Digital Commons Network^™

Deepbend: An Interpretable Model Of Dna Bendability, Samin Rahman Khan, Sadman Sakib, M Sohel Rahman, Md Abul Hassan Samee

Faculty, Staff and Students Publications

The bendability of genomic DNA impacts chromatin packaging and protein-DNA binding. However, we do not have a comprehensive understanding of the motifs influencing DNA bendability. Recent high-throughput technologies such as Loop-Seq offer an opportunity to address this gap but the lack of accurate and interpretable machine learning models still remains. Here we introduce DeepBend, a convolutional neural network model with convolutions designed to directly capture the motifs underlying DNA bendability and their periodic occurrences or relative arrangements that modulate bendability. DeepBend consistently performs on par with alternative models while giving an extra edge through mechanistic interpretations. Besides confirming the known …

Batf2 Promotes Hsc Myeloid Differentiation By Amplifying Ifn Response Mediators During Chronic Infection, Duy T Le, Marcus A Florez, Pawel Kus, Brandon T Tran, Bailee Kain, Yingmin Zhu, Kurt Christensen, Antrix Jain, Anna Malovannaya, Katherine Y King

Faculty, Staff and Students Publications

Basic leucine zipper ATF-like transcription factor 2 (BATF2), an interferon-activated immune response regulator, is a key factor responsible for myeloid differentiation and depletion of HSC during chronic infection. To delineate the mechanism of BATF2 function in HSCs, we assessed Batf2 KO mice during chronic infection and found that they produced less pro-inflammatory cytokines, less immune cell recruitment to the spleen, and impaired myeloid differentiation with better preservation of HSC capacity compared to WT. Co-IP analysis revealed that BATF2 forms a complex with JUN to amplify pro-inflammatory signaling pathways including CCL5 during infection. Blockade of CCL5 receptors phenocopied Batf2 KO differentiation …

Transcriptome, Proteome, And Protein Synthesis Within The Intracellular Cytomatrix, Tattym E Shaiken, Sandra L Grimm, Mohamad Siam, Amanda Williams, Abdol-Hossein Rezaeian, Daniel Kraushaar, Emily Ricco, Matthew J Robertson, Cristian Coarfa, Antrix Jain, Anna Malovannaya, Fabio Stossi, Antone R Opekun, Alyssa P Price, Julien Dubrulle

Faculty, Staff and Students Publications

Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, …

Alternative Polyadenylation Alters Protein Dosage By Switching Between Intronic And 3’Utr Sites, Nicola De Prisco, Caitlin Ford, Nathan D Elrod, Winston Lee, Lauren C Tang, Kai-Lieh Huang, Ai Lin, Ping Ji, Venkata S Jonnakuti, Lia Boyle, Maximilian Cabaj, Salvatore Botta, Katrin Õunap, Karit Reinson, Monica H Wojcik, Jill A Rosenfeld, Weimin Bi, Kristian Tveten, Trine Prescott, Thorsten Gerstner, Audrey Schroeder, Chin-To Fong, Jaya K George-Abraham, Catherine A Buchanan, Andrea Hanson-Khan, Jonathan A Bernstein, Aikaterini A Nella, Wendy K Chung, Vicky Brandt, Marko Jovanovic, Kimara L Targoff, Hari Krishna Yalamanchili, Eric J Wagner, Vincenzo A Gennarino

Faculty, Staff and Students Publications

Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' untranslated region (3'UTR), introns, or exons. Most studies focus on APA within the 3'UTR; however, here, we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function …

Endothelial-To-Osteoblast Transition In Normal Mouse Bone Development, Song-Chang Lin, Guoyu Yu, Yu-Chen Lee, Jian H Song, Xingzhi Song, Jianhua Zhang, Theocharis Panaretakis, Christopher J Logothetis, Yoshihiro Komatsu, Li-Yuan Yu-Lee, Guocan Wang, Sue-Hwa Lin

Faculty, Staff and Student Publications

Metastatic prostate cancer (PCa) in bone induces bone-forming lesions. We have previously shown that PCa-induced bone originates from endothelial cells (ECs) that have undergone EC-to-osteoblast (OSB) transition. Here, we investigated whether EC-to-OSB transition also occurs during normal bone formation. We developed an EC and OSB dual-color reporter mouse (DRM) model that marks EC-OSB hybrid cells with red and green fluorescent proteins. We observed EC-to-OSB transition (RFP and GFP co-expression) in both endochondral and intramembranous bone formation during embryonic development and in adults. Co-expression was confirmed in cells isolated from DRM. Bone marrow– and lung-derived ECs underwent transition to OSBs and …

