Digital Commons Network^™

Integration Of Mechanism-Driven Computational Modeling And Public Data Resources For Chemical Toxicity Assessment, Elena Chung

Theses and Dissertations

Regulatory toxicology depends primarily on animal testing, which limits throughput, mechanistic interpretability, and applicability to human-relevant endpoints. This dissertation presents computational approaches that integrate publicly available bioactivity data with machine learning to support chemical safety evaluation. Oral carcinogenicity was modeled using curated chemicals from the US Environmental Protection Agency’s Integrated Risk Information System (IRIS) and activity data from over 1,900 PubChem assays. Quantitative structure-activity relationship (QSAR) models trained on statistically prioritized assays demonstrated strong predictive performance and were applied to rank the carcinogenic potential of more than 16,000 compounds. Hepatotoxicity was evaluated using a hybrid modeling approach that combined structural …

Antibiofilm Activity Of Amylases Isolated From The Bacteria Associated With The Soft Coral Sarcophyton Trocheliophorum, Asmaa Marshoud Al Harbi, Mamdoh T Jamal, Sathianeson Satheesh

Journal of King Abdulaziz University: Marine Science

Amylases are one of the important enzymes with tremendous biotechnological applications. In this study, the amylase enzyme producing bacterial strains associated with the soft coral Sarcophyton trocheliophorum was isolated and identified. The amylases were produced in a specific growth medium and the stability was tested under different pH and temperature conditions. The crude amylases were tested for the antibiofilm activity against two biofilm-forming bacterial strains. The amylase enzyme extracted from two bacterial strains (KAU-AS1 and KAU-AS3) showed good activity in the antibiofilm activity assays. The amylases reduced the growth and attachment of the biofilm bacteria. Also, the amylase enzymes degraded …

Morphological Observations Of Ophioderma Hybridum (Echinodermata: Ophiuroidea) From Western Of Libya, Najla Mohamed Abushaala, Edris Mansour, Ignazio Sparacio, Abdulfattah Elfituri

Journal of King Abdulaziz University: Marine Science

The distribution of the species of Ophioderma in the Mediterranean is still incompletely known. In this paper, Ophioderma hybridum (Ophiuroidea, Ophiodermatidae) is reported for the first time from the coast of Tajura, in the southern Mediterranean Sea, Libya. This recently described species was until now known only from the coast of Tunisia. Description of external appearance and taxonomic characteristics: Specimens had a dark reddish brown body colour on disc and arms, the radial shields not covered by granules. As a result of these morphological observations, O. hybridum is added to the Ophiuroidea fauna of the Libyan coast, southern Mediterranean Sea, …

Isolation And Importance Of Endophytic Actinomycetes Of Some Red Sea Algae And Their Biological Activities, Najla Ali Alburae

Journal of King Abdulaziz University: Marine Science

Endophytic Actinomycetes attract scientist's attention and in particular, endophytes from marine algae were documented and showed many biological activities that maintain ecological balance in various habitats that solve many health problems. This research aimed at the development of antimicrobial and antioxidant agent from endophytic Actinomycetes. Three seaweed algal samples were collected from the Red Sea Umluj corniche, nestled in northwestern of Saudi Arabia and identified as Ulva lactuca (Chlorophyta), Dictyota dichotoma (Phyaephyta) and Gelidium sp. (Rhodophyta). The collected algal samples were washed, surface sterilized, cut into small squares for Endophytic Actinomycete isolation on Starch nitrate medium containing 10% NaCl. Twelve …

Accumulation And Distribution Of Microplastic Particles In Recent Coastal Sediments From Specific Areas Of The Syrian Coast And Determination Of Medium Energy, Samer Ghadeer, Yousef Rslan

Journal of King Abdulaziz University: Marine Science

Despite the numerous benefits plastics have brought to our daily lives, they have also introduced many unexpected and serious environmental challenges, particularly for marine environments, their ecosystems, and sediments. This research holds significant importance as it addresses microplastic pollution, a pressing contemporary issue that demands solutions. It marks the first study of its kind on the Syrian coast, utilizing sediments to identify and quantify microplastics, as well as to determine their sizes and the primary human activities contributing to their spread. A comprehensive study was conducted on sediment samples from specific areas along the Syrian coast-Wadi Qandel, Banias, and Al-Mantar-to …

