Life Sciences Commons^™

A Disorder-Aware Computational Framework To Identify Structurally Tractable Targets In Proliferative Vitreoretinopathy, Mak B. Djulbegovic, Nedym Hadzijahic, David J. Taylor Gonzalez, Michael Antonietti, Sidra Zafar, Ajay E. Kuriyan

Wills Eye Hospital Papers

OBJECTIVE: Proliferative vitreoretinopathy (PVR) remains a major cause of failure after rhegmatogenous retinal detachment repair and lacks effective pharmacologic therapies. Although epithelial-mesenchymal transition (EMT) is central to PVR pathogenesis, the structural determinants governing the tractability of EMT regulators, particularly those involving intrinsic disorder, remain poorly defined. We developed a disorder-aware, artificial intelligence-enabled computational framework to evaluate EMT-associated proteins in PVR and prioritize structurally tractable regulators for structure-based targeting.

DESIGN: A computational, hypothesis-generating study employing an in silico screening and structural modeling pipeline.

SUBJECTS: No human subjects or biological specimens were included. The dataset comprised 25 EMT-associated proteins implicated in PVR, …

Popgenhelpr: An R Package To Streamline And Facilitate Informed Population Genomic Analyses And Visualization Of Genetic Ancestry, Diversity And Differentiation, Keaka Farleigh, Mason O. Murphy, Christopher Marie Blair, Tereza Jezkova

Publications and Research

Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and FST. PopGenHelpR also provides five …

Phytochemical Composition And Bioactivities Of Roselle (Hibiscus Sabdariffa L.) Extracts Obtained By Infusion, Ethanolic Maceration, And Maltodextrin-Assisted Drying, Risna Silvianti, Warsito Warsito, Elok Zubaidah, Zubaidah Ningsih, Aqidatul Izza

Karbala International Journal of Modern Science

Roselle (Hibiscus sabdariffa L.) is rich in phenolic compounds and anthocyanins, but the extraction method may influence its chemical composition and biological activity. This study compared hot-water infusion, ethanolic maceration, and maltodextrin-assisted drying. It aimed to examine the relationship between the extraction method, chemical profile, and bioactivity. The resulting extracts (EI, EM, and EP) were analyzed for total phenolic, flavonoid, and anthocyanin, LC-HRMS profiles, and antioxidant capacity by the FRAP assay. Antibacterial analysis was conducted against Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 25923) using agar well diffusion. Cytotoxicity tests (MTT, 24 h) were performed against HT-29, 4T1, …

Effects Of Warming On Growth And Leaf Colonization By Litter Mat-Forming Fungi In A Wet Tropical Forest In Puerto Rico, Ari E. Puentes, D. Jean Lodge, Deyaneira A. Ortiz-Iglesias, Tatiana Barreto-Vélez, Laura C. Rubio-Lebrón, Hieu Chu, Christine S. O'Connell, Sasha C. Reed, Tana E. Wood

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Wet tropical forests are experiencing rising temperatures and increased frequency and intensity of extreme climatic events, such as cyclones, which can increase rates of soil erosion and surface runoff. Fungal litter mats, formed by agaric decomposer fungi, play a crucial role in stabilizing slopes, preventing erosion, and aiding nutrient cycling; however, little is known about how warming affects litter mat growth and function. We investigated two litter mat-forming fungi, Gymnopus johnstonii and Marasmius aff. crinis-equi, in warmed (+4°C above ambient) and control plots in the Luquillo Experimental Forest, Puerto Rico. Growth and time-to-leaf colonization were monitored over 6 weeks …

Brain Age Prediction In Generalized Anxiety Disorder Using A Convolutional Neural Network, Corey Richier, André Zugman, Anita Harrewijn, Elise M. Cardinale, Parmis Khosravi, Moji Aghajani, Willem B. Bruin, Kevin Hilbert, Narcis Cardoner, Anderson M. Winkler

Human Genetics Publications

Higher predicted brain age difference has been associated with several psychiatric disorders. Generalized anxiety disorder (GAD) is associated with markers of accelerated aging. In this study, we determined brain predicted age difference (PAD) in individuals with GAD and healthy controls (HC) as well as group differences in PAD variability using voxel-wise structural MRI. The training dataset included 3511 controls, and the testing dataset included 1595 individuals with GAD and 4552 HC from the ENIGMA-Anxiety GAD Working Group. A convolutional neural network model using four input modalities per subject and a model ensemble approach was used to predict brain age. The …

