Digital Commons Network^™

Dynamic Contrast-Enhanced Mri Processing Comparison For Distinguishing True Progression From Pseudoprogression In High-Grade Glioma, Ahmad Amer, Shehbaz Ansari, Apollo Krayyem, Suprateek Kundu, Swapnil Khose, Halyna Pokhylevych, Susana Calle, Chirag B Patel, Zixi Yang, Ho-Ling Anthony Liu, Jason M Johnson

Faculty, Staff and Student Publications

Background: Treatment-related changes may occur due to radiation and temozolomide in glioblastoma and can mimic tumor progression on conventional MRI. DCE-MRI enables quantification of the extent of blood-brain barrier (BBB) disruption, providing information about areas of suspicious postcontrast T1 enhancement. We compared DCE-MRI processing methods for distinguishing true disease progression from pseudoprogression in high-grade gliomas (HGGs).

Methods: We identified 110 patients with HGG treated with surgery and chemoradiation who underwent DCE-MRI to further interrogate areas of new/increasing enhancement. All patients had confirmatory surgery/biopsy with pathology-confirmed progression or pseudoprogression. Scans were performed at 3T and analyzed using nordicICE. The MCA, SSS, …

Heat Shock Induces Alternative Polyadenylation Through Dynamic Dna Methylation And Chromatin Looping, Emily E Fink, Yi Zhang, Briana Santo, Anwita Siddavatam, Rosie Ou, Vishal Nanavaty, Byron H Lee, Angela H Ting

Faculty, Staff and Student Publications

Alternative cleavage and polyadenylation (APA) is a gene regulatory mechanism used by cells under stress to upregulate proteostasis-promoting transcripts, but how cells achieve this remains poorly understood. Previously, we elucidated a DNA methylation-regulated APA mechanism, in which gene body DNA methylation enhances distal poly(A) isoform expression by blocking CCCTC-binding factor (CTCF) binding and chromatin loop formation at APA control regions. We hypothesized that DNA methylation-regulated APA is one mechanism cells employ to induce proteostasis-promoting poly(A) isoforms. At the DNAJB6 cochaperone locus, acute heat shock resulted in binding of stress response transcription factors heat shock factor 1, ATF6, and YY1 at …

Functional Regulation Of Macrophages By Ces1d-Mediated Lipid Signaling In Immunometabolism, Long J Shao, Fathima Elizondo, Feng Gao, Rabie Habib, Xin Li, Katherine Pham, Jazmin Ysaguirre, Maryam Elizondo, Shirindokht Shirazi, Kristin L Eckel-Mahan, Sean Hartig, Huaizhu Wu, Kai Sun

Faculty, Staff and Student Publications

Objective: Macrophage accumulation in metabolically active tissues during obesity is common in both animals and humans, but the lipid signaling mechanisms that trigger macrophage inflammation remain unclear. This study investigates the role of Ces1d, an unconventional lipase, in regulating macrophage inflammation under nutritional stress.

Methods: A myeloid-specific Ces1d knockout (LysM-Cre-Ces1d floxed/floxed, KO) mouse model was used for the studies. For in vitro tests, bone marrow-derived macrophages (BMDMs) from control (Ces1d floxed/floxed, WT) and KO mice were assessed for migration, polarization, and activation. For in vivo experiments, WT and KO mice were induced to obesity via a high-fat diet (HFD) and …

Incomplete Toxicity Reporting And Use Of Toxicity-Minimizing Language In Phase Iii Oncology Trials, Avital M Miller, Adina H Passy, Alexander D Sherry, Ramez Kouzy, Joseph Abi Jaoude, Timothy A Lin, Gabrielle S Kupferman, Esther J Beck, Pavlos Msaouel, Ethan B Ludmir

Faculty, Staff and Student Publications

Purpose: This study aimed to determine complete toxicity reporting (CTR), and the use of subjective toxicity-minimizing language (TML) among phase III oncology trials.