Yield And Composition Of Forage Maize: Interaction Of Harvest Date, Cultivar And Plastic Mulch, E. M. Little, P. O'Kiely, J. C. Crowley, G. P. Keane

IGC Proceedings (1977-2023)

Forage maize is established as a crop with the potential to consistently supply high yields of quality forage on some Irish farms. Despite its success, considerable variability in crop yield, quality and maturity at harvest can exist from year to year. These reflect differing prevailing weather conditions, particularly temperature during May to September. The use of plastic mulch has increased the likelihood of achieving higher yields of high quality crops and has permitted maize production to extend into areas once considered unsuitable for the crop. In this experiment two cultivars of differing maturity were grown with or without plastic mulch …

Fermentation Characteristics Of Maize/Sesbania Bi-Crop Silage, M. Kondo, J. Yanagisawa, K. Kita, H. Yokota

IGC Proceedings (1977-2023)

Maize is one of the main forages for dairy production and is a suitable material for silage making because of high fermentable carbohydrates, high counts of lactic acid bacteria (LAB) and low buffering capacity (BC) (Nishino et al. 2003; McDonald et al. 1991). Whole crop maize silage is high in energy but low in crude protein (CP). On the other hand, legumes are high in CP but difficult to conserve because of their low water soluble carbohydrates (WSC) and high BC. It might be possible that maize/legume bi-crop silage compensate for their negative points. Sesbania is a legume originated …

Ensiling Of Tannin-Containing Sorghum Grain, E. M. Ott, Y. Acosta Aragón, M. Gabel

IGC Proceedings (1977-2023)

Sorghum is known as important feed-stuff in tropical regions where rainfall is insufficient for the cultivation of maize. Furthermore, those sorghum cultivars rich in tannins are naturally protected to a certain extent against bird damage, insect pests and moulds. Nevertheless, tannins impair the feed quality. Thus, the objectives of this study were to investigate whether ensiling could be a suitable preservation method for sorghum grain originally rich in tannins and if it is possible to reduce tannin content during fermentation.

Salivary Cortisol Analysis In Collegiate Female Lacrosse Athletes, Jenna L. Carter, Stephanie L. Mathews, Yvette L. Figueroa, Jennifer A. Bunn

International Journal of Exercise Science

International Journal of Exercise Science 16(6): 242-251, 2023. Cortisol is a hormone that corresponds to physiological and emotional stress. The purpose of this study was to 1) evaluate the changes in cortisol in female Division I collegiate lacrosse players (n = 15) throughout the competitive season, and 2) evaluate the correlation between cortisol and athlete wellness and workload. Salivary cortisol samples were collected weekly in the morning throughout the entirety of the 2021 competitive season (12 weeks). Subjective athlete total wellness scores and sub-scores (muscle soreness, sleep quality, fatigue, and stress) were taken on the same days. Objective total …

Adoption Ouroboros: Repeating The Cycle Of Adoption As Rescue, Malinda L. Seymore

Pepperdine Law Review

Ouroboros—the circular symbol of the snake eating its tail; an endless cycle. As the U.S. recently withdrew from Afghanistan in chaos and Russia invaded Ukraine, the attention of Americans turned, as it frequently has in times of international conflict, to the plight of children in need of rescue. For many Americans, rescue is synonymous with adoption. The history of international adoption began with rescues following America’s wars in Europe and Asia and continues today through other violent upheavals. International adoption is an ouroboros, repeating the pattern of adoption as a response to humanitarian crises. But as human and charitable as …

Effects Of Varying Dietary Ratios Of Lucerne To Maize Silage On Production And Microbial Protein Synthesis In Lactating Dairy Cows, G. A. Broderick, A. F. Brito

IGC Proceedings (1977-2023)

Lucerne silage (LS) is high in total CP and rumen degraded protein (RDP) but low in fermentable energy, while maize silage (MS) is a good source of fermentable energy but low in RDP. Thus, these silages are complementary and feeding them at optimum ratio should increase nutrient efficiency in lactating cows. Dhiman & Satter (1997) observed greater milk yield when the dietary forage was 2/3 LS and 1/3 MS. The objective of this experiment was to optimise the dietary LS:MS ratio for production, microbial protein and N utilisation.

