proposed and tested a multi-stage, multi-model framework that detects vegetation trends and attributes them to ten independent social-environmental system (SES) drivers in Kazakhstan (KZ). The time series segmented residual trend analysis showed …

Dominant Role Of Grazing And Snow Cover Variability On Vegetation Shifts In The Drylands Of Kazakhstan, Venkatesh Kolluru, Ranjeet John, Jiquan Chen, Preethi Konkathi, Srinivas Kolluru, Sakshi Saraf, Geoffrey M. Henebry, Jingfeng Xiao, Khushboo Jain, Maira Kussainova

Faculty Publications

Decomposing the responses of ecosystem structure and function in drylands to changes in human-environmental forcing is a pressing challenge. Though trend detection studies are extensive, these studies often fail to attribute them to potential spatiotemporal drivers. Most attribution studies use a single empirical model or a causal graph that cannot be generalized or extrapolated to larger scales or account for spatial changes and multiple independent processes. Here, we proposed and tested a multi-stage, multi-model framework that detects vegetation trends and attributes them to ten independent social-environmental system (SES) drivers in Kazakhstan (KZ). The time series segmented residual trend analysis showed …

Acousto-Dielectric Tweezers Enable Independent Manipulation Of Multiple Particles, Liang Shen, Zhenhua Tian, Kaichun Yang, Joseph Rich, Jinxin Zhang, Jianping Xia, Wesley Collyer, Brandon Lu, Nanjing Hao, Zhichao Pei, Chuyi Chen, Tony Jun Huang

Faculty Publications

Acoustic tweezers have gained substantial interest in biology, engineering, and materials science for their label-free, precise, contactless, and programmable manipulation of small objects. However, acoustic tweezers cannot independently manipulate multiple microparticles simultaneously. This study introduces acousto-dielectric tweezers capable of independently manipulating multiple microparticles and precise control over intercellular distances and cyclical cell pairing and separation for detailed cell-cell interaction analysis. Our acousto-dielectric tweezers leverage the competition between acoustic radiation forces, generated by standing surface acoustic waves (SAWs), and dielectrophoretic (DEP) forces, induced by gradient electric fields. Modulating these fields allows for the precise positioning of individual microparticles at points where …