Lifecycle Of Greater Wax Moth Galleria Mellonella (Lepidoptera: Pyralidae) And Its Control By Natural Products, Tahani A. Alzahrani, Hanan S. Alyahya, Shatha I. Alqurashi, Jazem A. Mahyoub

Journal of King Abdulaziz University: Meteorology, Environment and Arid Land Agriculture

The great wax moth (Galleria mellonella) is a major pest that affects honeybee colonies, causing serious damage to the honeycomb and disrupting beekeeping operations. This paper aims to review the life cycle of this insect and the natural control strategies used to manage its populations. This paper examines the different stages of growth of the great wax moth, including the stages of eggs, larva, pupae, and adults. The life cycle of this insect depends largely on environmental conditions, especially temperature, humidity and food quality, in addition, this paper focuses on natural control strategies, such as the use of plant extracts …

Production And Characterization Of Biodiesel From Malapari Seed Oil (Pongamia Pinnata L.): Evaluation Of Quality Parameters Based On The Indonesian National Standard (Sni) 04-7182-2015, Desi Adriyanti Nina Taebenu, Ni Luh Arpiwi, Ida Ayu Astarini

Makara Journal of Science

This study produced biodiesel from Malapari seed oil (Pongamia pinnata L.) by optimizing the esterification and transesterification processes. The objectives of this study were to determine the sulfuric acid (H₂SO₄) catalyst concentration in the esterification reaction that can reduc the free fatty acid (FFA) content of the seed oil to ≤2%, analyze the oil to methanol molar ratio (i.e.,1:6, 1:9, and 1:12) and KOH concentration (i.e.,2%, 4%, and 6%) that will produce the highest biodiesel yield, and evaluate the quality of the produced biodiesel according to the Indonesian National Standar (SNI) 04-7182-2015. The research was …

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, …

Phase Ii Basket Trial Of Dual Anti-Ctla-4 And Anti-Pd-1 Blockade In Rare Tumors (Dart) Swog S1609: Pancreatic Neuroendocrine Neoplasm (Pnen) Cohort, Sandip Pravin Patel, Jillian Fisher, Young Kwang Chae, Luisa Solis Soto, Anup Kasi, Bhavana Konda, Mark Walshauser, Edwin Parra, Jiexin Zhang, Caroline Duault, Edgar Gonzalez-Kozlova, Ganiraju Manyam, Jianhua Zhang, Hong Chen, Dzifa Yawa Duose, Caddie Laberiano Fernandez, Raja Luthra, Gheath Al-Atrash, Seunghee Kim-Schulze, Holden T Maecker, Ignacio I Wistuba, Sacha Gnjatic, J Jack Lee, Jianjun Zhang, Christine M Magner, Helen X Chen, Elad Sharon, Megan Othus, Christopher W Ryan, Charles Blanke, Cara L Haymaker, Razelle Kurzrock

Faculty, Staff and Student Publications

Purpose: SWOG S1609 Dual Anti-CTLA-4 and anti-PD-1 blockade in Rare Tumors (DART) studied the efficacy of ipilimumab combined with nivolumab across multiple rare tumor types. We report the results of the pancreatic neuroendocrine neoplasm (PNEN) cohort.

Experimental design: Treatment consisted of ipilimumab 1 mg/kg intravenously every 6 weeks with nivolumab 240 mg intravenously every 2 weeks. The primary endpoint was overall response rate (ORR) (Response Evaluation Criteria In Solid TumorsRECIST V.1.1). Secondary endpoints include progression-free survival (PFS), overall survival (OS), and toxicity. Clinical benefit rate (includes ORR plus stable disease (SD)>6 months was examined. Correlative …

Vitamin D3 Toxicity-Induced Hypercalcemia In Staphylococcal Arthritis: A Focus On Il-6, Ali Jabbar Abd Al-Hussain Alkawaz, Maryam Sabah Naser, Ali Jalil Obaid, Zakaria M. Al-Ghazaly

Karbala International Journal of Modern Science

Background: Vitamin D3  over-supplementation can induce toxicity through the development of hypercalcemia and may disturb immune modulation. This study examines the relationship between hypercalcemia  resulting from Vitamin D3 Overdose and serum Interleukin-6 (IL-6) levels in patients diagnosed with staphylococcal arthritis.