Sustained Aerobic Stability Of By-Products Silage Stored As A Total Mixed Ration, N. Nishino, H. Hattori, H. Wada

IGC Proceedings (1977-2023)

Ensiling a total mixed ration (TMR) has been practiced in Japan when high-moisture by-products are used as ruminant feed. Wet brewers grains (BG) are a common feed resource and approximately one million t are produced annually. Nishino et al. (2003; 2004) reported that, although silage would easily deteriorate in the presence of air when wet BG were ensiled alone, the spoilage could be avoided when stored as a TMR. Interestingly, the resistance to deterioration was consistently found whether high (> 106 cfu/g) or no (/g) yeasts were detected at unloading. In this study, changes during ensilage and after exposure …

Effect Of Variety And Species On The Chemical Composition Of Lotus When Ensiled, C. L. Marley, R. Fychan, R. Jones

IGC Proceedings (1977-2023)

Research has shown that there are positive benefits from using Lotus as a grazing forage for ruminants. These findings warrant studies into the suitability of different varieties for silage production. In this experiment, we investigated the chemical composition of 13 birdsfoot trefoil varieties and 1 greater birdsfoot trefoil when ensiled.

Cob Development In Forage Maize: Influence Of Harvest Date, Cultivar And Plastic Mulch, E. M. Little, P. O'Kiely, J. C. Crowley, G. P. Keane

IGC Proceedings (1977-2023)

Forage maize grown for silage tends to be a compromise between reproductive and vegetative yield, and the cob component is the main driver of feeding value (Keane et al., 2003). Thus the aim is to produce a well-developed crop of high dry matter (DM) and starch content reflecting large cobs of well-filled grains rather than crops with low DM and starch contents reflecting poorly developed (immature) cob components at harvest. The use of plastic mulch can increase total DM yields with the increase in cob yield accounting for 75% of the total yield increase (Easson & Fearnehough, 1997). In …

The Influence Of Crop Maturity And Type Of Baler On Whole Crop Barley Silage Production, P. Lingvall, M. Knicky, B. Frank, B. Rustas, J. Wallsten

IGC Proceedings (1977-2023)

Bale ensiling is based on long cut forages. Earlier studies (Honig, 1984; 1987) have shown the importance of laceration and high density in preventing fungi growth and storage instability. On the other hand use of an efficient baling technology reduces the time between moving and wrapping of bale to less than 10 minutes with a combi-baler compared to two hours with a separate wrapper. Even during feeding late fermentation is restricted as the bale is fed within some hours after opening. Ensiling of whole crop cereals needs the addition of silage additives to avoid clostridial fermentation (Weissbach et al., …

Ndf Digestion In Dairy Cows Fed Grass Or Red Clover Silages Cut At Two Stages Of Growth, K. Kuoppala, S. Ahvenjärvi, M. Rinne, A. Vanhatalo

IGC Proceedings (1977-2023)

Increasing demand for organic dairy products has encouraged research on red clover, as it is an important plant species in organic farming systems. The objective of this experiment was to investigate the effects of plant species and growth stage on NDF digestion in dairy cows.

Effect Of Stage Of Maturity On The Nutrient Content Of Alfalfa, Y. Tyrolova, A. Vyborna

IGC Proceedings (1977-2023)

Alfalfa (Medicago sativa), one of the major agricultural crops in the Czech Republic, is grown on 15.8% of the arable land. Alfalfa silage forms a substantial part of diets for farm animals. It is very important to choose a suitable term of harvesting for ensilage from the view of optimal nutrient content. The stage of maturity at cutting has large effects on each component, except crude protein (Yu et al., 2004). Alfalfa can be difficult to ensile due to a high buffering capacity and a low WSC content.

Parameters Of Ensiled Maize With Biological And Chemical Additives, J. Grajewski, A. Potkański, K. Raczkowska-Werwińska, M. Twarużek, B. Miklaszewska

IGC Proceedings (1977-2023)

The amount of maize grown in Poland has increased rapidly. Nowadays it takes about 600,000 ha, 40% of which is used as silage. Changing climate in Poland, with dry summer followed by wet autumn with ground frost causes extensive moulds contamination and high presence of the fusarium toxins in the maize during the harvest. The norms accepted in the EU concerning the acceptable level of deoxynivalenol (DON) and zearalenol (ZON) in feedstuffs for cattle require detailed examination of this problem as it decides on the health quality and production results. The aim of the study was to evaluate the effects …