The Role Of Media In Enhancing The Awareness Of Jordanian University Students About The Risks Of Energy Drinks, Rasha Salameh, R. Abuhasirah

Middle East Journal of Communication Studies

This article aimed to explore the role of media in enhancing the awareness of Jordanian university students regarding the health risks associated with energy drink consumption. The article employed a media audience survey method, applied to a Quota sample of 300 students from diverse academic disciplines (humanities, health sciences, and natural sciences) at Yarmouk University (public) and Middle East University (private). Data were collected between March 10 and April 15, 2025. The results indicated that energy drink consumption was higher among Middle East University students (55.4%) compared to Yarmouk University students (44.6%). Furthermore, students in the humanities reported higher consumption …

The Role Of Artificial Intelligence In Developing Science Journalism Strategies And Enhancing Political Awareness, Enad Akif Al-Jallad

Middle East Journal of Communication Studies

This study aimed to analyze the role of artificial intelligence in developing science journalism strategies and enhancing its capacity to raise political awareness. The study adopted a descriptive-analytical methodology through a review of relevant literature and an analysis of scientific content related to artificial intelligence technologies and their media applications. It also relied on a set of applied experiences in science journalism, including The Guardian’s coverage of climate issues and Al Jazeera Net’s reporting on the COVID-19 pandemic and its connection to health policies.

The findings revealed that science journalism serves as a fundamental tool for transferring knowledge to the …

The Use Of Social Media By Jordanian Science Journalists And Its Implications For The Accuracy Of Journalistic Content, Farah Yahya Zaatreh

Middle East Journal of Communication Studies

This study aimed to explore the use of social media by Jordanian science journalists and its implications for the accuracy of journalistic content. The descriptive-analytical method was adopted, utilizing a questionnaire as the primary research tool. The study sample consisted of 178 journalists, all members of the Jordanian Press Association who use social media in covering scientific issues. The results revealed that the majority of journalists primarily rely on social media to gather scientific information, with Facebook being the most preferred platform (61.8%). Furthermore, the spread of unverified scientific news was identified as a significant threat to journalistic credibility, with …

The Role Of Public Relations Practitioners In Jordanian Hospitals In Managing The Covid-19 Crisis In 2020., Dana Khalil Basheer Al-Shloul

Middle East Journal of Communication Studies

This study aimed to identify the departments and divisions that contributed to public relations in Jordanian hospitals during the COVID-19 pandemic, as well as to determine the procedures undertaken by public relations practitioners and the challenges they faced. Utilizing a descriptive-survey methodology guided by the Crisis and Emergency Risk Communication (CERC) model, the research collected data from a comprehensive sample of 16 individuals using a questionnaire.

The findings revealed that senior management’s participation in pandemic management in the surveyed hospitals was 37.93%, followed by the Ministry of Health at 27.59%. The public relations department’s actions varied by phase. Before the …

Jordanian Digital Media Organizations Rely On Artificial Intelligence To Produce Scientific Content, Baraa Kamal Abdul Latif Abu Humam

Middle East Journal of Communication Studies

The research aims to identify the extent to which workers in Jordanian digital media organizations rely on artificial intelligence in the production of scientific content, by knowing the extent of Jordanian digital media's coverage of scientific content, and the most prominent types of scientific content that rely on artificial intelligence techniques in its production, what are the most prominent roles that artificial intelligence plays during the production of scientific content, and what are the most prominent artificial intelligence techniques used in the production of scientific content, and the  study belongs to descriptive research, and relies on the field survey method, …

Lowland Tropical Forests Remain A Methane Sink Under Warming And Long-Term Hurricane Disturbance Recovery, Gabriele Larocca Conte, Lucia Zuvela, Rachel Cruz-Pérez, Tatiana Barreto-Vélez, Nibia Becerra-Santillan, Sophia F. Campbell, Hieu P. Chu, Trung Dam, Iana F. Grullón-Penkova, Miriam Kleit, Deyaneira A. Ortiz-Iglesias, Laura C. Rubio-Lebrón, Molly A. Cavaleri, Sasha C. Reed, Debjani Sihi, Tana E. Wood, Christine S. O'Connell

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Methane (CH₄) is a potent greenhouse gas, and tropical forests account for roughly one–third of global atmospheric CH₄ uptake by soils. Projected warming and more frequent hurricanes in these ecosystems may alter soil CH₄ sink strength, as warmer and wetter soils enhance methanogenesis activity. We measured soil CH₄ and CO₂ efflux during the calendar summer months of 2023 and 2024 alongside continuous records of soil moisture, soil and air temperature, and precipitation in an in–situ warming experiment (TRACE) located in a lowland tropical forest in Puerto Rico, six to seven years after Hurricanes Irma …