Methods: Two-arm superiority-design phase III oncology trials published from 2002 to 2020 were reviewed for toxicity data. CTR was defined as reporting total adverse events (TAEs), total serious adverse events (SAEs), total deaths, and study therapy discontinuations because of toxicity. Guideline concordance was defined according to guidelines published in the BMJ (defined as reporting total SAEs, total deaths, and study therapy discontinuations because of toxicity). TML was defined as a set of terms that subjectively downplay the …

Arum Palaestinum Extracts: A Natural Solution For Root-Knot Nematode Control, Samaher Ghaith, Michel Afram, Jamilah Borjac

BAU Journal - Science and Technology

Root-knot nematodes (RKNs), Meloidogyne spp., have a destructive effect on a wide range of the crops. Arum palaestinum is a wild plant in levant that has a lot of different phytochemicals. The aim of this study is to evaluate the nematicidal potential of A. palaestinum extracts against RKN. The nematicidal efficiency of three types of extracts (aqueous, ethanolic and chloroform) of leaves, flowers and rhizomes of A. palaestinum on second stage juveniles (J2s) and hatching egg rate (RHI) of RKNs were evaluated in vitro using 6 concentrations of each extract (50mg/mL, 37.5mg/mL, 25mg/mL, 12.5mg/mL, 5mg/mL and 2.5mg/mL) and compared …

From Differentiation To Disease: Cyclin C Directly Coordinates Transcription And Mitochondrial Dynamics, Alicia Campbell

Theses and Dissertations

Organelle crosstalk is essential for coordinating cellular responses to various external cues, including stress and differentiation. Two key organelles, the nucleus and mitochondria, engage in extensive crosstalk to manage responses to a range of environmental and developmental signals. Complex processes such as stem cell differentiation and neuronal development rely on organelle crosstalk. Both processes integrate changes in gene expression with cytosolic and organellar remodeling. However, it remains unclear how these two complex processes are coordinated to achieve the desired outcome. This project concentrates on cyclin C (CCNC), a component of the Mediator Kinase Module (MKM), and its role in directly …

The Effort To Improve Students’ Problem-Solving Ability: Physics E-Modules For High School Students, Hidayatullah Hana Putra, Edi Supriana, Nasikhuddin Nasikhuddin, Annisa U. Yana, Suhailee Sohnui

Jurnal Pendidikan Sains

Physics teachers in Indonesia still face obstacles during learning, such as students who are less active and have difficulty in solving physics problems. The physics learning media used are also still not very interesting and are not based on authentic problem solving. Therefore, this study focuses on the development of PBL-based e-modules on work and energy to improve the physics problem-solving abilities of high school students. This research and development used the ADDIE design and was tested on 90 high school students in High School 1 Sumber Pucung Malang in the 2022/2023 academic year. The questionnaire instrument was used in …

Ethnoscience-Based Science Learning Through Composite Board Making Utilizing Eggshell Waste And Water Hyacinth Fiber (Eichornia Crassipes), Asep Khaidir Arpan, Yulia Sukmawardani, Pina Pitriana, Ade Yeti Nuryantini

Jurnal Pendidikan Sains

The demand for boards continues to increase every year, while overexploitation of wood leads to environmental degradation and forest loss. On the other hand, eggshell and water hyacinth waste continues to grow without optimal utilization. This research aims to make composite boards based on eggshell waste and water hyacinth fibers and analyze the potential of ethnoscience in science learning. This research used a qualitative descriptive method with a literature and documentation study approach. The materials used in this experiment are eggshell waste, water hyacinth fiber, and polyester resin. The composite board was made by mixing water hyacinth fiber and eggshell …

Teaching Materials Containing Kse To Support Character Education In Mathematics Subjects In Elementary Schools, Kunaenah Kunaenah, Rasiman Rasiman, Bagus Ardi Saputro

Jurnal Pendidikan Sains

The purpose of the study was to determine the validity, practicality, and effectiveness of teaching materials containing KSE to support character education in mathematics lesson content. This study employs a development research approach based on Borg and Gall's research design. The subjects of the study were in class V at public elementary school Kaliboyo. The data collection instruments used were validity sheets, response questionnaires, validation sheets, and observation sheets. The findings show that experts carried out the validity test, achieving a value of 93.30% in the very valid category. The practicality test results were derived from various sources: students' questionnaires, …

Development Of Differentiated Teaching Modules With A Scientific Approach To Improve Elementary School Students’ Science Literacy, Supriyanto Supriyanto, Joko Sulianto, Achmad Buchori