Assessing The Impacts Of Global Warming On Mangrove Plants Growth In Malaysia, Baseem Tamimi, Wan Juliana Wan Ahmad, Mohd Nizam Mohd Said, Che Radziah Che Mohd Zain

Al-Bahir

Climate change issues have sparked intense debate around the world in recent years. Malaysia faces critical issues with global warming, which has changed the local climate, threatening critical ecosystems, including mangrove forests, and creating challenges in their habitat. This study was conducted to investigate the morphological and physiological attributes of the mangrove Rhizophora apiculata in response to air temperature for the selection of tree species that can adapt to climate change. The seedlings were grown in controlled growth chambers with temperatures, of 21,28, and 38°C, under elevated CO2 at 650 ppm for three months. The plants were watered with three …

Gloria - A Globally Representative Hyperspectral In Situ Dataset For Optical Sensing Of Water Quality, Moritz K. Lehmann

School of Natural Resources: Faculty Publications

The development of algorithms for remote sensing of water quality (RSWQ) requires a large amount of in situ data to account for the bio-geo-optical diversity of inland and coastal waters. The GLObal Reflectance community dataset for Imaging and optical sensing of Aquatic environments (GLORIA) includes 7,572 curated hyperspectral remote sensing reflectance measurements at 1nm intervals within the 350 to 900nm wavelength range. In addition, at least one co-located water quality measurement of chlorophyll α, total suspended solids, absorption by dissolved substances, and Secchi depth, is provided. The data were contributed by researchers affiliated with 59 institutions worldwide and come from …

Point/Counterpoint: Transgender Sport Participation Policy, Matt Moore, Nafees Alam

Social Work Faculty Publications and Presentations

I am looking forward to a spirited point/counterpoint regarding the NCAA (2022) policy on transgender sport participation. The NCAA Board of Governors voted in support of a sport-by-sport approach to transgender participation that preserves opportunity for transgender student-athletes while balancing fairness, inclusion, and safety for all who compete. The national governing bodies for each sport will determine policies for transgender participation (e.g., USA Swimming). The NCAA policy became effective in January. The policy requires transgender student-athletes to document sport specific testosterone levels beginning four weeks before their sport’s championship selections. In the 2022-2023 competition season, transgender student-athletes will need documented …

The Integration Of Biopolymer-Based Materials For Energy Storage Applications: A Review., Shrey Dalwadi, Arnav Goel, Constantine Kapetanakis, David Salas-De La Cruz, Xiao Hu

College of Science & Mathematics Departmental Research

Biopolymers are an emerging class of novel materials with diverse applications and properties such as superior sustainability and tunability. Here, applications of biopolymers are described in the context of energy storage devices, namely lithium-based batteries, zinc-based batteries, and capacitors. Current demand for energy storage technologies calls for improved energy density, preserved performance overtime, and more sustainable end-of-life behavior. Lithium-based and zinc-based batteries often face anode corrosion from processes such as dendrite formation. Capacitors typically struggle with achieving functional energy density caused by an inability to efficiently charge and discharge. Both classes of energy storage need to be packaged with sustainable …

Breast Cancer Knowledge Among Students At A State Comprehensive University, Calvin Odhiambo, Shimia Hunter

Teacher-Scholar: The Journal of the State Comprehensive University

Background: Breast cancer is the most common cancer among women worldwide and the second-leading cause of death among women in the United States. While lack of knowledge about breast cancer is a key factor in breast cancer mortality, little is known about breast cancer knowledge among women and men under the age of 30. The goal of the current study was to investigate the knowledge and awareness of breast cancer among female and male undergraduate students at a State Comprehensive University in the Southeastern United States.

Methods: This was a cross-sectional survey of 265 male and female undergraduate …

Medical Leave And Unrealistic Ministry Expectations A Study At Zion Lutheran Church, Aaron G. Flatau

Doctor of Ministry Major Applied Project

A medical leave of absence due to a kidney transplant resulted in feelings of guilt and failure for a pastor when he was unable to fulfill his desired ministry tasks. These feelings of guilt and failure were speculated to be unwarranted.