Examining The Ligands, Location, And Function Of Toll-Like Receptor 10, Kiefer Keanu Tam

Master's Theses

Toll-like receptors are a class of innate immune pattern recognition receptors that detect pathogen-associated molecular patterns and regulate downstream inflammatory responses. Toll-like receptor 10 remains the only human TLR whose ligand specificity, cellular localization, and immunological function are not fully defined. Emerging evidence suggests that TLR10 may play an anti-inflammatory role and can heterodimerize with TLR2 to modulate immune signaling. Previous studies from our laboratory demonstrated that stimulation with heat-killed Mycobacterium tuberculosis promotes TLR2-TLR10 heterodimerization and trafficking to the cell surface. In this study, we expanded our ligand panel to include additional gram-positive bacteria, particularly anti-inflammatory probiotic species, to further …

Effects Of Normothermic Hepatic Ischemia–Reperfusion Injury On The Hepatic Disposition Of Arachidonic Acid And Its Cytochrome P450-Generated Metabolites In Rats, Vindhya Edpuganti, Reza Mehvar

Pharmacy Faculty Articles and Research

Purpose

Cytochrome P450 (P450) metabolites of arachidonic acid (AA) are potential therapeutic targets in ischemia–reperfusion (IR) injury, yet their disposition and actions in hepatic IR are unknown. Cellular AA and its P450 metabolites are primarily bound to lipid membranes, resulting in negligible free concentrations. This study investigates how hepatic IR injury impacts the disposition of free AA and its major P450 metabolites in rats.

Methods

Rats underwent 60 min of partial (70%) ischemia or sham surgery, followed by 5 min, 3 h, or 24 h of reperfusion. The effects of IR injury on free concentrations of AA and its major …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Structure And Diversity Of Play Behavior In Juvenile Belding's Ground Squirrels, Paul O'Driscoll Ii

Master's Theses

Play behavior is ubiquitous among juvenile mammals and can promote motor, social, and cognitive development, providing multiple adaptive benefits to young animals in some cases. The structure of play can be linked to the benefits it confers on individuals. I evaluated the structure of play in juvenile Belding’s ground squirrels (Urocitellus beldingi), a species for which multiple adaptive benefits of play have been identified. I compared juvenile play in U. beldingi to adult sexual and aggressive behavior to determine and classify similarities between juvenile play and adult behavior. I evaluated diversity in the behaviors expressed during play interactions and diversity …

Improving Human-Wildlife Coexistence: An Ecological And Educational Approach To Rewilding Grizzly Bears (Ursus Arctos Horribilis) In California, Amanda C. D. Rosales

Master's Projects and Capstones

Megafauna extinction during the Holocene has been both caused and amplified by climatic changes and human influence. By the last half century, large carnivores were diminished in Europe and the United States, but policies increasingly addressed species decline and their territories expanded. This research examined large carnivore rewilding across the European Union and United States, specifically for rewilding brown bears, Ursus arctos, in historic habitat. Next, case studies for the health status of climate-impacted whitebark pine, Pinus albicaulis, a high energy food for bears, was assessed. Ultimately, research case studies, human perspective surveys, and the California Department of Education content …

Deforestation Dynamics In The Amazon: Impacts, Socio-Environmental Drivers And Restoration Pathways, Maria Natalia Rodriguez

Master's Projects and Capstones

The Amazon, which is the largest tropical rainforest in the world, experienced 542,581 km² of forest loss between the years 2000 and 2020. The process of deforestation endangers the ecological system results which maintain ecosystem connectivity and the Earth's climate system. The Amazon rainforest supplies essential ecological services which include maintaining soil fertility, storing carbon, purifying water and climate stability. The fundamental ecosystem of this area faces new threats because of increasing forest destruction. The research study adopts a combined methodology that uses Geographic Information Systems (GIS) with a comprehensive literature review to study Amazon deforestation patterns and its driving …

Kev's Dinghy Boat Workshops, Ruiyang Xiao

Masters Theses

In a culture where convenience replaces process, this project argues that making — even when inefficient, imperfect, or unnecessary — enables forms of engagement that buying cannot.