Jurnal Pendidikan Sains

The study aim is to determine the validity, practicality, and effectiveness of teaching materials. This type of research involves the development and creation of teaching module products. The research design used is ADDIE (Analysis, Design, Development, Implementation, Evaluation). The instruments used are validity sheets for experts and practitioners, teacher response questionnaires, teaching module validation sheets, and pretest and posttest questions. The findings show that experts conducted the validity test, achieving a score of 92.22 in the very valid category. The practicality test was obtained from the teacher questionnaire, which was stated as practical with an average value of 91.25, and …

Differentiated Teaching Module Using Problem Solving Model: Numerical Ability Of Elementary School Students, Risa Alifatin, Agus Sutono, Ida Dwijayanti

Jurnal Pendidikan Sains

This study aims to develop a differentiated teaching module using the problem-solving model that is valid, practical, and effective to improve students' numerical abilities. This study uses the ADDIE Model research and development approach. The sample in this study was class III of elementary school Tenggulangharjo as an experimental class totaling 22 students and class III of elementary school Karangtengah as a control class totaling 19 students. Data analysis used the t-test and N-Gain test. The study found that (1) the average validity score of the three parts of the Differentiated Teaching Module was 3.74, which is 93.62%, placing it …

Analysis Of Students' Creative Thinking Skills In Learning Hydrocarbons By Using Daily Life-Based Practicum Method, Yenni Kurniawati, Laras Dyaz Handayani, Dea Ramadani, Nurhikmah Sari

Jurnal Pendidikan Sains

Creative thinking skill is a competence of the 21st century that is needed very much and needs to be increased by utilizing chemistry in life. This research aimed at analyzing student creative thinking skills in experimental and control groups and finding out the effect of the daily life-based practical work learning method on student creative thinking skills. This research was conducted in the eleventh grade at High School 1 Pekanbaru on the hydrocarbon lesson. The quasi-experimental method was used in this research with pretest-posttest and non-equivalent control group designs. The instruments used in this research were essay tests, observation, and …

Exploring Students’ Perceptions Of Science Laboratory Practices: A Comparative Study Between Rural And Urban Schools, Safrida Dwiningsih, Ina Lestari, Roma Ismi, Sri Wahyu Rahmadina, Masdalena Sinaga, M. Rahmad

Jurnal Pendidikan Sains

This study aims to analyze students' perceptions of the implementation of science laboratory practicums at public middle school 020 Pekanbaru and public middle school 7 Pangkalan Kuras, Riau Province. Using a quantitative survey method, this study involved 75 student respondents. The instrument used was a questionnaire consisting of 26 statements, analyzed descriptively. The results show that students' perceptions of the preparation, implementation, and conclusion stages of the practicum fall into the "good" category, with urban schools having a higher percentage. In conclusion, the implementation of practicums in urban schools is better than in rural schools, bringing attention to the need …

Digital Comic Learning Media (E-Comic) To Increase Student Learning Interest In Reaction Rate Material At High School, Berliana Afsohin Nabila, Achmad Lutfi

Jurnal Pendidikan Sains

This study aims to develop digital comic learning media that is effective in increasing students' interest in learning about reaction rate material, focusing on the media's validity, practicality, and overall effectiveness. This research utilizes the research and development method with the ADDIE model. Research instruments were used, including validity sheets to assess the media's validity, student activity observations, and student response questionnaires to evaluate the media's practicality, as well as student interest questionnaires and learning outcomes to measure the effectiveness of the learning media. The findings show that validity results showed a mode score of 4, indicating a very valid …

Analysis Of Misconceptions In Learning Biology Mutation Material At High School, Fitri Hayati Kurnia, Tri Wahyu Agustina, Wahyuni Handayani

Jurnal Pendidikan Sains

This research aims to analyze student misconceptions regarding mutation material in class XII. The research method uses a descriptive approach with mixed methods, which combines qualitative and quantitative methods. Qualitative data was obtained through interviews with biology teachers, while quantitative data was obtained through questionnaires and essay tests on students. The research results indicate that the material that students like is growth and development, while the material they don't like is gene mutation and genetic material. Students' misconceptions occur due to preconception aspects, associative thinking, and a lack of understanding of genetic concepts. It was found that students' understanding of …