Methods: Forty male patients (mean age: 31 years; range: 17–45 years) were enrolled from Dec. 2024 to Feb. 2025. Twenty cases of staphylococcal arthritis were compared with twenty healthy male controls. Serum concentrations of Vitamin D3, calcium, IL-6, and other biochemical markers (urea, creatinine, ESR, WBC, and potassium) were analyzed. Staphylococcus aureus was isolated from synovial fluid and confirmed using …

Bite By Bite: How Ungulate Browsing Shapes North America's Forest Future, Darius Hardalau, Vladut Stefanescu, Mindaugas Bakševičius, Michael Manton, Charles Ruffner, Gediminas Brazaitis, Georgeta Ionescu, Ovidiu Ionescu

Aspen Bibliography

Ungulate browsing represents a contemporary issue for forest development, influencing forest regeneration, composition, and management practices across the world, especially in North America. This review synthesizes findings from 101 studies conducted between 1980 and 2025 to examine patterns of herbivory damage through browsing by moose, elk, white-tailed deer, black-tailed deer, and bison. Despite regional variation, high ungulate density consistently emerges as the primary factor driving browsing intensity and ecological and economic impact, leading to decreased social acceptance of coexistence with ungulates. This review highlights the selective suppression of palatable species such as balsam fir, red oak, and white cedar, leading …

Beyond Silence: A Review- Exploring Sensory Intelligence, Perception And Adaptive Behaviour In Plants, Taranisen Panda, Nirlipta Mishra, Shaik Rahimuddin, Bikram Pradhan, Rajballav Mohanty

Journal of Bioresource Management

Plants, traditionally viewed as passive organisms, exhibit sensory and adaptive abilities that challenge conventional notions of plant biology. All organisms evolve ways to sense and interact with their surroundings, and plants, although lacking eyes, ears, or brains, perceive the world in sophisticated ways. Despite lacking a nervous system and other features typically associated with animals, plants can see, smell, hear, feel, learn, remember, and act similarly to animals. This review examines how plants perceive and respond to their environment using mechanisms analogous to vision, hearing, smell, taste, and touch, adjusting their morphology, physiology, and phenotype accordingly. Drawing from plant physiology, …

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 …

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 …

On The Possibility Of Predicting The Approximate Fatty Acid Composition Of Blends Based On The Iodine Number, Adiba M. Serkaeva, Akhror A. Abdurakhimov, Nafisa S. Husanova, Kamar P. Serkaev

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of the study was to conduct research to determine the possibility of predicting the approximate fatty acid composition of blends based on the iodine number. The fatty acid composition was determined by the chromatographic method and the results were subsequently used to identify the composition of blends by determining the iodine number. The iodine number was determined by calculation and titrimetric methods, comparing the differences between the obtained values. The detected deviations in values between the two methods do not exceed 0.4%, which means that it is possible to predict the approximate fatty acid composition of blends based …

Digital Infrastructure For The Regenerative Movement: A Case Study Of The Mycelium Learning Network, Abigail Karparis

Journal of Nonprofit Innovation

The regenerative movement is gaining momentum worldwide, driven by communities working to restore ecological and social systems through place-based, culturally rooted action. Yet many of the groups leading this work, especially in the Global South or in hyper-local contexts, remain digitally invisible due to structural barriers, including limited access to appropriate technology, funding constraints, and misalignment between available tools and local values. Conventional digital infrastructures often exclude or marginalize these efforts, leaving regenerative practitioners disconnected from each other and from potential sources of support.