Technologies and Services nowadays are able to fulfill human’s desire to travel and explore at ease. However, this convenience proposes a mode of engagement based only in deeper knowledge of context and thus our experience with the world around us is hence diminished. Our engagement with the world becomes heavily mediated, regulated and controlled.

This project investigates how hands-on engagement with water can reintroduce + restore our sense of joy, curiosity, consequence, and …

Replication And Architectural Enhancement Of Omni Aggregation Networks, Matteo Calviello

Rose-Hulman Undergraduate Research Publications

Single Image Super-Resolution (SISR) reconstructs high-resolution images from low-resolution inputs, a capability valuable across many application domains. This thesis focuses on the replication and architectural enhancement of the Omni Aggregation Network (OAN), a lightweight super-resolution architecture designed to balance reconstruction quality with computational efficiency through a novel omni-axis self-attention mechanism.

Independent replication remains a persistent challenge in machine learning research, and this work addresses that issue directly. Initial replication attempts trailed the original reported results by approximately 6-10% in performance metrics before several undocumented implementation details were identified. After correcting these discrepancies, the replicated implementation achieved results within 4% of …

Insects And Arthropods And Their Role In Human Society, Emily Marie Perez-Medina

Whittier Scholars Program

With brightly colored exoskeletons, an excess of both eyes and legs, and seemingly  unpredictable behaviors, insects and arthropods come across as unusual and strange to general audiences. For this reason, they are often classified as “gross,” “ugly,” or “scary,” antagonists  in popular culture. What is not recognized when being represented to the masses is how much human society depends on their presence, and how a world without insects would be a world without most things humans know and love. In order to help reduce the stigma of these tiny, yet mighty creatures, this project serves as a call to action …

Somatic Prosthetics For Planetary Resonance, Disha Dharesh Kumar R

Masters Theses

This thesis investigates how industrial design can transcend extractive technological paradigms in favor of relational interfaces that foster planetary attunement. Framing the climate crisis as a 'crisis of imagination', the research challenges the Western bifurcation of nature and culture by drawing on Indic cosmologies- which recognize stones, plants, and ecosystems as conscious at different levels and participants in a shared cosmic field. By synthesizing research in Biosemiotics, Quantum Information Pansycishm, and Neuroscience, the project redefines intelligence as a distributed, more-than-human phenomenon.

The research materializes as a speculative design artifact: a device that functions as a somatic prosthetic for planetary resonance. …

Coenzyme Q10 Improves Functional And Structural Parameters Of Dairy Goat Sperm During Cooling And Cryopreservation, Ranadheer Narlagiri, Abdallah M. Shahat, Courtney Henry, Ashvini Pawar, Niki C. Whitley, Iman B. Shaheed, Mahipal Singh, Brou Kouakou, Irina A. Polejaeva, Adel R. Moawad

Animal, Dairy, and Veterinary Science Faculty Publications

Cryopreservation of gametes is crucial for conserving genetic diversity in livestock and endangered species, but the process can significantly impair sperm quality due to oxidative stress. Our aim was to evaluate the impacts of coenzyme Q10 (CoQ10) supplementation on the in vitro quality of cooled and cryopreserved goat semen. Semen samples collected from six mature Saanen bucks were pooled then diluted with AndroMed^® semen extender to a final concentration of 800 × 10⁶ sperm/mL. Diluted semen was supplemented with 0, 1, 2, 5, 10, and 20 µM CoQ10. Extended semen was either cooled at 4 °C for 72 …

Bat Species Acoustic Detections And Mist Net Captures 2017, 2018, 2019, 2022, 2023, 2025., Laroy Brandt

Faculty Peer-Reviewed Publications

No abstract provided.

Slouching Towards Inefficiency? The Cardiometabolic And Cognitive Costs Of Poor Posture, Ava Mae Fitzenrider

Honors Projects

Posture affects all of our lives. It is both static and dynamic, adapting continuously to environmental demands. One postural alteration frequently observed in occupational settings is hyperkyphosis, which can be induced by sitting position. During computer use, individuals commonly adopt a slouched posture, which can exacerbate hyperkyphosis, and contribute to dis-ease within the body. Previous research has demonstrated that such postural deviations can negatively affect pulmonary function, as well as other bodily functions. Despite these findings, the effects of acute hyperkyphosis (“slouching”) on cardiometabolic function and cognition remain largely unexplored. Therefore, the purpose of this study was to examine the …

Foveate, Dahlia Aggarwal

Masters Theses

This thesis investigates how textiles can unsettle visual assumptions, encouraging a perceptual shift. Through weaving, upholstery, and spatial installation, the work stages a tension between what a surface appears to be and how it is encountered by the body. Through woven pattern, tactile texture, and trompe l’oeil textile surfaces, perception is something negotiated rather than fixed: the eye anticipates one reality while the hand discovers another.