To determine if these feelings were unwarranted, this paper researched sickness as presented in the Bible. Biblical research found illness to be a personal reminder of a global fall, found a link between forgiveness of sin and healing of sickness, and examined illness in the context of the Kingdom of God. Historical examination found that illness within the context …

Parp1 Associates With R-Loops To Promote Their Resolution And Genome Stability, Natalie Laspata, Parminder Kaur, Sofiane Yacine Mersaoui, Daniela Muoio, Zhiyan Silvia Liu, Maxwell Henry Bannister, Hai Dang Nguyen, Caroline Curry, John M. Pascal, Guy G. Poirier, Hong Wang, Jean-Yves Masson, Elise Fouquerel

Student Papers, Posters & Projects

PARP1 is a DNA-dependent ADP-Ribose transferase with ADP-ribosylation activity that is triggered by DNA breaks and non-B DNA structures to mediate their resolution. PARP1 was also recently identified as a component of the R-loop-associated protein-protein interaction network, suggesting a potential role for PARP1 in resolving this structure. R-loops are three-stranded nucleic acid structures that consist of a RNA-DNA hybrid and a displaced non-template DNA strand. R-loops are involved in crucial physiological processes but can also be a source of genome instability if persistently unresolved. In this study, we demonstrate that PARP1 binds R-loops in vitro and associates with R-loop formation …

The Student Movement Volume 107 Issue 16: Soul Lounge, Self-Care, And Stripple Breakfast Burritos: There's Something For Everyone, Solana Campbell, Gloria Oh, Caryn Cruz, Terika Williams, Skyler Campbell, Marcel Mattox, Andrew Francis, Katie Davis, Alexander J. Hess, Abby Shim, Reagan Mccain, Abraham Bravo, Lily Burke

The Student Movement v. 107 (2022-2023)

HUMANS

AU's Favorite Classes, Solana Campbell

Becoming Multilingual, Gloria Oh

Greatest Gazebo Orders, Solana Campbell

Interview with VP Nixon, Caryn Cruz

ARTS & ENTERTAINMENT

Currently: Babel, Terika Williams

That 90's Love: BSCF Soul Lounge, Skyler Campbell

The Therapist, Marcel Mattox

NEWS

Experience Andrews University's Community Adult Education, Gloria Oh

Joyful Resilience: An Art Experience at AU, Solana Campbell

Students Share Their African Heritage at Short Course, Andrew Francis

IDEAS

The Future of Self-Care, Katie Davis

The Straw that Breaks the Camel's Back? Beyoncé and the 2023 Grammys, Alexander J. Hess

Death Toll Passes 41,000: Turkey and Syria Earthquakes, Abby Shim …

Importance Of Snowmelt On Soil Nitrate Leaching To Groundwater – A Model Study, Sahila Beegum, Arindam Malakar, Chittaranjan Ray, Daniel D. Snow

Nebraska Water Center: Faculty Publications

The movement of nitrate to surface water bodies during snow accumulation and melting has been extensively studied, but there are only limited studies on the influence of snow processes on nitrate leaching to groundwater. The present study investigated the impact of snow processes on nitrate leaching to groundwater based on a simulation modeling approach using HYDRUS-1D. HYDRUS-1D model has a temperature threshold-based snow model in addition to water, solute, and heat simulation components. The snow component in HYDRUS-1D was previously not applied to snow simulation studies since the method does not consider a detailed physical and process-based representation of snow …

Characterizing The Consensus Residue Specificity And Surface Of Bcl-2 Binding To Bh3 Ligands Using The Knob-Socket Model, Jennifer Yi, Vivian Kellner, Hyun Joo, Nathaniel Chien, Shivarni Patel, Zaina Chaban, Jerry Tsai

Pacific Faculty Work

Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of …

Personalized Semantic Annotation Recommendations On Biomedical Content Through An Expanded Socio-Technical Approach, Asim Abbas, Steve Mbouadeu, Tahir Hameed, Syed Ahmad Chan Bukhari

Management Faculty Publications

There are huge on-going challenges to timely access of accurate online biomedical content due to exponential growth of unstructured biomedical data. Therefore, semantic annotations are essentially required with the biomedical content in order to improve search engines’ context-aware indexing, search efficiency, and precision of the retrieved results. In this study, we propose a personalized semantic annotation recommendations approach to biomedical content through an expanded socio-technical approach. Our layered architecture generates annotations on the users’ entered text in the first layer. To optimize the yielded annotations, users can seek help from professional experts by posing specific questions to them. The socio-technical …

I.V.A: Benjamin 'Frankie' Franklin Brown, Jr._Sibling, Betty L. Brown-Chappell Phd

Visual Materials [Series I]

Benjamin 'Frankie' Franklin Brown, Jr._Sibling