Effect Of Mercury Dose Variation On Growth And Nitrate Reductase Activity In Aquarius Palifolius (Nees & Mart.) Christenh. & Byng, Tsurayya Nurhanifah, Dwi Umi Siswanti

Makara Journal of Science

Mercury, a byproduct of mining, can harm the environment. One method to reduce this impact is through phytoremediation. This study used the Mexican sword (Aquarius palifolius), a plant with the potential to absorb and accumulate mercury. The aim of this study was to examine the effect of mercury stress on nitrate reductase activity, which plays a role in plant productivity, and to assess its impact on growth parameters, including plant height growth rate, leaf length, and number of leaves. Three-month-old A. palifolius plants obtained from rice fields in Sleman were treated with mercury at doses of 0, 14, …

A Demand Systems Analysis Of Energy Sources In The United States, Rafael Bakhtavoryan

Faculty Publications

This study estimates a Generalized Exact Affine Stone Index model to quantify demand structure among such energy sources as natural gas, coal, nuclear, wind, solar, and geothermal energy, employing monthly time-series data ranging from January of 2009 through December of 2020. The demand for natural gas, coal, and nuclear energy emerges as inelastic. A significant substitutability relationship is empirically established between the energy sources. All the computed expenditure elasticities are positive, with natural gas being the most sensitive and nuclear energy being the least sensitive to energy source expenditures. Pre-committed consumption is found for geothermal energy. Finally, the welfare implications …

Ifi16 Mediates Deacetylation Of Kshv Chromatin Via Interaction With Nurd And Sin3a Co-Repressor Complexes, Anandita Ghosh, Bala Chandran, Arunava Roy

School of Medicine Faculty Publications

IFI16 is a well-characterized nuclear innate immune DNA sensor that detects foreign dsDNA, including herpesviral genomes, to activate the inflammasome and interferon pathways. Beyond immune signaling, IFI16 also functions as an antiviral restriction factor, promoting the silencing of invading viral genes through transcriptional and epigenetic mechanisms. We recently demonstrated another role of IFI16, in which it interacts with and recruits the class I histone deacetylases, HDAC1 and 2, to the KSHV latency protein LANA, modulating its acetylation and function. In this study, we asked whether these IFI16-HDAC1/2 interactions contribute to broader epigenetic regulation of the KSHV chromatin. Our findings reveal …

Soil Degradation Of Solvent-Cast Pha Films Produced By Bacillus Tequilensis Pwf Using Waste Polyethylene Terephthalate (Pet), Rafeya Sohail, Rida Batool, Nazia Jamil

Journal of Bioresource Management

Polyhydroxyalkanoate (PHA) aliphatic polymers however efficiently biodegradable, still pose a contradiction with the principles of green chemistry. Use of bacterial strains capable of degrading synthetic plastics for the production of biopolymers i.e., PHAs may aid in reduction of plastic pollution. Bacterial strains PWA; Bacillus subtilis (MH142143), PWF; Bacillus tequilensis (MH142145), and PWG; Bacillus safensis (MH142146) were grown on waste shredded PET and PET flakes. Highest bioconversion of PET to PHA was observed using PET flakes. Strain PWF produced 40.47 % (0.815 g/L) and 31.80 % (0.626 g/L) PHA using PET flakes and shredded PET at 48 h, respectively. Whereas highest …

A Customizable Ligand-Conjugate System For Investigation And Detection Of Ghrelin O-Acyltransferase, Amber Ford

Dissertations - ALL

Ghrelin is a 28 amino acid peptide hormone responsible for a variety of physiological functions. Ghrelin signals these functions via its cognate receptor, GHSR, after an essential post translational modification which acylates its third serine. The acylation of ghrelin is facilitated by the enzyme ghrelin O-acyltransferase (GOAT) for which ghrelin is the only known substrate. Canonically, GOAT acylates ghrelin in the endoplasmic reticulum before it is further processed and secreted in circulation. Recent studies, however, have detected GOAT in the cytoplasm, plasma membrane, and in circulation in extracellular vesicles. Furthermore, GOAT has been identified as a potential prostate cancer (PCa) …

Impact Of Oceanographic Gradients And Marine Heatwaves On The Picophytoplankton Community In The Northern California Current System, Kristin E. Forgrave, Carey P. Sweeney, Melissa Steinman, Anvita U. Kerkar, Timothy M. Pettit, Anne W. Thompson