Drawing on a range of sensations gathered from observing landscape formations and textures, it translates enduring scale and material qualities into an interior landscape of woven surfaces and textile-based furniture. Rather than serving as …

Colonization Of Southern Flying Squirrels (Glaucomys Volans) To Urban Nebraska: Range Expansion Or Human Assisted Translocation?, Jennifer Wettschreck, James Wilson, Robert E. Wilson, Abby May, Megan Cary, Jeffrey Huebschman, Sarah A. Sonsthagen

Biology Faculty Publications

Southern flying squirrels (Glaucomys volans; Linnaeus 1758) were first observed in Lincoln, Nebraska, in 2018, 80 km north of their described range. Given that southern flying squirrels are a species of concern within Nebraska, determining the origin of this new population (natural expansion or pet-trade) garnered interest from state biologists. Further, the recent colonization of Lincoln by southern flying squirrels presents a unique opportunity to investigate the genetic implications of a founding event on a small arboreal mammal. The Lincoln population had genetic characteristics suggestive of a single-event colonization with fewer rare alleles and lower genetic diversity than potential …

The Marathon Without Running: Experiencing A Runner's Sensorial Journey, Harin Kim

Masters Theses

The marathon is defined not by motion alone, but by the changing conditions a body moves through—and remains within—over time. Breath, cadence, heat, sound, crowd compression and attention fluctuate, producing phases that structure the race from within. These interior states are difficult to access by spectators from the sidelines, yet they are precisely what shape the runner’s experience.

This thesis begins with a simple but unconventional question: How can an exhibition translate the runner’s physical sensations and emotions into a multidimensional experience for spectators who do not run? Through a sequence of pop-up exhibitions placed along the New York City …

Watershed Amendments: Assembling New Pervious Ground From Landscape Waste, Sophie Kaplan-Bucciarelli

Masters Theses

In Providence, Rhode Island, much of the downtown area is built over a vast historic tidal estuary. Though we no longer see the salt marshes, wooded bluffs, or meadows that once characterized this landscape, we recognize their absence in contemporary crises of urban heat, flooding, polluted soils and stormwater runoff, and habitat loss. These conditions are particularly acute along the city’s industrialized river corridors, where vacant lots and parking areas sit idle, their history paved over and potential constrained by limited imagination and resources.

These lots - already experiments in fill and land building after centuries of disturbance - can …

Integrating Consumer-Grade Wearable Data Into Orthopedic Risk Stratification For Amateur Athletes: A Perspective On An Untapped Clinical Tool, Youssef Salama, William Gadbois, Kevin Reck, Scott Yaekle

Medical Student Research Symposium

Background:

Consumer-grade wearables have rapidly expanded beyond fitness tracking, providing continuous physiologic and biomechanical data. Metrics such as heart rate variability (HRV), sleep efficiency, and training load have been validated as markers of both recovery and overtraining. However, orthopedic care has not yet translated these data into clinical use. Given the rising burden of overuse injuries in recreational athletes, wearable-derived information may offer a practical opportunity for early detection and prevention within outpatient settings.

Methods:

A narrative perspective review of literature from 2010–2025 was performed using PubMed. Studies addressing wearable device validity, physiologic correlates of musculoskeletal injury, and training-load modeling …

Environmental Mercury Alters Immune Pathways Linked To Autoimmune Risk In Mice Mirroring Humans, Maurgan Lee, Paul Stemmer, Randall Gill, Allen Rosenspire, Anil Aranha, Heather Gibson

Medical Student Research Symposium

Background and Purpose: Mercury is a pervasive environmental contaminant, and human epidemiologic studies have linked chronic low-level exposure to increased autoimmune disease-risk. Dysregulated lymphocyte activation and impaired signaling tolerance are central mechanisms in human autoimmunity. Protein phosphorylation governs lymphocyte differentiation and function, alterations in phosphoproteomic networks may represent a signature of immune disruption. This study evaluates how low dose mercury exposure modifies B and T cell abundance and intracellular signaling patterns in BALB/c and Diversity Outbred (DO) mice.

Methods: BALB/c and DO mice were exposed to low dose HgCl2 in their water for two weeks or provided standard water controls. …