This article explores these challenges and presents a case study response: the co-creation of accessible, relational …

Annotated Checklist And Distribution Of The Jewel Beetles (Coleoptera: Buprestidae) Of Idaho, Luc Leblanc, Emma L. Eakins

Insecta Mundi

An annotated checklist of the 102 species of Buprestidae (Coleoptera) known to be present in the state of Idaho is provided, with photographs and detailed distribution maps for each species. The checklist is based on label data from 7,506 museum specimens, 21 observations obtained from iNaturalist.org and Bug-Guide.net, and 63 distribution records from published literature. Buprestis consularis Gory is a new record for Idaho, formerly reported as Buprestis nutalli Kirby, which is not known to occur in the state. Obscure past records of Anthaxia retifera LeConte and Melanophila occidentalis Obenberger published in the literature are regarded as dubious and are …

Genomics-Based Taxonomic Refinement Of Emesis Fabricius (Lepidoptera: Riodinidae), Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

Insecta Mundi

Expanded genomic sequencing of Emesis [Fabricius], 1807 (Lepidoptera: Riodinidae Grote, 1895) reveals additional taxonomic insights. As a result of this study, one subgenus and 10 species are proposed as new (type species or type localities in parenthesis): Sinuata Grishin, new subgenus (Emesis sinuatus Hewitson, 1877) of Exoplisia Godman and Salvin, 1886; Emesis (Mandania) mandaca Grishin, new species (Mexico: Oaxaca); Emesis (Mandania) mantunga Grishin, new species (Ecuador: Tungurahua); Emesis (Tenedia) hidalga Grishin, new species (Mexico: Hidalgo); Emesis (Tenedia) vera Grishin, new species (Mexico: Veracruz); Emesis (Tenedia) nica Grishin, new species …

A New Species Of Leaf Litter Inhabiting Species Of Stevenaltica Konstantinov, Linzmeier And Savini From The United States (Coleoptera: Chrysomelidae: Galerucinae: Alticini), Amy L. Brown, Shawn M. Clark, Alexander S. Konstantinov

Insecta Mundi

A new species, Stevenaltica parvarotunda Bown, Clark, and Konstantinov (Coleoptera: Chrysomelidae), is described from Ohio, U.S.A. This is the first report of this genus in North America. Brief comments are made regarding Exoceras Jacoby and Leptophysa Baly.

Three New Species Of Dichotomius Hope, 1838 (Coleoptera: Scarabaeidae: Scarabaeinae) From Mexico And Central America, Ángel Solís, Burt Kohlmann

Insecta Mundi

Three new species assigned to the satanas species-group of Dichotomius Hope (Coleoptera: Scarabaeidae: Scarabaeinae) are described from North and Central America: Dichotomius pisuicas Solís and Kohlmann, new species, from the Caribbean slope of Honduras to Panama; D. lucifer Solís and Kohlmann, new species, from the Costa Rican and Panamanian Pacific rainforests; and D. chamuco Solís and Kohlmann, new species, from Mexico to Honduras. A description, diagnosis, images, and distributional map are presented for each species.

The Millipede Genus Alocodesmus Silvestri, 1896 (Polydesmida: Chelodesmidae: Batodesmini): Description Of A New Species From Colombia And The Identity Of A. Hanseni (Silvestri, 1898), Juan Romero-Rincon, Santiago Alvear

Insecta Mundi

The genus Alocodesmus Silvestri, 1896 (Polydesmida: Chelodesmidae: Batodesmini) currently comprises six valid species, three of which are recorded for Colombia, including A. danielae Romero-Rincon and Alvear, new species, from Yondó, Antioquia Department. Two species are known from Panama and one from Venezuela. The new species differs from its congeners by having a spoon-shaped prefemoral process that is ventrally extended forming a conspicuous concave space with branch Z being shorter than branches X and Y. The identity of A. hanseni Silvestri, 1898, previously of uncertain status, is revised, and the species is herein proposed as a new synonymy …

A Battle Of Armies: Massive Attack Of Natural Enemies To The True Armyworm Mythimna Unipuncta (Haworth, 1809) (Lepidoptera: Noctuidae) In Forage Crops, Armando Falcon-Brindis, Raul T. Villanueva