Biology Faculty Publications and Presentations

The Northern California Current (NCC) system is a productive coastal ecosystem with a mosaic of temporal and spatial features. The phytoplankton community plays a crucial role in supporting the rich ecosystem and economically important fisheries of the NCC. Our study integrates data across two years (2022-2023) and multiple transects to investigate the community composition of two major phytoplankton groups in the NCC: picocyanobacteria and photosynthetic picoeukaryotes (PPE). The abundances and cell sizes of the phytoplankton were measured using flow cytometry. We found PPE present at similar concentrations in both summer and winter, while picocyanobacteria were much more abundant in the …

Living Heritage, Resilience And Ethically Informed Infrastructures In Malawi, Martha B. Lerski, Frank Puluputu Mwale

Publications and Research

Rooted in a rural community’s needs, this paper explores how historically, and ethically informed infrastructures can support community engagement towards identification, documentation, and dissemination of local, traditional, and indigenous knowledge relating to climate change. The paper examines climate adaptation and sustainability issues through the lenses of community organizing and Library & Information Science best practices. It draws on a growing body of literature identifying a role for expanded epistemological and subject discipline perspectives. While the impacts of climate on material culture are increasingly recognized, intangible, and biocultural heritage have not received as much attention. Living heritage traditions and knowledge systems …

Development Of Biolymer And Essential Oils-Based Edible Coatings To Enhance The Shelf Life Of Strawberries, Katie Wiseman, Lily Jaiswal, Shiv Shankar

Level 3

No abstract provided.

American Kestrels (Falco Sparverious) In Row Crop Agriculture Of The Lower Mississippi Alluvial Valley Of Northeast Arkansas: Factors Influencing Nest And Roost Box Use, Nest Success, And Effects On Agricultural Pests, Ty Spencer Sharrow

Student Theses and Dissertations

Utilizing birds of prey for pest control is a sustainable, environmentally friendly approach to pest management that can benefit not just the environment and human health but also the birds themselves. The American Kestrel (Falco sparverius; hereafter ‘kestrel’) is one such species that can provide pest management services while benefiting from nest boxes used to attract them in agricultural areas. I examined how box and habitat characteristics influenced kestrel box use for nesting, winter roosting, and nest success in the row crop-dominated landscape of northeast Arkansas’ Lower Mississippi Alluvial Valley. In addition, I assessed kestrel impact on pests by systematically …

Insights Into Therapeutic Discovery Through The Kelch Domain Structure Of Keap1 At Ambient Temperature, Merve Yilmaz, Belgi̇n Sever, Yi̇ği̇t Kutlu, Mehmet Gül, Ceren Okuducu, Serra Tavli, Masami Otsuka, Mikako Fujita, Turkan Hali̇loğlu, Hali̇li̇brahi̇m Çi̇ftçi̇, Hasan Demi̇rci̇

Turkish Journal of Biology

Background/aim: The Kelch-like-ECH associated protein 1 (Keap1) is an integral component of the E3-ubiquitin ligase complex, which binds to Nuclear factor erythroid 2-related factor 2 (Nrf2) and facilitates its degradation by the 26S proteasome. The Kelch domain of Keap1, composed of six repeated structural motifs, plays a key role in this interaction. This study aims to investigate the dimeric structure of the Keap1 Kelch domain at ambient temperature and to examine its implications for conformational dynamics, particularly in relation to the DMF and Nrf2 binding sites.Materials and methods: The dimeric crystal structure of the Keap1 Kelch domain was determined at …

Deliberately Queer Journal Editors' Note For Volume One, Sean Te Maulding, Mel Monier

Deliberately Queer Journal

No abstract provided.