Insecta Mundi

Understanding the interactions between plant-host-parasitoid plays a major role in insect pest management. Farmers in the southeastern United States rely on pasture systems for cattle milk and beef production, but the benefits of parasitoids and predators on major lepidopteran pests on pasture lands are still overlooked. Here, we aimed to identify and quantify the effect of parasitism on the true armyworm Mythimna unipuncta (Haworth, 1809) (Lepidoptera: Noctuidae) attacking teff grass Eragrostis tef (Zucc.) Trotter (Poaceae) and crabgrass Digitaria sanguinalis (L.) Scop. (Poaceae) in western Kentucky. In early August of 2023, 547 larvae of M. unipuncta were collected from experimental …

In Memoriam: Donald B. Thomas, Jr., January 26, 1949–November 10, 2024, Brett C. Ratcliffe, Joseph E. Eger Jr., David Rider

Insecta Mundi

We honor the life and contributions of Donald Byron Thomas, Jr. (January 26, 1949–November 10, 2024) with a short review of his professional life followed by three appendices listing his published papers, taxa described, and patronyms.

Erratum To Golovatch Et Al. (2025): Contributions To The Taxonomy Of The Neotropical Millipede Genus Iulidesmus Silvestri, 1895 (Diplopoda: Polydesmida: Paradoxosomatidae: Catharosomatini), Sergei I. Golavatch, Juan Romero-Rincon, Nesrine Akkari, Santiago Alvear

Insecta Mundi

After publication of Golovatch et al. (2025), it was noticed that Figure 3 was accidentally omitted. The authors and the Insecta Mundi editorial staff apologize for this error. Figure 3 is reproduced here. Insecta Mundi has also released a revised version of the Golovatch et al. (2025) manuscript, with this error corrected. However, the revised version is not an official version of record, and anyone wishing to reference the findings of Golovatch et al. (2025) should cite the original manuscript or this erratum.

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 …

Political Agroecology In Syracuse: Local Understandings, Possibilities, And Barriers To Food System Transformation, Cooper Olds

Theses - ALL

In recent years, agroecology has begun to receive increasing attention from international institutions such as the United Nations Food and Agriculture Organization (UN FAO). For some, this is seen as a valuable case of up-scaling agroecology which will lead to greater institutional support for the framework. However, critical agroecologists have raised concerns that such institutional adoption is rather a form of co-optation where the social and political elements of agroecology are omitted to facilitate the integration of the framework into a wider program of food system reform. As a result, there is ongoing contestation over the framework between these co-opted …

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) …

An Fgfr-P53 Developmental Signaling Axis Drives Salivary Cancer Progression, Julia M. R. Billington

USF Tampa Graduate Theses and Dissertations

Mucoepidermoid carcinoma (MEC) is the most frequently occurring salivary gland malignancy.Here, we investigated transcriptomic profiles of human fetal and adult salivary glands and MEC tumors to assess programs involved in MEC progression. Molecular and genetic analyses revealed that MEC tumors and fetal salivary glands share proliferative and developmental gene expression profiles that implicate an FGFR-p53 signaling axis in salivary MEC progression. Based on these findings, we developed a genetically engineered mouse model of advanced MEC via targeted expression of the CRTC1-MAML2 oncogene in salivary ductal cells. Specifically, CRTC1- MAML2 expression combined with p53 dysregulation in salivary ducts rewires FGF signaling …

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 …

The Dynamics Of Daily Area And Depth Of Grazing And Herbage Intake Of Cows In A Five Day Paddock System, M H. Wade, J L. Peyraud, G Lemaire, E A. Comeron

IGC Proceedings (1977-2023)

Optimisation of animal production per unit area results in a penalty to individual animal production and herbage intake. The objective of the present study was to examine the dynamic changes in a grass sward in relation to declining production and herbage intake in five day paddocks grazed by dairy cows. The study formed part of a larger project to examine the effects of stocking rate and grazing method upon milk production and herbage intake that is reported by Peyraud et al. (1989).