Antiinflammatory Effects Of Cucurbitacins And Sorafenib In Hepg2 Cells By Modulating The Iκb/Nf-Κb/Cox-2 Pathway Through Akt Signaling, Muhammed Mehdi̇ Üremi̇ş, Yusuf Türköz, Nuray Üremi̇ş

Turkish Journal of Biology

Aim: Cucurbitacins possess antitumor, antiproliferative, and antiinflammatory properties. This study aims to examine the antiinflammatory effects of CuD, CuI, and CuE on NF-κB, iNOS, COX-2, and Akt and compare their cytotoxic and antiinflammatory effects on HepG2 cells with sorafenib, the primary chemotherapeutic agent used in HCC treatment. Methods: Cytotoxic effects of cucurbitacins and sorafenib on HepG2 cells were evaluated using MTT and LDH assays, along with Annexin V, MMP, and comet assays. Levels of proteins related to the Akt/NF-κB pathway and COX-2, iNOS, and NO were also measured. Results: Our study showed that CuD, CuI, CuE, and sorafenib have antiproliferative …

Mis-Splicing-Derived Neoantigens And Cognate Tcrs In Splicing Factor Mutant Leukemias, Won Jun Kim, Edie I Crosse, Emma De Neef, Inaki Etxeberria, Erich Y Sabio, Eric Wang, Jan Philipp Bewersdorf, Kuan-Ting Lin, Sydney X Lu, Andrea Belleville, Nina Fox, Cynthia Castro, Pu Zhang, Takeshi Fujino, Jennifer Lewis, Jahan Rahman, Beatrice Zhang, Jacob H Winick, Alexander M Lewis, Robert F Stanley, Susan Dewolf, Brigita Meškauskaitė Urben, Meril Takizawa, Tobias Krause, Henrik Molina, Ronan Chaligne, Priya Koppikar, Jeffrey Molldrem, Mathieu Gigoux, Taha Merghoub, Anthony Daniyan, Smita S Chandran, Benjamin D Greenbaum, Christopher A Klebanoff, Robert K Bradley, Omar Abdel-Wahab

Faculty, Staff and Student Publications

Mutations in RNA splicing factors are prevalent across cancers and generate recurrently mis-spliced mRNA isoforms. Here we identified a series of bona fide neoantigens translated from highly stereotyped splicing alterations promoted by neomorphic, leukemia-associated somatic splicing machinery mutations. We utilized feature-barcoded peptide-MHC dextramers to isolate neoantigen-reactive T cell receptors (TCRs) from healthy donors, patients with active myeloid malignancy, and following curative allogeneic stem cell transplant. Neoantigen-reactive CD8+ T cells were present in the blood of patients with active cancer and had a distinct phenotype from virus-reactive T cells with evidence of impaired cytotoxic function. T cells engineered with TCRs recognizing …

In Vitro Regeneration Potential Of Pistacia Integerrima And Pistacia Khinjuk Rootstocks: A Modeling Approach For Optimal Medium Formulation, Heydem Eki̇nci̇, Beki̇r Erol Ak

Turkish Journal of Agriculture and Forestry

Micropropagation involves the development of whole plants from small meristematic tissues by culturing them in vitro under aseptic conditions on a nutrient medium. However, identifying a single nutrient medium suitable for propagating Pistacia, a recalcitrant species, remains challenging. While some species exhibit good growth on Murashige and Skoog (MS) medium, Pistacia species generally yield insufficient results. To address this, a five-dimensional experimental design was developed using Design- Expert software (Stat-Ease Inc., Minneapolis, MN, USA). Thirty-three experimental databases were generated by the software using the modified I-optimal criterion. MS medium served as the control treatment. A response surface model (RSM) employing …

Comprehensive Characterization Of Purified Naringinase: Effect On Naringin Content, Antioxidant Activity, Phenolic Profile, And Grapefruit Juice Quality, Arzu İmece, Memnune Şengül, Bülent Çeti̇n, Ömer İrfan Küfrevi̇oğlu, Arzu Öztürk Kesebi̇r

Turkish Journal of Agriculture and Forestry

Bitterness arising from naringin is a problem in citrus juices, especially grapefruit juice, in terms of consumer preference. Naringinase enzyme is used to eliminate the bitterness. In this study, naringinase was extracellularly extracted, isolated, and characterized from an Aspergillus niger strain in different media. The extracted enzyme was added to grapefruit juice at different concentrations (0.1%, 0.5%, 1%) (0.078, 0.39 and 0.78 EU) and stored at different temperatures (25, 35, and 45 °C) for 5 h. At the end of the first and fifth h, the amount of naringin, physicochemical properties, phenolic profiles, and antioxidant activities of the grapefruit juice …